diff --git a/misc-scripts/production_database/sql/data/ensembl_production.dump b/misc-scripts/production_database/sql/data/ensembl_production.dump
index e167e1e606d6d5d36f1394ae14137c8ca8aaac13..9e86e3ea23da06454985eb9189a1911245f00b16 100644
--- a/misc-scripts/production_database/sql/data/ensembl_production.dump
+++ b/misc-scripts/production_database/sql/data/ensembl_production.dump
@@ -59,23 +59,23 @@ INSERT INTO `analysis_description` VALUES (20,'celegans_est','Caenorhabditis ele
INSERT INTO `analysis_description` VALUES (21,'celegans_mrna','Caenorhabditis elegans mRNA are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','C.elegans cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (22,'chicken_cdna','Chicken cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Chicken cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (23,'chicken_est','Chicken \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Chicken EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (24,'chicken_protein','Chicken protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Chicken protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (24,'chicken_protein','Chicken protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Chicken protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (25,'chicken_repeatmask','<a rel=\"external\" href=\"http://www.repeatmasker.org\">RepeatMasker</a> is used to find repeats and low-complexity sequences using a chicken repeat library. This track usually shows repeats alone (not low-complexity sequences).','Repeats (Chicken)',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (26,'chimp_cdna','Pan troglodytes cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Chimpanzee cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (27,'chimp_est','Pan troglodytes \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Chimpanzee EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (28,'chimp_human_protein','Human protein sequence aligned to the chimp genome by projection or by using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Human protein',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (29,'chimp_protein','Pan troglodyes protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Chimpanzee protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (29,'chimp_protein','Pan troglodyes protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Chimpanzee protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (30,'cint_cdna','Ciona intestinalis cDNA sequences from the <a rel=\"external\" href=\"http://ghost.zool.kyoto-u.ac.jp/indexr1.html\">Ghost Database</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','C.intestinalis cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (31,'cint_est','Ciona intestinalis \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> and the <a rel=\"external\" href=\"http://ghost.zool.kyoto-u.ac.jp/indexr1.html\">Ghost Database</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','C.intestinalis EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (32,'cow_cdna','Cow cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Cow cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (33,'cow_est','Cow \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Cow EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (34,'cow_protein','Cow protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Cow protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (34,'cow_protein','Cow protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Cow protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (35,'cpg','CpG islands are regions of nucleic acid sequence containing a high number of adjacent cytosine guanine pairs (along one strand). Usually unmethylated, they are associated with promoters and regulatory regions. They are determined from the genomic sequence using a program written by G. Miklem, similar to <a rel=\"external\" href=\"http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgreport.html\">newcpgreport</a> in the EMBOSS package.','CpG islands',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (36,'cyt','Cytokine model, manually curated by Genoscope','Cytokine',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (37,'deletion','Feature imported from <a rel=\"external\" href=\"http://www.flybase.org\">FlyBase</a>.','Deletion',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (38,'dog_ensembl_protein','Selected Ensembl-predicted dog peptide sequences aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Dog Ensembl protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (39,'dog_est','Dog \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Dog EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (40,'dog_protein','Dog proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Dog protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (40,'dog_protein','Dog protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Dog protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (41,'drosophila_cdna_all','Drosophila melanogaster cDNA sequences from <a rel=\"external\" href=\"http://www.fruitfly.org\">BDGP</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Fly cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (42,'drosophila_est','Drosophila melanogaster \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Fly EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (43,'drosophila_gold_cdna','Medaka cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Fly gold cDNA',NULL,NULL,NULL,NULL,1);
@@ -112,13 +112,13 @@ INSERT INTO `analysis_description` VALUES (73,'fantom_gsc_pet','These are short
INSERT INTO `analysis_description` VALUES (74,'fantom_gsc_pet_raw','These are short sequence tags from the start sites of polyA transcripts. These ditags were downloaded from the <a rel=\"external\" href=\"http://fantom.gsc.riken.go.jp/\">Riken Fantom</a> project and aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Fantom GSC raw',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (75,'fgenesh','Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel=\"external\" href=\"http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10779491\">AA Salamov et al., Genome Res. 2000 4:516-22</a>.','FGENESH prediction',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (76,'firstef','First Exon Finder (<a rel=\"external\" href=\"http://www.nature.com/ng/journal/v29/n4/full/ng780.html\">First EF</a>) predicts positions of the first exons of transcripts, both coding and non-coding, using the sequence to identify features such as CpG islands and promoter regions.','First EF',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (77,'fish_protein','Fish proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Fish protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (77,'fish_protein','Fish protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Fish protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (78,'flybase','Feature imported from <a rel=\"external\" href=\"http://www.flybase.org\">FlyBase</a>.','FlyBase feature',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (79,'fosends','End sequences of Fosmid library clones used in the sequencing project aligned to the genome using <a rel=\"external\" href=\"http://www.sanger.ac.uk/Software/analysis/SSAHA2/\">SSAHA2</a>.','FOS ends',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (80,'fosmid','Vancouver fosmids mapped to the C.elegans genome (available through GeneService)','fosmid',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (81,'fugu_cdna','Takifugu cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Takifugu cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (82,'fugu_est','Takifugu \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Takifugu EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (83,'fugu_protein','Takifugu proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Takifugu protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (83,'fugu_protein','Takifugu protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Takifugu protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (84,'gadflyp','FlyBase proteins aligned by WU-BlastP','GadflyP',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (85,'gadflyx','FlyBase proteins aligned by WU-BlastX','GadflyX',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (86,'gene3d','Gene3D analysis as of interpro_scan.pl','gene3d',NULL,NULL,NULL,NULL,1);
@@ -126,31 +126,31 @@ INSERT INTO `analysis_description` VALUES (87,'genedensity','Gene density as cal
INSERT INTO `analysis_description` VALUES (88,'genefinder','Ab initio prediction of protein coding genes by Genefinder (C. Wilson, L. Hilyer, and P. Green, unpublished).','Genefinder prediction',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (89,'genscan','Ab initio prediction of protein coding genes by <a rel=\"external\" href=\"http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc\">Genscan</a>. The splice site models used are described in more detail in C. Burge, Modelling dependencies in pre-mRNA splicing signals. 1998 In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology, Elsevier Science, Amsterdam, 127-163.','Genscan prediction',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (90,'gid','Ab initio prediction of protein coding genes by <a rel=\"external\" href=\"http://www1.imim.es/software/geneid/\">Geneid</a>, with parameters customised for accuracy in Tetraodon sequences.','Geneid prediction',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (91,'gorilla_cdna','Gorilla proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Gorilla RefSeq/ENA cDNA',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (92,'gorilla_protein','Gorilla proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Gorilla protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (91,'gorilla_cdna','Gorilla protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Gorilla RefSeq/ENA cDNA',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (92,'gorilla_protein','Gorilla protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Gorilla protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (93,'gorilla_rnaseq','Illumina paired-end reads from Western lowland gorilla generated at the Wellcome Trust Sanger Institute (WTSI) aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','RNASeq',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (94,'green_anole_cdna','Green anole cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Green anole cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (95,'green_anole_est','Green anole \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Green anole EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (96,'green_anole_protein','Green anole proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Green anole UniProtKB protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (96,'green_anole_protein','Green anole protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Green anole UniProtKB protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (97,'gsc','Ab initio prediction of protein coding genes by <a rel=\"external\" href=\"http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc\">Genscan</a>, with parameters customised for accuracy in Tetraodon sequences','GSC',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (98,'gsten','Annotation generated by <a rel=\"external\" href=\"http://www.genoscope.cns.fr/spip/\">Genoscope</a>, combining evidence from <a rel=\"external\" href=\"http://www1.imim.es/software/geneid/\">Geneid</a>, <a rel=\"external\" href=\"http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45VGF7T-9&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=aa15a5f8122912c172ddb9dd15b237dc\">Genscan</a>, <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> and <a rel=\"external\" href=\"http://www.nature.com/ng/journal/v25/n2/abs/ng0600_235.html\">Exofish</a> predictions with alignments of Tetraodon cDNAs to the genome. This was done automatically using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/full/12/9/1418\">GAZE</a> with a custom-designed configuration and gene structure model.','Genoscope',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (99,'guineapig_cdna','Guineapig cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Guineapig cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (100,'guineapig_est','Guineapig \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Guineapig EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (101,'guineapig_protein','Guineapig proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Guineapig protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (101,'guineapig_protein','Guineapig protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Guineapig protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (102,'gws_uni','Alignment of a <a rel=\"external\" href=\"http://www.uniprot.org/\">Uniprot protein</a> to the genome by <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','UniProt protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (103,'havana','Manual annotation (determined on a case-by-case basis) from the <a rel=\"external\" href=\"http://www.sanger.ac.uk/HGP/havana/havana.shtml\">Havana</a> project.','Havana',NULL,NULL,5132,'2011-05-11 14:48:25',1);
INSERT INTO `analysis_description` VALUES (104,'havana_ig_gene','Immunoglobulin (Ig) and T-cell receptor (TcR) annotation imported from the manually curated IG gene set from the <a rel=\"external\" href=\"http://www.sanger.ac.uk/HGP/havana/havana.shtml\">Havana</a> project.','Havana Ig/T-cell receptor',NULL,NULL,5132,'2011-05-11 14:48:25',1);
INSERT INTO `analysis_description` VALUES (105,'hmmpanther','HMM-Panther families','hmmpanther',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (106,'horse_cdna','Horse cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Horse cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (107,'horse_est','Horse \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Horse EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (108,'horse_protein','Horse protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Horse protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (108,'horse_protein','Horse protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Horse protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (109,'hox','HOX genes were manually curated by <a rel=\"external\" href=\"http://www.genoscope.cns.fr/spip/\">Genoscope</a>.','HOX',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (110,'human_cdna','Human cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Human RefSeq/ENA cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (111,'human_cdna2genome','Homo Sapiens cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">EMBL</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate cdna2genome model</a>.','Human RefSeq/ENA cdna2genome',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (112,'human_ensembl_protein','Selected Ensembl-predicted human peptide sequences aligned to the genome using the whole genome alignment to gene (WGA2Gene) projection method or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Human Ensembl protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (112,'human_ensembl_protein','Selected Ensembl-predicted human peptide sequences aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a> or <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Human Ensembl protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (113,'human_est','Homo sapiens \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Human EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (114,'human_one2one_mus_orth','Human ensembl transcripts that are <a href=\"http://www.ensembl.org/info/docs/compara/homology_method.html\" class=\"cp-external\">one-to-one orthologues</a> with mouse are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Human protein',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (115,'human_protein','Human proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Human protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (115,'human_protein','Human protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Human protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (116,'human_refseq','Human proteins from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> used in the <a href=\"http://www.ensembl.org/info/docs/genebuild/index.html\" class=\"cp-external\">genebuild</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Human RefSeq protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (117,'ikmc_es_cells_available','IKMC_ES_cells_available','IKMC ES cells available',NULL,NULL,NULL,NULL,0);
INSERT INTO `analysis_description` VALUES (118,'ikmc_mice_available','IKMC_Mice_available','IKMC Mice available',NULL,NULL,NULL,NULL,0);
@@ -169,7 +169,7 @@ INSERT INTO `analysis_description` VALUES (130,'kyotograil_2005','C. intestinali
INSERT INTO `analysis_description` VALUES (131,'lrg_import','Data from LRG database','LRG',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (132,'macaque_cdna','Macaque cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Macaque cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (133,'macaque_est','Macaque \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Macaque EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (134,'macaque_protein','Macaque proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Macaque UniProt protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (134,'macaque_protein','Macaque protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Macaque UniProt protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (135,'macaque_refseq','Macaque proteins from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> used in the <a href=\"http://www.ensembl.org/info/docs/genebuild/index.html\" class=\"cp-external\">genebuild</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Macaque RefSeq protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (136,'mammal_protein','Mammalian proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Mammal UniProt protein',NULL,NULL,NULL,NULL,0);
INSERT INTO `analysis_description` VALUES (137,'marker','Markers, or sequence tagged sites (STS), from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists\">UniSTS</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/full/7/5/541\">Electronic PCR (e-PCR)</a>.','Marker',NULL,NULL,NULL,NULL,1);
@@ -181,11 +181,11 @@ INSERT INTO `analysis_description` VALUES (142,'medaka_5psage','Medaka 5pSAGE da
INSERT INTO `analysis_description` VALUES (143,'medaka_cdna','Medaka cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">EMBL</a> are aligned to the genome aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Medaka RefSeq/ENA cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (144,'medaka_est','Medaka \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Medaka EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (145,'medaka_genome_project','Annotation provided by the Medaka Genome Project, viz. the University of Tokyo (http://medaka.utgenome.org/) and the National Institute of Genetics (http:// dolphin.lab.nig.ac.jp/medaka/).','Medaka Genome Project',NULL,NULL,5132,'2011-05-12 13:24:25',1);
-INSERT INTO `analysis_description` VALUES (146,'medaka_protein','Medaka proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Medaka UniProtKB protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (146,'medaka_protein','Medaka protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Medaka UniProtKB protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (147,'medaka_transcriptcoalescer','ESTs are mapped on the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>. Genes (including isoforms) are inferred using the gene-predicting module TranscriptCoalescer','EST-based',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (148,'mouse_cdna','Mouse cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Mouse RefSeq/ENA cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (149,'mouse_est','Murine \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Mouse EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (150,'mouse_protein','Murine proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Mouse protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (150,'mouse_protein','Murine protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Mouse protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (151,'mt_genbank_import','Mitochondrial gene models imported from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/Genbank/\">Genbank</a>. Genbank is part of the International Nucleotide Sequence Database Collaboration, which also includes the DNA DataBank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL).','Imported MT',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (152,'mus_one2one_human_orth','Mouse ensembl transcripts that are <a href=\"http://www.ensembl.org/info/docs/compara/homology_method.html\" class=\"cp-external\">one-to-one orthologues</a> with human are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Mouse protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (153,'ncoils','Prediction of coiled-coil regions in proteins is by <a rel=\"external\" href=\"http://www.sciencemag.org/cgi/reprint/252/5009/1162\">Ncoils</a>.','Coiled-coils (Ncoils)',NULL,NULL,NULL,NULL,1);
@@ -194,10 +194,10 @@ INSERT INTO `analysis_description` VALUES (155,'ncrna_pseudogene','ncRNA pseudog
INSERT INTO `analysis_description` VALUES (156,'nembase_contig','NemBase EST contigs','nembasecontig',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (157,'operon','Multi-gene feature imported from <a rel=\"external\" href=\"http://www.wormbase.org\">Wormbase</a> annotation.','Operon',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (158,'opossum_cdna','Opposum cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Opossum cDNA',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (159,'opossum_protein','Opposum proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Opossum UniProtKB protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (159,'opossum_protein','Opposum protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Opossum UniProtKB protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (160,'orangutan_cdna','Orangutan cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Orangutan cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (161,'orangutan_est','Orangutan \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Orangutan EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (162,'orangutan_protein','Orangutan proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Orangutan protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (162,'orangutan_protein','Orangutan protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Orangutan protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (163,'ost','Caenorhabditis elegans OSTs of the Vidal Lab aligned to the genome using BLAT','C.elegans OST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (164,'other_est','For various species, \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Various EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (165,'other_protein','For various species, proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> are aligned to the genome with <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Other species protein',NULL,NULL,NULL,NULL,1);
@@ -210,14 +210,14 @@ INSERT INTO `analysis_description` VALUES (171,'pfam','Protein domains and motif
INSERT INTO `analysis_description` VALUES (172,'pfscan','Protein domains and motifs from the <a rel=\"external\" href=\"http://www.ebi.ac.uk/ppsearch/\">PROSITE</a> profiles database are aligned to the genome.','PROSITE profiles',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (173,'pig_cdna','Pig cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','pig cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (174,'pig_est','Pig \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','pig EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (175,'pig_protein','Pig proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','pig protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (175,'pig_protein','Pig protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','pig protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (176,'pirsf','Protein domains and motifs from the <a rel=\"external\" href=\"http://pir.georgetown.edu/pirwww/index.shtml\">PIR (Protein Information Resource)</a> Superfamily database.','PIRSF domain',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (177,'platypus_454_cdna','Platypus reads from 454 sequencing are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Sequence reads (454)',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (178,'platypus_cdna','Platypus cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Platypus cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (179,'platypus_est','Platypus \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Platypus EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (180,'platypus_olfactory_receptors','Manually curated olfactory receptor sequences from <a rel=\"external\" href=\"http://www.funpecrp.com.br/gmr2008b/issue.asp?volume=541&capitulo=551#anc_206\">Tsviya Olender</a>','Olfactory receptor',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (181,'platypus_olfactory_receptor_cdna','Manually curated olfactory receptor sequences from <a rel=\"external\" href=\"http://www.funpecrp.com.br/gmr2008b/issue.asp?volume=541&capitulo=551#anc_206\">Tsviya Olender</a>','Olfactory receptor',NULL,NULL,5132,'2011-05-12 13:24:25',1);
-INSERT INTO `analysis_description` VALUES (182,'platypus_protein','Platypus proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Platypus protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (182,'platypus_protein','Platypus protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Platypus protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (183,'polya_site','Feature imported from <a rel=\"external\" href=\"http://www.flybase.org\">FlyBase</a>.','PolyA Site',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (184,'ppapepp','Pristionchus pacificus proteins aligned by WU-BlastP','PpapepP',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (185,'ppapepx','Pristionchus pacificus proteins aligned by WU-BlastX','PpapepX',NULL,NULL,NULL,NULL,1);
@@ -227,7 +227,7 @@ INSERT INTO `analysis_description` VALUES (188,'pseudogene','Pseudogenes are ide
INSERT INTO `analysis_description` VALUES (189,'qtl','Quantitative Trait Loci (QTL) features.','QTL',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (190,'rabbit_cdna','Rabbit cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Rabbit cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (191,'rabbit_est','Oryctolagus cuniculus \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Rabbit EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (192,'rabbit_protein','Rabbit proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Rabbit protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (192,'rabbit_protein','Rabbit protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Rabbit protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (193,'rat_cdna','Rattus cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Rat RefSeq/ENA cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (194,'rat_cdna2genome','Rattus norvegicus cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">EMBL</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate cdna2genome model</a>.','Rat RefSeq/ENA cdna2genome',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (195,'rat_est','Rattus norvegicus \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Rat EST',NULL,NULL,NULL,NULL,1);
@@ -241,7 +241,7 @@ INSERT INTO `analysis_description` VALUES (202,'rescue_fragment','Feature (Fly)
INSERT INTO `analysis_description` VALUES (203,'rfamblast','<a href=\"http://www.ensembl.org/info/docs/genebuild/ncrna.html\" class=\"cp-external\">Positions</a>Positions of ncRNAs (non-coding RNAs) from the <a rel=\"external\" href=\"http://rfam.sanger.ac.uk/\">Rfam </a> database are shown. Initial BLASTN hits of genomic sequence to RFAM ncRNAs are clustered and filtered by E value. These hits are supporting evidence for ncRNA genes.','RFAM ncRNA',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (204,'rna-seq_exon_supporting_feat','Supporting feature for exons of RNA-Seq gene model','RNA-Seq exon supp feat',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (205,'rnai','Aligned probes from RNA interference experiments.','RNAi',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (206,'rodent_protein','Rodent proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Rodent RefSeq/TrEMBL protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (206,'rodent_protein','Rodent protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Rodent RefSeq/TrEMBL protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (207,'rrna','ribosomal RNA genes','rRNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (208,'savignyi_est','Ciona savignyi \'Expressed Sequence Tags\' (ESTs) were aligned to corrected cDNA sequences from the <a rel=\"external\" href=\"http://ghost.zool.kyoto-u.ac.jp/indexr1.html\">Kyoto-EST-set</a> using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','C.savignyi EST',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (209,'scanprosite','Protein domains and motifs from the <a rel=\"external\" href=\"http://www.ebi.ac.uk/ppsearch/\">PROSITE</a> profiles database are aligned to the genome.','PROSITE patterns',NULL,NULL,NULL,NULL,1);
@@ -265,12 +265,12 @@ INSERT INTO `analysis_description` VALUES (226,'snpdensity','Density of Single N
INSERT INTO `analysis_description` VALUES (227,'snrna','small nuclear RNA genes','snRNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (228,'stickleback_cdna','Gasterosteus aculeatus cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Stickleback cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (229,'stickleback_est','Gasterosteus aculeatus \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Stickleback EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (230,'stickleback_protein','Gasterosteus aculeatus proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Stickleback protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (230,'stickleback_protein','Gasterosteus aculeatus protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Stickleback protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (231,'superfamily','Protein domains and motifs in the <a rel=\"external\" href=\"http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457CXWM-3D&_user=776054&_coverDate=11%2F02%2F2001&_rdoc=17&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232001%23996869995%23286382%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=17&_acct=C000042238&_version=1&_urlVersion=0&_userid=776054&md5=a921e84cd71c59f75644aa28f3224b58\">SUPERFAMILY</a> database.','Superfamily domain',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (232,'supp_repeatmask','Interspersed repeats and low complexity sequence identified by <a rel=\"external\" href=\"http://www.repeatmasker.org\">RepeatMasker</a> using a supplemental repeat database specific to the species.','Supp. Repeats (Recon)',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (233,'tetraodon_cdna','Tetraodon cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Tetraodon cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (234,'tetraodon_est','Tetraodon \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Tetraodon EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (235,'tetraodon_protein','Tetraodon proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Tetraodon protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (235,'tetraodon_protein','Tetraodon protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Tetraodon protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (236,'tigrfam','Protein domains and motifs in the <a rel=\"external\" href=\"http://nar.oxfordjournals.org/cgi/content/full/31/1/371?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&author1=Haft&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&fdate=1/1/2003&tdate=12/31/2003&resourcetype=HWCIT\">TIGRFAM</a> database.','TIGRFAM domain',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (237,'tmhmm','Prediction of transmembrane helices in proteins by <a rel=\"external\" href=\"http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D7V9-K&_user=776054&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=776054&md5=a113464457fa5206c6699b9d464cbfee\">TMHMM</a>.','Transmembrane helices',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (238,'transposable_element','Feature imported from <a rel=\"external\" href=\"http://www.flybase.org\">FlyBase</a>.','TE',NULL,NULL,NULL,NULL,1);
@@ -289,7 +289,7 @@ INSERT INTO `analysis_description` VALUES (250,'uniprot_vertebrate','Vertebrate
INSERT INTO `analysis_description` VALUES (251,'vertrna','Positions of vertebrate mRNAs along the genome. mRNAs are from the <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">European Nucleotide Archive</a> database. Initial alignments are performed using TBLASTN of Genscan-predicted peptides against the European Nucleotide Archive mRNAs.','ENA vertebrate cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (252,'vertrna_other','Genomic positions of non-coding vertebrate mRNAs, annotated by the Anacode team at the Wellcome Trust Sanger Institute and used in <a rel=\"external\" href=\"http://www.sanger.ac.uk/HGP/havana/havana.shtml\">Havana</a> manual curation as supporting evidence for exons. Each repeat-masked clone (not an entire chromosome) is searched against non-coding RNA molecules of type \"Other RNA\" from the <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">European Nucleotide Archive</a> database using NCBI BLAST. Since each clone is searched, there will be edge effects where clones overlap in the chromosome assembly.','ENA vertebrate non-coding cDNA (Havana)',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (253,'washu_contig','Washington University Nematode clusters aligned by BLAT','Washu. contig',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (254,'wga2genes','Alignment to a human Ensembl protein inferred by projecting through a BLASTZ DNA alignment to the human genome','BLASTZ protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (254,'human_projected_protein','Alignment to a human Ensembl protein inferred by projecting through a BLASTZ DNA alignment to the human genome','Human projected protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (255,'wormbase','This model was annotated and aligned to the genome by <a rel=\"external\" href=\"http://www.wormbase.org\">Wormbase</a> through a process of automatic and manual curation.','Worm',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (256,'wormpepp','C. elegans proteins aligned by WU-BlastP','wormpepP',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (257,'wormpepx','C. elegans proteins aligned by WU-BlastX','wormpepX',NULL,NULL,NULL,NULL,1);
@@ -301,12 +301,12 @@ INSERT INTO `analysis_description` VALUES (262,'xrefexonerateprotein','match','P
INSERT INTO `analysis_description` VALUES (263,'xtrop_cdna','Xenopus tropicalis cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','X.tropicalis cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (264,'xtrop_cluster','Xenopus laevis \'Expressed Sequence Tag Clusters\' (ESTs) from <a rel=\"external\" href=\"http://informatics.gurdon.cam.ac.uk/cgi-bin/public.exe\">Gurdon Institute Xenopus tropicalis Full-Length Database</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','X.laevis EST cluster',NULL,NULL,NULL,NULL,0);
INSERT INTO `analysis_description` VALUES (265,'xtrop_est','Xenopus tropicalis \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','X.tropicalis EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (266,'xtrop_protein','Xenopus tropicalis proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','X.tropicalis protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (266,'xtrop_protein','Xenopus tropicalis protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','X.tropicalis protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (267,'yeastp','S. cerevisiae proteins aligned by WU-BlastP','yeastP',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (268,'yeastx','S. cerevisiae proteins aligned by WU-BlastX','yeastX',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (269,'zebra_finch_cdna','Taeniopygia guttata cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Zebra finch cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (270,'zebra_finch_est','Taeniopygia guttata \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Zebra finch EST',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (271,'zebra_finch_protein','Taeniopygia guttata protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Zebra finch UniProtKB protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (271,'zebra_finch_protein','Taeniopygia guttata protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Zebra finch UniProtKB protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (272,'zfish_14dpf_intron','Spliced RNASeq read support for intron from 14 days post fertilization embryos','14dpf intron',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (273,'zfish_1dpf_intron','Spliced RNASeq read support for intron from 1 day post fertilization embryos','1dpf intron',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (274,'zfish_2cells_intron','Spliced RNASeq read support for intron from 2 cell stage','2 cell intron',NULL,NULL,NULL,NULL,1);
@@ -321,7 +321,7 @@ INSERT INTO `analysis_description` VALUES (282,'zfish_female_head_intron','Splic
INSERT INTO `analysis_description` VALUES (283,'zfish_male_body_intron','Spliced RNASeq read support for intron from male body','Male body intron',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (284,'zfish_male_head_intron','Spliced RNASeq read support for intron from male head','Male head intron',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (285,'zfish_ovary_intron','Spliced RNASeq read support for intron from ovary','Ovary intron',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (286,'zfish_protein','Zebrafish proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Zebrafish protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (286,'zfish_protein','Zebrafish protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Zebrafish protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (287,'zfish_rnaseq','Annotation generated using only <a href=\"http://www.ensembl.org/info/docs/genebuild/rnaseq_annotation.html\" class=\"cp-external\">Zebrafish RNASeq</a> data.','RNASeq',NULL,NULL,5132,'2011-05-12 13:24:25',1);
INSERT INTO `analysis_description` VALUES (288,'est2genome_fish','Alignment of zebrafish ESTs (expressed sequence tags) to the genome using the program <a rel=\"external\" href=\"http://emboss.sourceforge.net/apps/cvs/emboss/apps/est2genome.html\">Est2genome</a>. ESTs are from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a>','Zebrafish EST (EST2genome)',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (289,'vertrna_havana','Positions of vertebrate mRNAs along the genome. mRNAs are from the <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">European Nucleotide Archive</a> database. Initial alignments are performed using TBLASTN of Genscan-predicted peptides against the European Nucleotide Archive mRNAs.','ENA vertebrate cDNA (Havana)',NULL,NULL,NULL,NULL,1);
@@ -385,7 +385,7 @@ INSERT INTO `analysis_description` VALUES (346,'thyroid_rnaseq','Models built us
INSERT INTO `analysis_description` VALUES (347,'liver_rnaseq','Models built using Human liver total RNA, lot 040000124, caucasian male, suicide/36 foot fall, Illumina Human Bodymap 2.0 Data','liver',NULL,NULL,5132,'2011-05-11 13:59:25',1);
INSERT INTO `analysis_description` VALUES (348,'gibbon_repeatmask','<a rel=\"external\" href=\"http://www.repeatmasker.org\">RepeatMasker</a> is used to find repeats and low-complexity sequences using a gibbon repeat library. This track usually shows repeats alone (not low-complexity sequences).','Repeats (Gibbon)',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (349,'mammal_repeatmask','<a rel=\"external\" href=\"http://www.repeatmasker.org\">RepeatMasker</a> is used to find repeats and low-complexity sequences using a mammal repeat library. This track usually shows repeats alone (not low-complexity sequences).','Repeats (Mammal)',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (350,'gibbon_protein','Gibbon proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Gibbon protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (350,'gibbon_protein','Gibbon protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Gibbon protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (351,'gibbon_cdna','Gibbon cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Gibbon RefSeq cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (352,'refseq_mouse_import','Mouse RefSeq gene models from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> were imported into Ensembl in December 2010.','Mouse RefSeq import',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (353,'refseq_human_havana','Human cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Human RefSeq cDNA',NULL,NULL,NULL,NULL,1);
@@ -411,15 +411,15 @@ INSERT INTO `analysis_description` VALUES (372,'syntenic_region','syntenic_regio
INSERT INTO `analysis_description` VALUES (373,'tandem_repeat','tandem_repeat','tandem_repeat',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (374,'transposable_element_insertion_site','transposable_element_insertion_site','transposable_element_insertion_site',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (375,'dna_motif','DNA_motif','DNA_motif',NULL,NULL,NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (376,'microbat_protein','Microbat protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Microbat protein',NULL,NULL,NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (376,'microbat_protein','Microbat protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Microbat protein',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (377,'microbat_cdna','Microbat cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Microbat cDNA',NULL,NULL,NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (378,'riken_cage_tss','Female K562 CAGE-defined Transcription Start Sites produced by Riken as part of the ENCODE collaboration.','K562 CAGE-defined TSS',5132,'2011-06-03 15:02:04',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (379,'lamprey_cdna','Lamprey cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Lamprey cDNA',97245,'2011-06-24 13:12:19',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (380,'lamprey_est','Lamprey \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Lamprey EST',97245,'2011-06-24 13:14:36',NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (381,'lamprey_protein','Lamprey protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Lamprey protein',97245,'2011-06-24 13:22:20',NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (381,'lamprey_protein','Lamprey protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Lamprey protein',97245,'2011-06-24 13:22:20',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (382,'lamprey_consortium_abinitio_set','Ab initio gene prediction by <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/5/59\">SNAP</a>, <a rel=\"external\"http://genomebiology.com/2006/7/S1/S11\">Augustus</a> and other tools provided by the lamprey_consortium.','Additional prediction',97245,'2011-06-24 13:48:08',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (383,'devil_cdna','devil cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','devil cDNA',97245,'2011-07-05 15:19:02',NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (384,'devil_protein','devil protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','devil protein',97245,'2011-07-05 15:19:13',NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (384,'devil_protein','devil protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','devil protein',97245,'2011-07-05 15:19:13',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (385,'devil_rnaseq','Annotation generated using only Tasmanian devil RNASeq data.','RNASeq gene',8,'2011-07-08 14:34:47',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (386,'devil_introns','Spliced RNASeq read support','introns',8,'2011-07-08 14:35:06',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (387,'cow_cdna2genome','Cow cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">EMBL</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate cdna2genome model</a>.','Cow Refseq/ENA cdna2genome',97245,'2011-07-15 11:49:25',NULL,NULL,1);
@@ -435,18 +435,18 @@ INSERT INTO `analysis_description` VALUES (396,'proj_havana_ig_gene','Immunoglob
INSERT INTO `analysis_description` VALUES (397,'proj_ncrna','Non-coding RNAs (ncRNAs) predicted using sequences from <a href=\"http://rfam.sanger.ac.uk\">RFAM</a> and <a href=\"http://microrna.sanger.ac.uk/sequences/index.shtml\">miRBase</a>. See <a href=\"http://www.ensembl.org/info/docs/genebuild/ncrna.html\" class=\"cp-external\">article</a>. These were projected to the <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml\">alternate locus</a> via a mapping from the <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml\">primary assembly</a>.','Projected ncRNA',NULL,'2011-08-08 14:07:01',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (398,'proj_ncrna_pseudogene','ncRNA pseudogenes imported from the manual annotation produced by Sean Eddy group and projected to the <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml\">alternate locus</a> via a mapping from the <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml\">primary assembly</a>.','Projected ncRNA pseudogene',NULL,'2011-08-08 14:07:01',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (399,'proj_ensembl_havana_transcript','Transcript where the Ensembl genebuild transcript and the <a rel=\"external\" href=\"http://vega.sanger.ac.uk/index.html\">Vega</a> manual annotation have the same sequence, for every base pair. See <a href=\"http://www.ensembl.org/info/docs/genebuild/genome_annotation.html\" class=\"cp-external\">article</a>. This was projected to the <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml\">alternate locus</a> via a mapping from the <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml\">primary assembly</a>.','Projected Ensembl/Havana merge',NULL,'2011-08-08 15:27:49',NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (400,'ferret_protein','Ferret proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Ferret protein',101214,'2011-08-17 09:28:37',NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (400,'ferret_protein','Ferret protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Ferret protein',101214,'2011-08-17 09:28:37',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (401,'ferret_est','Ferret \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Ferret EST',101214,'2011-08-17 09:44:28',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (402,'ferret_cdna','Ferret cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Ferret cDNA',101214,'2011-08-17 09:48:13',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (403,'tilapia_est','Tilapia \'Expressed Sequence Tags\' (ESTs) from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Tilapia EST',101214,'2011-08-17 16:04:22',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (404,'tilapia_cdna','Tilapia cDNAs from <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> and <a rel=\"external\" href=\"http://www.ebi.ac.uk/embl/\">ENA</a> are aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Tilapia cDNA',101214,'2011-08-17 16:05:47',NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (405,'tilapia_protein','Tilapia proteins from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Tilapia protein',101214,'2011-08-17 16:08:20',NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (405,'tilapia_protein','Tilapia protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Tilapia protein',101214,'2011-08-17 16:08:20',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (406,'zebrafish_ensembl_protein','Selected Ensembl-predicted zebrafish peptide sequences aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Zebrafish Ensembl protein',101214,'2011-08-17 16:12:26',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (407,'stickleback_ensembl_protein','Selected Ensembl-predicted stickleback peptide sequences aligned to the genome using <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Stickleback Ensembl protein',101214,'2011-08-17 16:14:12',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (408,'repeatmask_cod_consortium','<a rel=\"external\" href=\"http://www.repeatmasker.org\">RepeatMasker</a> is used to find repeats using a cod repeat library provided by the Cod Consortium. This track usually shows repeats alone (not low-complexity sequences).','Repeats (Cod)',5132,'2011-08-18 10:20:41',NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (409,'ensembl_stickleback_projection','Models were annotated by projecting stickleback Ensembl transcripts through a BLASTZ DNA alignment to the stickleback genome','Projected stickleback',5132,'2011-08-26 15:02:39',NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (409,'stickleback_projected_protein','Models were annotated by projecting stickleback Ensembl transcripts through a BLASTZ DNA alignment to the stickleback genome','Stickleback projected protein',5132,'2011-08-26 15:02:39',NULL,NULL,1);
INSERT INTO `analysis_description` VALUES (410,'wga2genes_stickleback','Alignment to a stickleback Ensembl protein inferred by projecting through a BLASTZ DNA alignment to the stickleback genome','BLASTZ protein',5132,'2011-08-26 15:04:18',NULL,NULL,1);
-INSERT INTO `analysis_description` VALUES (411,'bushbaby_protein','Bushbaby protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a>.','Bushbaby protein',97245,'2011-09-01 10:06:01',NULL,NULL,1);
+INSERT INTO `analysis_description` VALUES (411,'bushbaby_protein','Bushbaby protein sequences from <a rel=\"external\" href=\"http://uniprot.org\">UniProtKB</a> and <a rel=\"external\" href=\"http://www.ncbi.nlm.nih.gov/RefSeq/\">NCBI RefSeq</a> are aligned to the genome using <a rel=\"external\" href=\"http://genome.cshlp.org/cgi/content/abstract/14/5/988?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=14&firstpage=988&resourcetype=HWCIT\">GeneWise</a> or <a rel=\"external\" href=\"http://www.biomedcentral.com/1471-2105/6/31\">Exonerate</a>.','Bushbaby protein',97245,'2011-09-01 10:06:01',NULL,NULL,1);
--
-- Table structure for table `analysis_web_data`
@@ -544,7 +544,7 @@ INSERT INTO `analysis_web_data` VALUES (66,22,32,1,'otherfeatures',1,NULL,NULL,N
INSERT INTO `analysis_web_data` VALUES (67,243,9,2,'core',1,NULL,NULL,NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (68,251,9,2,'core',1,NULL,NULL,NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (69,32,9,2,'core',0,NULL,NULL,NULL,NULL);
-INSERT INTO `analysis_web_data` VALUES (70,32,9,2,'otherfeatures',1,NULL,NULL,NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (70,32,32,2,'otherfeatures',1,NULL,NULL,NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (73,243,9,4,'core',1,NULL,NULL,NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (74,251,9,4,'core',1,NULL,NULL,NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (75,138,9,4,'core',0,NULL,NULL,NULL,NULL);
@@ -2905,7 +2905,7 @@ INSERT INTO `analysis_web_data` VALUES (2482,250,50,20,'core',1,97245,'2011-07-2
INSERT INTO `analysis_web_data` VALUES (2483,245,50,20,'core',1,97245,'2011-07-22 16:48:18',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2484,261,NULL,14,'core',0,97245,'2011-07-28 10:25:13',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2485,226,NULL,39,'core',1,97245,'2011-07-28 10:27:16',NULL,NULL);
-INSERT INTO `analysis_web_data` VALUES (2486,388,50,21,'otherfeatures',1,NULL,'2011-08-05 17:49:24',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2486,388,73,21,'otherfeatures',1,NULL,'2011-08-05 17:49:24',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2487,389,5,21,'otherfeatures',0,NULL,'2011-08-08 11:46:04',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2488,390,17,21,'otherfeatures',1,NULL,'2011-08-08 14:22:42',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2489,391,17,21,'otherfeatures',1,NULL,'2011-08-08 14:23:09',NULL,NULL);
@@ -2978,6 +2978,12 @@ INSERT INTO `analysis_web_data` VALUES (2555,250,50,33,'core',1,97245,'2011-09-0
INSERT INTO `analysis_web_data` VALUES (2556,261,NULL,33,'core',0,97245,'2011-09-01 10:33:10',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2557,411,NULL,33,'core',1,97245,'2011-09-01 10:34:21',NULL,NULL);
INSERT INTO `analysis_web_data` VALUES (2558,110,9,33,'otherfeatures',1,97245,'2011-09-02 10:03:44',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2559,151,66,52,'core',1,97245,'2011-09-23 14:12:16',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2560,151,66,1,'core',1,97245,'2011-09-27 11:28:20',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2561,151,66,51,'core',1,97245,'2011-09-27 11:38:22',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2562,151,66,31,'core',1,97245,'2011-09-27 11:51:55',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2563,151,66,22,'core',1,97245,'2011-09-27 14:14:00',NULL,NULL);
+INSERT INTO `analysis_web_data` VALUES (2564,151,66,56,'core',1,NULL,'2011-10-07 15:40:00',NULL,NULL);
--
-- Table structure for table `biotype`
@@ -2992,6 +2998,7 @@ CREATE TABLE `biotype` (
`is_dumped` tinyint(1) NOT NULL DEFAULT '1',
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega') NOT NULL DEFAULT 'core',
+ `attrib_type_id` int(11) DEFAULT NULL,
`description` text,
`created_by` int(11) DEFAULT NULL,
`created_at` datetime DEFAULT NULL,
@@ -3007,158 +3014,158 @@ SET character_set_client = @saved_cs_client;
--
-- ORDER BY: `biotype_id`
-INSERT INTO `biotype` VALUES (1,'IG_C_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (2,'IG_C_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (3,'IG_D_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (4,'IG_D_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (5,'IG_J_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (6,'IG_J_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (7,'IG_J_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (8,'IG_J_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (9,'IG_V_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (10,'IG_V_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (11,'IG_V_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (12,'IG_V_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (13,'IG_gene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (14,'IG_gene',1,1,'transcript','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (15,'IG_pseudogene',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (16,'IG_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (17,'LRG_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (18,'LRG_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (19,'Mt_rRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (20,'Mt_rRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (21,'Mt_tRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (22,'Mt_tRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (23,'Mt_tRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (24,'Mt_tRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (25,'RNA-Seq_gene',1,1,'gene','otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (26,'RNA-Seq_gene',1,1,'transcript','otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (27,'TEC',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (28,'TEC',1,1,'transcript','core,vega','',NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (29,'TR_gene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (30,'TR_gene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (31,'TR_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (32,'TR_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (33,'ambiguous_orf',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (34,'antisense',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (35,'cDNA_update',1,1,'gene','cdna',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (36,'cDNA_update',1,1,'transcript','cdna',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (37,'cdna',1,1,'gene','otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (38,'cdna',1,1,'transcript','otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (39,'disrupted_domain',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (40,'est',1,1,'gene','otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (41,'est',1,1,'transcript','otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (42,'lincRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (43,'lincRNA',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (44,'miRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (45,'miRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (46,'miRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (47,'miRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (48,'misc_RNA',1,1,'gene','core,otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (49,'misc_RNA',1,1,'transcript','core,otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (50,'misc_RNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (51,'misc_RNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (52,'ncRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (53,'ncRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (54,'non_coding',1,1,'gene','core,otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (55,'non_coding',1,1,'transcript','core,otherfeatures,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (56,'nonsense_mediated_decay',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (57,'polymorphic',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (58,'polymorphic_pseudogene',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (59,'polymorphic_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (60,'processed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (61,'processed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (62,'processed_transcript',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (63,'processed_transcript',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (64,'protein_coding',1,1,'gene','core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (65,'protein_coding',1,1,'transcript','core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (66,'pseudogene',1,1,'gene','core,otherfeatures,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (67,'pseudogene',1,1,'transcript','core,otherfeatures,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (68,'rRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (69,'rRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (70,'rRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (71,'rRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (72,'retained_intron',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (73,'retrotransposed',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (74,'retrotransposed',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (75,'scRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (76,'scRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (77,'snRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (78,'snRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (79,'snRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (80,'snRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (81,'snlRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (82,'snlRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (83,'snoRNA',1,1,'gene','core,otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (84,'snoRNA',1,1,'transcript','core,otherfeatures',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (85,'snoRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (86,'snoRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (87,'tRNA',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (88,'tRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (89,'tRNA_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (90,'tRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (91,'transcribed_processed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (92,'transcribed_processed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (93,'transcribed_unitary_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (94,'transcribed_unprocessed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (95,'transcribed_unprocessed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (96,'unitary_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (97,'unitary_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (98,'unprocessed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (99,'unprocessed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (100,'ccds_gene',1,0,'gene','otherfeatures','Imported CCDS gene models',NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (101,'protein_coding_in_progress',1,1,'gene','vega','occurs where the ORF is lost when remapping to a different assembly and the gene is awaiting reannotation',NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (102,'IG_Z_gene',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (103,'IG_M_gene',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (104,'ncrna_host',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (105,'TR_V_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (106,'TR_V_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (107,'IG_C_pseudogene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (108,'TR_C_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (109,'TR_J_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (110,'TR_V_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (111,'TR_V_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (112,'IG_C_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (113,'TR_C_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (114,'TR_J_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (115,'protein_coding_in_progress',1,1,'transcript','vega','occurs where the ORF is lost when remapping to a different assembly and the gene is awaiting reannotation',NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (116,'IG_M_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (117,'IG_Z_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (118,'3prime_overlapping_ncrna',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `biotype` VALUES (119,'snRNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:10:35',NULL,NULL);
-INSERT INTO `biotype` VALUES (120,'snRNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:11:25',NULL,NULL);
-INSERT INTO `biotype` VALUES (121,'miRNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:11:51',NULL,NULL);
-INSERT INTO `biotype` VALUES (122,'miRNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:11:59',NULL,NULL);
-INSERT INTO `biotype` VALUES (123,'antisense_RNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:12:32',NULL,NULL);
-INSERT INTO `biotype` VALUES (124,'antisense_RNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:12:40',NULL,NULL);
-INSERT INTO `biotype` VALUES (125,'scRNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:13:08',NULL,NULL);
-INSERT INTO `biotype` VALUES (126,'scRNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:13:15',NULL,NULL);
-INSERT INTO `biotype` VALUES (127,'RNase_MRP_RNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:14:03',NULL,NULL);
-INSERT INTO `biotype` VALUES (128,'RNase_MRP_RNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:14:09',NULL,NULL);
-INSERT INTO `biotype` VALUES (129,'RNase_P_RNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:14:40',NULL,NULL);
-INSERT INTO `biotype` VALUES (130,'RNase_P_RNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:14:46',NULL,NULL);
-INSERT INTO `biotype` VALUES (131,'telomerase_RNA',1,0,'gene','otherfeatures','From RefSeq import',5132,'2011-06-02 07:15:54',NULL,NULL);
-INSERT INTO `biotype` VALUES (132,'telomerase_RNA',1,0,'transcript','otherfeatures','From RefSeq import',5132,'2011-06-02 07:16:03',NULL,NULL);
-INSERT INTO `biotype` VALUES (133,'sense_intronic',1,1,'transcript','core',NULL,97245,'2011-07-18 10:14:50',NULL,NULL);
-INSERT INTO `biotype` VALUES (134,'sense_intronic',1,1,'transcript','vega',NULL,97245,'2011-07-19 13:29:32',NULL,NULL);
-INSERT INTO `biotype` VALUES (135,'sense_overlapping',1,1,'transcript','vega',NULL,97245,'2011-07-19 13:29:37',NULL,NULL);
-INSERT INTO `biotype` VALUES (136,'antisense',1,1,'gene','vega',NULL,97245,'2011-07-19 13:30:11',NULL,NULL);
-INSERT INTO `biotype` VALUES (137,'lincRNA',1,1,'gene','vega',NULL,97245,'2011-07-19 13:30:14',NULL,NULL);
-INSERT INTO `biotype` VALUES (138,'sense_intronic',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:24',NULL,NULL);
-INSERT INTO `biotype` VALUES (139,'ambiguous_orf',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:27',NULL,NULL);
-INSERT INTO `biotype` VALUES (140,'retained_intron',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:31',NULL,NULL);
-INSERT INTO `biotype` VALUES (141,'non_coding',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:35',NULL,NULL);
-INSERT INTO `biotype` VALUES (142,'3prime_overlapping_ncrna',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:38',NULL,NULL);
-INSERT INTO `biotype` VALUES (143,'ncrna_host',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:42',NULL,NULL);
-INSERT INTO `biotype` VALUES (144,'sense_overlapping',1,1,'gene','vega',NULL,97245,'2011-07-19 13:31:47',NULL,NULL);
-INSERT INTO `biotype` VALUES (145,'sense_overlapping',1,1,'transcript','core',NULL,97245,'2011-07-20 10:09:57',NULL,NULL);
-INSERT INTO `biotype` VALUES (146,'TR_D_gene',1,1,'transcript','core',NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
-INSERT INTO `biotype` VALUES (147,'TR_J_pseudogene',1,1,'transcript','core',NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
-INSERT INTO `biotype` VALUES (148,'TR_D_gene',1,1,'gene','core',NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
-INSERT INTO `biotype` VALUES (149,'TR_J_pseudogene',1,1,'gene','core',NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
-INSERT INTO `biotype` VALUES (150,'ncbi_pseudogene',1,0,'gene','otherfeatures','Imported annotation from RefSeq',5132,'2011-08-06 09:03:27',NULL,NULL);
-INSERT INTO `biotype` VALUES (151,'ncbi_pseudogene',1,0,'transcript','otherfeatures','Imported annotation from RefSeq',5132,'2011-08-06 09:04:11',NULL,NULL);
-INSERT INTO `biotype` VALUES (152,'ncbigene',1,0,'gene','otherfeatures','Imported annotation from RefSeq',5132,'2011-08-06 09:04:25',NULL,NULL);
+INSERT INTO `biotype` VALUES (1,'IG_C_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (2,'IG_C_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (3,'IG_D_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (4,'IG_D_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (5,'IG_J_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (6,'IG_J_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (7,'IG_J_pseudogene',1,1,'gene','core',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (8,'IG_J_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (9,'IG_V_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (10,'IG_V_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (11,'IG_V_pseudogene',1,1,'gene','core',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (12,'IG_V_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (13,'IG_gene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (14,'IG_gene',1,1,'transcript','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (15,'IG_pseudogene',1,1,'gene','core,vega',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (16,'IG_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (17,'LRG_gene',1,1,'gene','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (18,'LRG_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (19,'Mt_rRNA',1,1,'gene','core',73,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (20,'Mt_rRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (21,'Mt_tRNA',1,1,'gene','core',74,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (22,'Mt_tRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (23,'Mt_tRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (24,'Mt_tRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (25,'RNA-Seq_gene',1,1,'gene','otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (26,'RNA-Seq_gene',1,1,'transcript','otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (27,'TEC',1,1,'gene','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (28,'TEC',1,1,'transcript','core,vega',NULL,'',NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (29,'TR_gene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (30,'TR_gene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (31,'TR_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (32,'TR_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (33,'ambiguous_orf',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (34,'antisense',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (35,'cDNA_update',1,1,'gene','cdna',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (36,'cDNA_update',1,1,'transcript','cdna',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (37,'cdna',1,1,'gene','otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (38,'cdna',1,1,'transcript','otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (39,'disrupted_domain',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (40,'est',1,1,'gene','otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (41,'est',1,1,'transcript','otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (42,'lincRNA',1,1,'gene','core',190,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (43,'lincRNA',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (44,'miRNA',1,1,'gene','core',70,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (45,'miRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (46,'miRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (47,'miRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (48,'misc_RNA',1,1,'gene','core,otherfeatures',71,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (49,'misc_RNA',1,1,'transcript','core,otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (50,'misc_RNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (51,'misc_RNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (52,'ncRNA',1,1,'gene','core',99,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (53,'ncRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (54,'non_coding',1,1,'gene','core,otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (55,'non_coding',1,1,'transcript','core,otherfeatures,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (56,'nonsense_mediated_decay',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (57,'polymorphic',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (58,'polymorphic_pseudogene',1,1,'gene','core,vega',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (59,'polymorphic_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (60,'processed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (61,'processed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (62,'processed_transcript',1,1,'gene','core,vega',79,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (63,'processed_transcript',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (64,'protein_coding',1,1,'gene','core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (65,'protein_coding',1,1,'transcript','core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (66,'pseudogene',1,1,'gene','core,otherfeatures,vega',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (67,'pseudogene',1,1,'transcript','core,otherfeatures,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (68,'rRNA',1,1,'gene','core',66,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (69,'rRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (70,'rRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (71,'rRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (72,'retained_intron',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (73,'retrotransposed',1,1,'gene','core',77,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (74,'retrotransposed',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (75,'scRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (76,'scRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (77,'snRNA',1,1,'gene','core',68,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (78,'snRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (79,'snRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (80,'snRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (81,'snlRNA',1,1,'gene','core',78,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (82,'snlRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (83,'snoRNA',1,1,'gene','core,otherfeatures',69,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (84,'snoRNA',1,1,'transcript','core,otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (85,'snoRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (86,'snoRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (87,'tRNA',1,1,'gene','core',76,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (88,'tRNA',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (89,'tRNA_pseudogene',1,1,'gene','core',75,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (90,'tRNA_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (91,'transcribed_processed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (92,'transcribed_processed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (93,'transcribed_unitary_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (94,'transcribed_unprocessed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (95,'transcribed_unprocessed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (96,'unitary_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (97,'unitary_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (98,'unprocessed_pseudogene',1,1,'gene','vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (99,'unprocessed_pseudogene',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (100,'ccds_gene',1,0,'gene','otherfeatures',NULL,'Imported CCDS gene models',NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (101,'protein_coding_in_progress',1,1,'gene','vega',NULL,'occurs where the ORF is lost when remapping to a different assembly and the gene is awaiting reannotation',NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (102,'IG_Z_gene',1,1,'gene','core,vega',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (103,'IG_M_gene',1,1,'gene','core,vega',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (104,'ncrna_host',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (105,'TR_V_pseudogene',1,1,'gene','core',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (106,'TR_V_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (107,'IG_C_pseudogene',1,1,'gene','core',67,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (108,'TR_C_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (109,'TR_J_gene',1,1,'gene','core',100,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (110,'TR_V_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (111,'TR_V_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (112,'IG_C_pseudogene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (113,'TR_C_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (114,'TR_J_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (115,'protein_coding_in_progress',1,1,'transcript','vega',NULL,'occurs where the ORF is lost when remapping to a different assembly and the gene is awaiting reannotation',NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (116,'IG_M_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (117,'IG_Z_gene',1,1,'transcript','core',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (118,'3prime_overlapping_ncrna',1,1,'transcript','core,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `biotype` VALUES (119,'snRNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:10:35',NULL,NULL);
+INSERT INTO `biotype` VALUES (120,'snRNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:11:25',NULL,NULL);
+INSERT INTO `biotype` VALUES (121,'miRNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:11:51',NULL,NULL);
+INSERT INTO `biotype` VALUES (122,'miRNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:11:59',NULL,NULL);
+INSERT INTO `biotype` VALUES (123,'antisense_RNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:12:32',NULL,NULL);
+INSERT INTO `biotype` VALUES (124,'antisense_RNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:12:40',NULL,NULL);
+INSERT INTO `biotype` VALUES (125,'scRNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:13:08',NULL,NULL);
+INSERT INTO `biotype` VALUES (126,'scRNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:13:15',NULL,NULL);
+INSERT INTO `biotype` VALUES (127,'RNase_MRP_RNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:14:03',NULL,NULL);
+INSERT INTO `biotype` VALUES (128,'RNase_MRP_RNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:14:09',NULL,NULL);
+INSERT INTO `biotype` VALUES (129,'RNase_P_RNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:14:40',NULL,NULL);
+INSERT INTO `biotype` VALUES (130,'RNase_P_RNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:14:46',NULL,NULL);
+INSERT INTO `biotype` VALUES (131,'telomerase_RNA',1,0,'gene','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:15:54',NULL,NULL);
+INSERT INTO `biotype` VALUES (132,'telomerase_RNA',1,0,'transcript','otherfeatures',NULL,'From RefSeq import',5132,'2011-06-02 07:16:03',NULL,NULL);
+INSERT INTO `biotype` VALUES (133,'sense_intronic',1,1,'transcript','core',NULL,NULL,97245,'2011-07-18 10:14:50',NULL,NULL);
+INSERT INTO `biotype` VALUES (134,'sense_intronic',1,1,'transcript','vega',NULL,NULL,97245,'2011-07-19 13:29:32',NULL,NULL);
+INSERT INTO `biotype` VALUES (135,'sense_overlapping',1,1,'transcript','vega',NULL,NULL,97245,'2011-07-19 13:29:37',NULL,NULL);
+INSERT INTO `biotype` VALUES (136,'antisense',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:30:11',NULL,NULL);
+INSERT INTO `biotype` VALUES (137,'lincRNA',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:30:14',NULL,NULL);
+INSERT INTO `biotype` VALUES (138,'sense_intronic',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:24',NULL,NULL);
+INSERT INTO `biotype` VALUES (139,'ambiguous_orf',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:27',NULL,NULL);
+INSERT INTO `biotype` VALUES (140,'retained_intron',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:31',NULL,NULL);
+INSERT INTO `biotype` VALUES (141,'non_coding',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:35',NULL,NULL);
+INSERT INTO `biotype` VALUES (142,'3prime_overlapping_ncrna',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:38',NULL,NULL);
+INSERT INTO `biotype` VALUES (143,'ncrna_host',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:42',NULL,NULL);
+INSERT INTO `biotype` VALUES (144,'sense_overlapping',1,1,'gene','vega',NULL,NULL,97245,'2011-07-19 13:31:47',NULL,NULL);
+INSERT INTO `biotype` VALUES (145,'sense_overlapping',1,1,'transcript','core',NULL,NULL,97245,'2011-07-20 10:09:57',NULL,NULL);
+INSERT INTO `biotype` VALUES (146,'TR_D_gene',1,1,'transcript','core',NULL,NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
+INSERT INTO `biotype` VALUES (147,'TR_J_pseudogene',1,1,'transcript','core',NULL,NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
+INSERT INTO `biotype` VALUES (148,'TR_D_gene',1,1,'gene','core',100,NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
+INSERT INTO `biotype` VALUES (149,'TR_J_pseudogene',1,1,'gene','core',67,NULL,97245,'2011-07-20 10:10:01',NULL,NULL);
+INSERT INTO `biotype` VALUES (150,'ncbi_pseudogene',1,0,'gene','otherfeatures',NULL,'Imported annotation from RefSeq',5132,'2011-08-06 09:03:27',NULL,NULL);
+INSERT INTO `biotype` VALUES (151,'ncbi_pseudogene',1,0,'transcript','otherfeatures',NULL,'Imported annotation from RefSeq',5132,'2011-08-06 09:04:11',NULL,NULL);
+INSERT INTO `biotype` VALUES (152,'ncbigene',1,0,'gene','otherfeatures',NULL,'Imported annotation from RefSeq',5132,'2011-08-06 09:04:25',NULL,NULL);
--
-- Table structure for table `changelog`
@@ -3182,6 +3189,7 @@ CREATE TABLE `changelog` (
`biomart_affected` enum('N','Y') NOT NULL DEFAULT 'N',
`variation_pos_changed` enum('N','Y') NOT NULL DEFAULT 'N',
`db_status` enum('N/A','unchanged','patched','new') NOT NULL DEFAULT 'N/A',
+ `priority` tinyint(1) NOT NULL DEFAULT '2',
`created_by` int(11) DEFAULT NULL,
`created_at` datetime DEFAULT NULL,
`modified_by` int(11) DEFAULT NULL,
@@ -3196,381 +3204,463 @@ SET character_set_client = @saved_cs_client;
--
-- ORDER BY: `changelog_id`
-INSERT INTO `changelog` VALUES (1,59,'Changelog','<p>As of release 59, Ensembl will use a changelog to track detailed updates to the data and code. This will be separate from the release news, which will focus on major updates such as new species and web features.</p>\r\n\r\n<p>The changelog is stored in the new ensembl_production database, rather than ensembl_website.</p>','sauausatuhusahsu','handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2010-05-18 11:04:18',2,'2010-07-16 09:36:02',1);
-INSERT INTO `changelog` VALUES (3,59,'Ensembl marts for release 59','<p>Full build of seven marts:<br />- sequence mart.<br />- ensembl mart: possible orthologs added.<br />- snp mart: somatic data set added.<br />- ontology mart.<br />- vega mart<br />- functional genomics mart.<br />- genomic features mart.</p>','','handed_over','Mart','N','N','N','N','N','N','N','N/A',100169,'2010-05-27 16:32:04',36,'2010-07-27 14:38:25',1);
-INSERT INTO `changelog` VALUES (4,59,'external database references','<p>Update External database references for:-</p>\r\n<ul>\r\n<li>Human</li>\r\n<li>Mouse</li>\r\n<li>Cow</li>\r\n<li>Chicken</li>\r\n</ul>','','handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2010-05-28 09:35:36',36,'2010-07-27 14:36:03',1);
-INSERT INTO `changelog` VALUES (5,59,'Update to human RepeatMasking','<ul>\r\n<li>Update to human Repeatmasking: this involves re-running the RepeatMasker analysis on toplevel slices, with the \'-nolow\' flag, so that low complexity regions are not masked. </li>\r\n</ul>','','handed_over','Genebuild','Y','N','Y','N','N','N','N','new',5132,'2010-05-28 14:19:01',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (6,59,'Update human otherfeatures db','<p>Update human otherfeatures database:</p>\r\n<ul>\r\n<li>New CCDS models</li>\r\n</ul>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',5132,'2010-05-28 14:20:33',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (8,59,'New species name meta-values with corresponding helper methods','<p>A set of new meta key-value pairs are inserted into all Core databases:</p>\r\n<ul>\r\n<li>species.production_name (a string that may be used to refer to a particular species in e.g. database tables or file names)</li>\r\n<li>species.scientific_name (the full bi- or trinomial scientific name of the species)</li>\r\n<li>species.short_name (a short string, often based on the common name, useful for labels in GUIs etc.)</li>\r\n</ul>\r\n<p>For each of these, the Bio::EnsEMBL::DBSQL::MetaContainer class now also contains a get_* method for retrieval of the corresponding meta value (get_short_name(), etc.). There is also a new get_common_name() method.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',896,'2010-06-21 13:29:37',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (9,59,'ResultFeature Collection Normalisation','<p>All result_feature collections (Human & Mouse) have been normalised using a simple by read count method(RPKM), enabling more meaningful visual comparisons using the multi-wiggle displays. </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-01 10:45:56',1273,'2010-07-21 11:26:05',1);
-INSERT INTO `changelog` VALUES (10,59,'Mouse IKMC xrefs and features','<p>Support mouse IKMC (International Mouse Knockout Consortium) links by creating a set of simple features to show the genomic extent of the knockouts.</p>','','handed_over','Core','N','N','N','N','N','N','N','patched',36,'2010-06-01 10:56:32',36,'2010-07-16 09:37:58',1);
-INSERT INTO `changelog` VALUES (11,59,'Update Amazon data sets','<p>Update Amazon data sets for MySQL and FASTA dumps.</p>','','handed_over','Core','N','N','N','N','N','N','N','patched',36,'2010-06-01 10:57:48',36,'2010-07-27 14:46:21',1);
-INSERT INTO `changelog` VALUES (12,59,'Gene name and GO term projections','<p>Assign gene names and GO terms to species where they are not well covered by projection from well-annotated species, using Compara homologies.</p>','','handed_over','Core','N','N','N','N','N','N','N','patched',36,'2010-06-01 10:58:59',36,'2010-07-16 09:38:24',1);
-INSERT INTO `changelog` VALUES (13,59,'Schema patch: annotated_feature.summit','<p>The annotated_feature table now has a dedicated peak \'summit\' field (patch_58_59_c.sql). API support has been added both to the eFG and the ensembl-analysis APIs.</p>\r\n<p> </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-01 16:18:51',1273,'2010-07-21 11:26:38',1);
-INSERT INTO `changelog` VALUES (14,59,'Update to human ensembl-vega','<p>Update to the human havana annotation shown in the \'Vega Havana\' gene track</p>','','postponed','Genebuild','N','Y','N','N','N','N','N','new',161,'2010-06-01 16:33:58',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (15,59,'Schema patch: probe.description','<p>The probe table has been patched (patch_58_59_b) to add a description column. Appropriate API support has also been added to the eFG and ensembl-analysis APIs</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-02 10:50:35',1273,'2010-07-21 11:27:43',1);
-INSERT INTO `changelog` VALUES (16,59,'Schema path: regulatory_feature.binary_string_project','<p>The regulatory_feature table has been redefined (patch_58_59_d) to add a new binary_string and projected columns to store information generated from the Regulatory Build. API has also be added to the RegulatoryFeature class and associated adaptor.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-02 10:54:49',1273,'2010-07-21 11:28:08',1);
-INSERT INTO `changelog` VALUES (17,59,'Mouse Projection Regulatory Build','<p>The Mouse Regulatory Build has been regenerated using a new \'projection\' method. Core(MultiCell) RegulatoryFeatures are only be projected to these sparsely annotated cell lines if more annotation is available i.e. RegulatoryFeatures are not be built if there is no supporting evidence on the given cell line.</p>\r\n<p>This reintroduces some data from different cell lines which do not have associated \'core\' features (e.g. DNAse1) along with some new TFBS data.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-02 11:08:53',2,'2010-07-21 11:49:11',1);
-INSERT INTO `changelog` VALUES (18,59,'New chip-seq datasets','<p><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">Add ENCODE Chip-seq datasets for the following cell types:</span></p>\r\n<ul>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">K562: Update of the Current Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">GM12878: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">H1 ES: New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">HeLa: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">HepG2: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">HUVEC: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">No Regulatory Build for this cell line in this release </span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">NHEK: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n</ul>\r\n<p><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\"><br />Add mouse TF Chip-Seq datasets from Chen et all (2008)</span></p>\r\n<ul>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: small;\"><span style=\"border-collapse: collapse; font-size: 13px;\">Update of the Current Mouse ES Reg</span></span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">ulatory Build</span></li>\r\n</ul>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2010-06-02 11:24:50',100304,'2010-07-28 09:38:30',1);
-INSERT INTO `changelog` VALUES (19,59,'Schema change','<p>We will have the following schema patches to the Ensembl Core schema:</p>\r\n<ol>\r\n<li>Update schema version, as usual.</li>\r\n<li>Add new exception types (\'PATCH_NOVEL\' and \'PATCH_FIX\') to the assembly_exception table. This is to allow for patched assemblies.</li>\r\n<li>Modify the splicing_event table so that instead of a \'type\' field there is an \'attrib_type_id\' pointing to the attrib_type table. The short enumerated codes were too terse.</li>\r\n<li>A unique index in the object_xref table (\'object_type_idx\') is being extended to include the \'analysis_id\'. This is to allow two object Xrefs for the same object using two different analyses.</li>\r\n<li>A new meta key \'schema_type\' (with value \'core\' for Ensembl Core databases) will be inserted into all Core databases.</li>\r\n</ol>','','handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2010-06-02 13:21:16',36,'2010-07-27 14:37:17',1);
-INSERT INTO `changelog` VALUES (20,59,'Drosophila melanogaster update','<p>Update of D. melanogaster gene set to release 5.25 (FlyBase 2010_02).</p>','','handed_over','Core','N','Y','N','N','Y','N','N','new',98587,'2010-06-02 15:35:39',737,'2010-07-21 11:37:03',1);
-INSERT INTO `changelog` VALUES (21,59,'Drosophila melanogaster update','<ul>\r\n<li>Affy mapping update for D. melanogaster 5.25</li>\r\n<li>Regulatory elements update from REDfly v2.2</li>\r\n</ul>\r\n<p> </p>','','handed_over','Funcgen','N','Y','N','N','Y','N','N','new',98587,'2010-06-02 15:53:11',98587,'2010-07-28 13:40:44',1);
-INSERT INTO `changelog` VALUES (22,59,'Variation data','Import of dbSNP 131 for Human\r\n and calculation of variation consequences and tag SNPs<br />\r\nImport of the CNV probes from the Affymetrix Genome 6 array <br />\r\nImport new LRG sequences<br />\r\nCorrect population sizes (currently 1 or 0 only)<br />\r\nCorrect zebrafish display strain defaults <br />\r\nsomatic mutation substitutions from 70 genes involved in cancer (COSMIC) \r\nUpdate UniProt and DGVa data\r\n<p>Update variation consequences (in transcript_variation table ) for new gene sets in: cow, horse, chicken, platypus, mouse, orangutan</p>\r\n','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2010-06-02 17:15:57',3,'2010-07-21 13:25:43',1);
-INSERT INTO `changelog` VALUES (23,59,'Update of mouse gene set','<p>Update of mouse gene set incorporating new Vega genes, implementing new code for HavanaAdder.</p>','','handed_over','Genebuild','N','Y','N','Y','Y','N','N','patched',97238,'2010-06-02 21:21:11',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (24,59,'Selenocysteine update','<p>Update 172 transcripts across 25 species to remove 3<span class=\"misspell\"> base pair</span> introns where there should be a selenocysteine.</p>\r\n<p>The following species are affected:</p>\r\n<ul>\r\n<li>bos taurus</li>\r\n<li>choloepus hoffmanni </li>\r\n<li>dasypus novemcinctus </li>\r\n<li>dipodomys ordii </li>\r\n<li>echinops telfairi </li>\r\n<li>equus caballus </li>\r\n<li>erinaceus europaeus </li>\r\n<li>felis catus </li>\r\n<li>gallus gallus </li>\r\n<li>gorilla gorilla </li>\r\n<li>macropus eugenii </li>\r\n<li>microcebus murinus </li>\r\n<li>myotis lucifugus </li>\r\n<li>ochotona princeps </li>\r\n<li>ornithorhynchus anatinus </li>\r\n<li>otolemur garnettii</li>\r\n<li>pongo pygmaeus </li>\r\n<li>procavia capensis </li>\r\n<li>pteropus vampyrus </li>\r\n<li>sorex araneus </li>\r\n<li>spermophilus tridecemlineatus </li>\r\n<li>tarsius syrichta </li>\r\n<li>tupaia belangeri </li>\r\n<li>tursiops truncatus </li>\r\n<li>vicugna pacos </li>\r\n</ul>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',29,'2010-06-03 09:42:53',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (25,59,'New human assembly patches','<p>Update human assembly to include sequence for the new assembly patches provided by the GRC (patch_release_1).</p>\r\n<ul>\r\n<li>Assembly patches are toplevel and non-reference</li>\r\n</ul>','','handed_over','Genebuild','Y','N','Y','N','N','N','N','new',5132,'2010-06-03 10:09:15',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (26,59,'Human Regulatory Build - 6 New cell lines & data update','<p>The Human Regulatory Build has been regenerated to incorporate the 5 new ENCODE cell lines: GM12878, H1ES, HeLa, HepG2, and NHEK.</p>\r\n<p>The new data has also been used to update the core MultiCell and existing cell line specific build i.e. K562, IMR90, GM06990, CD4. </p>\r\n<p> </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-03 10:28:02',100304,'2010-07-28 09:55:38',1);
-INSERT INTO `changelog` VALUES (27,59,'Ensembl-Havana merge (GENCODE gene set)','<p>There will be a new Ensembl-Havana merge gene set incorporating new annotation from Vega database.</p>','','postponed','Genebuild','N','Y','Y','Y','N','N','N','new',9335,'2010-06-03 10:32:06',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (28,59,'Variation API','<p>Add a new 1000 Genomes set<br />modify call for nearest gene to variation feature<br />HGVS nomenclature on proteins</p>\r\nChanges to API and schema to separate somatic and germline variations','','handed_over','Variation','N','N','N','N','N','N','N','new',99616,'2010-06-03 10:59:21',3,'2010-07-21 11:58:01',1);
-INSERT INTO `changelog` VALUES (29,59,'Additional mapping for marmoset','<p>An additional contig to scaffold mapping for unplaced and unlocalized scaffolds</p>\r\n<p>Update of the corresponding gene coordinates</p>','','handed_over','Genebuild','N','N','Y','N','N','N','N','patched',97245,'2010-06-03 10:59:58',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (30,59,'Variation schema','<p><br />New enums for 1000 Genomes and also for precious SNPs in the validation status column<br />add schema type key into the meta table</p>','','handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2010-06-03 11:01:15',3,'2010-07-21 11:47:00',1);
-INSERT INTO `changelog` VALUES (31,59,'Mouse cDNA update','<p>Mouse cDNA update</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','new',97245,'2010-06-03 11:01:25',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (32,59,'cDNA based gene annotation of human assembly patches','<p>Annotate human assembly patches with cDNA based gene models.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',14183,'2010-06-03 11:07:24',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (33,59,'Array Mapping','<p>Array mapping and Transcript xrefs have been regenerated for species which have updated genome assemblies or genebuilds.</p>','','handed_over','Funcgen','N','N','N','N','Y','N','N','N/A',1273,'2010-06-03 11:12:51',100304,'2010-07-28 09:40:07',1);
-INSERT INTO `changelog` VALUES (34,59,'Mouse ChIP-Seq data','<p><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; color: #555555; white-space: pre;\">Transcription Factor Chip-Seq data has been added (Chen </span><span style=\"font-size: 13px; border-collapse: collapse; color: #555555; white-space: pre;\"><em>et al</em></span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; color: #555555; white-space: pre;\"> 2008)</span></p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-03 11:36:54',100304,'2010-07-28 09:55:05',1);
-INSERT INTO `changelog` VALUES (35,59,'Ontology database','<p>We will provide the ensembl_ontology_59 database with updated data from Gene Ontology (GO) and Sequence Ontology (SO).</p>','','handed_over','Core','N','N','N','N','N','N','N','new',896,'2010-06-03 12:07:02',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (36,59,'Saccharomyces cerevisiae core database','<p>Core database from Ensembl Genomes (updated March 2010 from SGD, currently in EG5) in 58 schema, patched to 59 schema when sql available. Also corresponding other_features database containing ESTs.</p>','Contact arnaud@ebi.ac.uk about yeast databases','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',101216,'2010-06-03 14:58:52',737,'2010-07-21 11:36:41',1);
-INSERT INTO `changelog` VALUES (37,59,'Saccharomyces cerevisiae funcgen database','<p>Database containing Affy array mapping data for Saccharomyces cerevisiae. Currently part of Ensembl Genomes Release 5. Currently 58, will be patched to 59.</p>','Contact arnaud@ebi.ac.uk','handed_over','Funcgen','N','N','N','N','Y','N','N','new',101216,'2010-06-03 15:00:29',101255,'2010-07-28 13:49:46',1);
-INSERT INTO `changelog` VALUES (38,59,'Saccharomyces cerevisiae variation database','<p>Variation database containing data from Saccharomyces Resequencing Project at the Sanger Institute. Present in Ensembl Genomes release 5 as schema 58. Will be patched to 59.</p>','contact: Arnaud Kerhornou \r\narnaud@ebi.ac.uk','handed_over','Variation','N','N','N','N','N','N','N','new',101216,'2010-06-03 15:02:01',101255,'2010-07-28 13:52:24',1);
-INSERT INTO `changelog` VALUES (39,59,'Drosophila melanogaster','<p>Drosophila melanogaster variation database based on DPGP 1.0</p>','','handed_over','Variation','N','Y','N','N','N','N','N','new',98587,'2010-06-03 17:15:59',98587,'2010-07-28 13:41:23',1);
-INSERT INTO `changelog` VALUES (40,59,'external db id','<p>Fixing dna align feature tables of otherfeatures databases for various species by adding external db ids</p>\r\n<p> </p>\r\n<p>WARNING, missing external_db_ids from Anolis_carolinensis DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Bos_taurus DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Bos_taurus DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Danio_rerio DATABASE_CORE dna_align_feature<br />WARNING, missing external_db_ids from Danio_rerio DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Drosophila_melanogaster DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Equus_caballus DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Saccharomyces_cerevisiae DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Taeniopygia_guttata DATABASE_OTHERFEATURES dna_align_feature</p>\r\n<p> </p>','','declared','Genebuild','N','N','N','N','N','N','N','patched',1011,'2010-06-04 12:13:42',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (41,59,'Pairwise alignments','<p>Add new haplotype alignments for human vs high coverage blastz-net alignments<br /><br /> * H.sap-P.tro<br /> * H.sap-G.gor<br /> * H.sap-P.pyg<br /> * H.sap-M.mul<br /> * H.sap-M.mus<br /> * H.sap-R.nor<br /> * H.sap-C.fam<br /> * H.sap-B.tau<br /> * H.sap-S.scr<br /> * H.sap-E.cab<br /> * H.sap-O.ana<br /> * H.sap-M.dom<br /> * H.sap-G.gal<br /><br />New blastz-net due to changes in marmoset assembly<br /><br /> * H.sap-C.jac</p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-06-04 12:15:46',49918,'2010-07-16 09:44:17',1);
-INSERT INTO `changelog` VALUES (42,59,'Multiple alignments','<p> * 33 way epo low coverage<br /> * 6 way epo primates<br /> * 11 way epo eutherian mammals<br /> * Add MT alignments for fish, 11 and 33 way EPO alignments<br /> * Map changes to marmoset assembly in 16-way mecator/pecan placental mammals</p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-06-04 12:17:11',49918,'2010-07-16 09:44:49',1);
-INSERT INTO `changelog` VALUES (43,59,'Compara dumps','<p> * EMF dumps for 6 way EPO multiple alignments<br /> * EMF dumps for 11 way EPO multiple alignments<br /> * EMF dumps for 16 way mecator/pecan multiple alignments<br /> * EMF dumps for 33 way EPO multiple aligments<br /> * BED files for 33 way GERP constrained elements<br /> * EMF dumps for GeneTrees</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-06-04 12:18:11',96753,'2010-07-27 14:39:16',1);
-INSERT INTO `changelog` VALUES (44,59,'Families','<p>Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.<br /><br /> * Clustering by MCL<br /> * Multiple Sequence Alignments with MAFFT<br /> * Family stable ID mapping</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-06-04 12:19:02',49918,'2010-07-16 09:45:08',1);
-INSERT INTO `changelog` VALUES (45,59,'Gene Homlogies','<p>GeneTrees with new/updated genebuilds and assemblies<br /><br /> * Updated build of ncRNA trees<br /> * Clustering using hcluster_sg<br /> * Multiple Sequence Alignments using consistency-based MCoffee meta-aligner<br />(mafftgins+muscle+kalign+probcons) and exon-skipping aware \"skipper\" algorithm<br /> * Homology inference including the recent \'possible_ortholog\' type and \'putative gene split\' and<br />\'contiguous gene split\' exceptions<br /> * Pairwise gene-based dN/dS calculations for high coverage species pairs only<br /> * GeneTree stable ID mapping</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-06-04 12:20:02',49918,'2010-07-16 09:45:33',1);
-INSERT INTO `changelog` VALUES (46,59,'Schema changes','<p>* Addition of extra column in dnafrag table to hold information on whether the fragment is reference or non-reference.</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-06-04 12:20:45',49918,'2010-07-16 09:45:52',1);
-INSERT INTO `changelog` VALUES (47,59,'assembly fixes','<p>The assembly / seq region tables of otherfeatures databaess for these species will be sync. with their core databases bos_taurus_otherfeatures_58_4g<br />sus_scrofa_otherfeatures_58_9b<br />pan_troglodytes_otherfeatures_58_21m<br />danio_rerio_otherfeatures_58_8d<br />pongo_pygmaeus_otherfeatures_58_1d<br /><br /></p>','','handed_over','Genebuild','Y','N','N','N','N','N','N','patched',1011,'2010-06-04 12:25:30',5132,'2010-07-16 13:16:15',1);
-INSERT INTO `changelog` VALUES (48,59,'human cdna update','<p>new human cdna update database with integrated assembly patches</p>','','handed_over','Genebuild','Y','Y','N','N','N','N','N','new',1011,'2010-06-04 12:29:08',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (49,59,'Change name of EMBL database to European Nucleotide Archive','<p>Change name of EMBL database to European Nucleotide Archive to reflect the new official name. External reference sources will be the most obvious change.</p>','','declared','Core','N','N','N','N','N','N','N','patched',36,'2010-06-04 12:36:07',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (50,59,'Meta schema_type','<p>A meta entry has been added to the eFG DBs to capture the schema type \'funcgen\' (patch_58_59_e).</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-08 14:32:26',100304,'2010-07-28 09:31:06',1);
-INSERT INTO `changelog` VALUES (51,59,'variation displays','The LRG display now has tables listing differences between the LRG and the reference sequence.<br />\r\nThe context panel of the variation page has been updated to show if the variant overlaps a regulatory region, structural variants or conserved region\r\n','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2010-06-09 17:29:51',3,'2010-07-21 13:24:37',1);
-INSERT INTO `changelog` VALUES (52,59,'Schema patch: result_feature partitions','<p>The result_feature table partitions have been modified slightly to reflect the true default zoom levels in the \'Region in Detail\' view (patch_58_59_f). Collection data has been regenerated accordingly.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-10 13:19:52',100304,'2010-07-28 09:40:54',1);
-INSERT INTO `changelog` VALUES (53,59,'Meta table changes','<p>These changes are intended to solidify the requirements for names in Ensembl and will reduce the amount of name conversion which occurs in the codebase.</p>\r\n<table class=\"confluenceTable\">\r\n<tbody>\r\n<tr>\r\n<th class=\"confluenceTh\">meta key</th> <th class=\"confluenceTh\">usage</th> <th class=\"confluenceTh\">required</th> <th class=\"confluenceTh\">stable</th> <th class=\"confluenceTh\">regular expression</th> <th class=\"confluenceTh\">example value</th>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.production_name</td>\r\n<td class=\"confluenceTd\">Used for a computing scenario e.g. writing a file to disk.</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">\r\n$[a-z0-9_]+^</pre>\r\n</div>\r\n</div>\r\n</td>\r\n<td class=\"confluenceTd\">homo_sapiens</td>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.scientific_name</td>\r\n<td class=\"confluenceTd\">The full name of the species, which should replace the call\r\nMetaContainer->get_Species()->binomial()\r\n</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">-</td>\r\n<td class=\"confluenceTd\">Homo sapiens</td>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.common_name</td>\r\n<td class=\"confluenceTd\">The common name of the species, which can equal the value from taxonomy</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">-</td>\r\n<td class=\"confluenceTd\">human</td>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.short_name</td>\r\n<td class=\"confluenceTd\">A name which is short enough to be used in space-constrained areas (such as tabs on the web site)</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">-</td>\r\n<td class=\"confluenceTd\">human</td>\r\n</tr>\r\n</tbody>\r\n</table>','The link between core to compara and web code to compara is a perfect example of the problem and with the introduction of more specific names (strain types from Ensembl Genomes and trinomial named species) this is something we need to put a stop to now.','handed_over','Core','N','N','N','N','N','N','N','N/A',737,'2010-06-11 11:27:13',2,'2010-08-05 10:27:39',1);
-INSERT INTO `changelog` VALUES (54,59,'Update mouse otherfeatures db','<p>Update mouse otherfeatures db</p>\r\n<ul>\r\n<li>New CCDS models</li>\r\n</ul>','','handed_over','Genebuild','N','Y','N','N','N','N','N','patched',5132,'2010-06-18 14:46:05',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (55,59,'miRanda miRNA Target update','<p>The human miRanda miRNA Targets set has been updated and a new mouse set has been added. These have been supplied by the Enright lab at the EBI . NOTE: These were generated using a revised conservative methodology and hence are a subset of those available via http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/ </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-06-25 14:50:49',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (56,59,'Public plugins','<p class=\"space-below\">We are overhauling public-plugins/admin, as it is very out of date. This will probably affect very few users, but for those that do use it, there will be quite a few changes in the next couple of releases so we wanted to give plenty of notice!</p>\r\n\r\n<p class=\"space-below\">Firstly, we are creating a new public plugin, \'orm\', which will reduce and ultimately remove our reliance on Class::DBI::Sweet by replacing it with Rose::DB::Object. Access to non-essential web functionality, including user accounts, will be ported to this plugin over the coming releases. This plugin will also be a requirement for the admin plugin, since the new CRUD interface uses Rose for its ORM (object relational mapping) component.</p>\r\n\r\n<p class=\"space-below\">Note that the core web code (in /modules) is in the process of being changed to use DBI directly for access to the ensembl_website database, for example for help and news. This is so that simple mirror sites do not need to install the Rose ORM suite and all its dependencies.<p>\r\n\r\n<p>If you have any questions, please email us at dev@ensembl.org.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2010-07-21 10:40:21',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (57,59,'Removal of Object::Help','<p>The module EnsEMBL::Web::Object::Help and its associated Factory, as well as the EnsEMBL::Web::Data classes for help records, have been removed from the web code, as they were no longer needed. If you have any custom modules in the Help namespace (e.g. Components), please change them to use Hub. See for example EnsEMBL::Web::Component::Help::View for examples of how to substitute \'hub\' for \'object\' and how to get data from the ensembl_website database using DBSQL::WebsiteAdaptor (you may need to extend the adaptor in your plugin).</p>\r\n',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2010-07-27 16:26:36',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (58,59,'Key and Zmenu for Xref','The xref display and description is now fixed on the vertical drawing (whole genome), now showing the exact xref and associated gene. Also a key has been added to describe which pointer is which. And finally the Zmenu is now working properly describing the gene and xref accordingly.',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2010-07-29 11:38:09',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (59,60,'data','<p>update of UniProt identifier links including phenotype information <br /> import of new information from NHGRI <br /> import of new data sets for structural variants from DGVa<br /> import of an expanded data set for all short somatic sequence variants from COSMIC <br /> GVF (Genome Variation Format) dumps for all variants<br /> update of variant consequences for new human gene set</p>\r\n<p>update of variant consequences for new zebrafish assembly and gene setimport new set of 150,000 Zebrafish variants</p>\r\n<p>import of variants submitted on LRG_7 from Uniprot</p>\r\n<p> </p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2010-08-13 10:36:14',3,'2010-10-06 12:13:22',1);
-INSERT INTO `changelog` VALUES (60,60,'Array Mapping','<p>The array mapping pipeline will be run for those species which have new assemblies, gene build or new array designs. This includes an update to the latest version of the Phalanx OneArray for human.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-08-13 11:10:09',1273,'2010-11-05 14:30:02',1);
-INSERT INTO `changelog` VALUES (61,60,'BindingMatrix','<p>A new BindingMatrix class will represent position weight matrices (PWMs) loaded from Jaspar or inferred directly from Chip-Seq data. This will ultimately be able to identify the consequence of a sequence change at a given location, with respect to the PWM score. patch_59_60_c.sql contains the relevant changes to update the schema to support this data.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',1273,'2010-08-13 11:19:34',100304,'2010-11-05 10:49:29',1);
-INSERT INTO `changelog` VALUES (62,60,'MotifFeature','<p>A new MotifFeature class has been added to represent the genomic mapping of a position weight matrix (BindingMatrix). patch_59_60_c.sql contains the relevant schema updates.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',1273,'2010-08-13 11:22:44',100304,'2010-11-05 10:49:09',1);
-INSERT INTO `changelog` VALUES (63,60,'Schema patch: Schema version','<p>patch_59_60_a.sql updates the meta table, changing the schema_version meta_value to 60.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',1273,'2010-08-13 11:24:05',100304,'2010-11-05 10:49:59',1);
-INSERT INTO `changelog` VALUES (64,60,'Schema patch: associated_feature_type','<p>patch_59_60_b.sql updates the associated_feature_type table to support feature_type to feature_type associations. The relevant adaptors have also been updated to reflect the new table fields and values.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',1273,'2010-08-13 11:26:09',100304,'2010-11-05 10:50:19',1);
-INSERT INTO `changelog` VALUES (65,60,'RegulatoryBuild update','<p>The human RegulatoryBuild has been updated and re-annotated based on the new ChIP-Seq data sets.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-08-13 11:30:20',100304,'2010-11-05 10:47:39',1);
-INSERT INTO `changelog` VALUES (66,60,'Position Weight Matrix (PWM) mapping and visualisation','<p>PWM mappings which used to be associated with the RegulatoryFeatures, are now associated with the AnnotatedFeatures representing the specific Transcription Factor Binding Site predictions. This utilises the new MotifFeature and BindingMatrix classes. These new data are available as new tracks in the Regulation panel as well as Region in Detail.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-08-13 11:33:19',100304,'2010-11-05 10:46:50',1);
-INSERT INTO `changelog` VALUES (67,60,'New chip-seq datasets from ENCODE','<p>93 new ENCODE Chip-Seq datasets for existing cell lines will be added.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',NULL,NULL,100304,'2010-11-05 10:46:00',1);
-INSERT INTO `changelog` VALUES (68,60,'Update to human vega annotation','<p>An update to Vega human annotation</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2010-08-13 15:12:56',161,'2010-09-23 14:28:41',1);
-INSERT INTO `changelog` VALUES (69,60,'Ensembl marts for release 60','<p>Release 60 Ensembl marts (all species)<br />Ensembl Genes 60<br /> • Addition of new species Ailuropoda melanoleuca (Panda)</p>\r\n<p> • GNF data has been updated via Gene Expression Atlas (http://www.ebi.ac.uk/gxa/)</p>\r\n<p> • Germ line and Somatic mutations are separated in both filter and attributes.</p>\r\n<p>Ensembl variation 60<br /> • Ensembl Variation mart and Ensembl Gene mart are connected via ensembl gene stable-ids for Human</p>',NULL,'handed_over','Mart','N','N','N','N','N','N','N','N/A',NULL,NULL,25629,'2010-11-03 10:21:15',1);
-INSERT INTO `changelog` VALUES (70,60,'Ontology database','A new ontology database (\"ensembl_ontology_60\") will be built using the latest data from GO and SO.',NULL,'handed_over','Core','N','N','N','N','N','N','N','new',896,'2010-08-19 09:55:26',896,'2010-08-24 12:01:02',1);
-INSERT INTO `changelog` VALUES (71,60,'Gencode gene set update','Update to the Ensembl/Havana Gencode gene set using the latest Vega gene set.',NULL,'handed_over','Genebuild','N','Y','Y','N','N','N','N','new',9335,'2010-08-19 09:58:12',9335,'2010-08-25 14:44:42',1);
-INSERT INTO `changelog` VALUES (72,60,'Human cDNA update','<p>Updated set of cDNA alignments to the human genome.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',14183,'2010-08-19 10:00:06',14183,'2010-09-24 09:38:40',1);
-INSERT INTO `changelog` VALUES (73,60,'Rabbit chromosomes','Chromosome mapping added for the rabbit genome\r\nCoordinates updated accordingly',NULL,'handed_over','Genebuild','Y','Y','Y','N','N','N','N','patched',97245,'2010-08-19 10:07:26',97245,'2010-08-19 12:00:37',1);
-INSERT INTO `changelog` VALUES (74,60,'Human (GRCh37) assembly patch release 2','<p>Addition of the GRCh37 patch release 2 patches. These are toplevel, non-reference regions of the assembly.</p>',NULL,'handed_over','Genebuild','Y','N','Y','N','N','N','N','new',14183,'2010-08-19 10:11:38',14183,'2010-09-24 09:40:02',1);
-INSERT INTO `changelog` VALUES (75,60,'Updated human otherfeatures db: EST alignments','Human ESTs were realigned.\r\nNew EST-based genes were produced from these EST alignments.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',5132,'2010-08-19 10:11:45',5132,'2010-08-24 11:55:59',1);
-INSERT INTO `changelog` VALUES (76,60,'Panda genebuild','<p>The first genebuild for the panda genome</p>',NULL,'handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',97245,'2010-08-19 10:13:59',97245,'2010-09-06 09:12:32',1);
-INSERT INTO `changelog` VALUES (77,60,'Update human otherfeatures db: new CCDS import','Update to CCDS set for human',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',5132,'2010-08-19 10:15:17',5132,'2010-08-24 11:56:25',1);
-INSERT INTO `changelog` VALUES (78,60,'Updated mouse otherfeatures db: New CCDS import','<p>Update to CCDS set for mouse</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2010-08-19 10:16:02',5132,'2010-09-23 21:46:32',1);
-INSERT INTO `changelog` VALUES (79,60,'cDNA based gene annotation of human assembly patches','<p>Annotate the human assembly patches using Exonerate\'s cDNA2genome model, which aligns cDNAs to the genome using annotation identifying the coding regions of the cDNAs.</p>','This annotation will be stored in the other features database.','handed_over','Genebuild','N','N','N','N','N','N','N','new',14183,'2010-08-19 10:17:33',14183,'2010-09-28 09:33:18',1);
-INSERT INTO `changelog` VALUES (80,60,'Families','<p>Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa</p>\r\n<p>Clustering by MCL</p>\r\n<p>Multiple Sequence Alignments with MAFFT</p>\r\n<p>Family stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',NULL,NULL,49918,'2010-11-05 10:53:26',1);
-INSERT INTO `changelog` VALUES (81,60,'Gene Homologies','<p>GeneTrees with new/updated genebuilds and assemblies</p>\r\n<p>Updated build of ncRNA trees</p>\r\n<p>Clustering using hcluster_sg</p>\r\n<p>Multiple Sequence Alignments using consistency-based MCoffee meta-aligner (mafftgins+muscle+kalign+probcons) and exon-skipping aware \"skipper\" algorithm</p>\r\n<p>Homology inference including the recent \'possible_ortholog\' type and \'putative gene split\' and \'contiguous gene split\' exceptions</p>\r\n<p>Pairwise gene-based dN/dS calculations for high coverage species pairs only</p>\r\n<p>GeneTree stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-08-19 11:06:43',49918,'2010-11-05 10:53:54',1);
-INSERT INTO `changelog` VALUES (82,60,'Zebrafish genebuild','<p>Full genebuild on the new Zv9 assembly</p>','This genebuild will include RNA-Seq gene models','handed_over','Genebuild','Y','Y','Y','Y','Y','N','N','new',29,'2010-08-23 09:37:17',29,'2010-11-05 10:49:48',1);
-INSERT INTO `changelog` VALUES (83,60,'Gene name and GO term projections','<p>Gene names and GO xrefs will be projected from species where there is high coverage to species where there is lower coverage. Panda will be included as a target for these projections.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','patched',36,'2010-08-24 09:40:04',23,'2010-11-05 10:46:30',1);
-INSERT INTO `changelog` VALUES (84,60,'external database references','<p>Update external database references for human, mouse and Xenopus</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2010-08-24 11:10:08',23,'2010-11-05 10:50:14',1);
-INSERT INTO `changelog` VALUES (85,60,'GO Xrefs are now Ontology Xrefs','<p>The go_xref table is renamed to ontology_xref. The Bio::EnsEMBL::GoXref Perl module is renamed to Bio::EnsEMBL::OntologyXref.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',NULL,NULL,23,'2010-11-05 10:50:50',1);
-INSERT INTO `changelog` VALUES (86,60,'Pairwise Alignments','<p>Lastz-net alignments</p>\r\n<ul>\r\n<li>H.sap-A.mel</li>\r\n<li>H.sap-O.cun</li>\r\n<li>C.fam-A.mel</li>\r\n</ul>\r\n<p>Blat-alignments</p>\r\n<ul>\r\n<li>H.sap-D.rer </li>\r\n<li>M.mus-D.rer</li>\r\n<li>R.nor-D.rer</li>\r\n<li>G.gal-D.rer</li>\r\n<li>T.rub-D.rer</li>\r\n<li>D.rer-X.tro</li>\r\n<li>C.int-D.rer</li>\r\n<li>C.sav-D.rer</li>\r\n<li>G.acu-D.rer</li>\r\n<li>O.lat-D.rer</li>\r\n<li>D.rer-T.nig</li>\r\n</ul>\r\n<p>Non-reference alignments for human vs high coverage blastz-net alignments</p>\r\n<ul>\r\n<li>H.sap-P.tro </li>\r\n<li>H.sap-G.gor</li>\r\n<li>H.sap-P.pyg</li>\r\n<li>H.sap-M.mul</li>\r\n<li>H.sap-M.mus</li>\r\n<li>H.sap-R.nor</li>\r\n<li>H.sap-C.fam</li>\r\n<li>H.sap-B.tau</li>\r\n<li>H.sap-S.scr</li>\r\n<li>H.sap-E.cab</li>\r\n<li>H.sap-O.ana</li>\r\n<li>H.sap-M.dom</li>\r\n<li>H.sap-G.gal</li>\r\n</ul>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-08-24 16:41:35',49918,'2010-11-05 10:54:21',1);
-INSERT INTO `changelog` VALUES (87,60,'Multiple alignments','<p>34 way epo low coverage</p>\r\n<p>12 way epo eutherian mammals</p>\r\n<p>5 way epo fish</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-08-24 16:43:34',49918,'2010-11-05 10:55:00',1);
-INSERT INTO `changelog` VALUES (88,60,'Mouse cDNA update','<p>Updated set of cDNA alignments to the mouse genome.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',101214,'2010-08-24 16:47:56',101214,'2010-09-27 14:19:42',1);
-INSERT INTO `changelog` VALUES (89,60,'Flagging Translation attribute where the evidence was removed','<p>Add a flag to the translation where a human Ensembl translation used as evidence was removed from the current human database. These are indicated on the web display by colouring them in grey on transcript supporting evidence view.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',101214,'2010-08-24 16:57:29',161,'2010-11-04 14:51:23',1);
-INSERT INTO `changelog` VALUES (90,60,'Flagging Translation attribute where the Uniprot evidence was removed','<p>Add a flag to the translation where a supporting evidence from Uniprot was removed from Uniprot database. These are indicated on the web display by colouring them in grey on transcript supporting evidence view.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',101214,'2010-08-24 17:02:12',161,'2010-11-04 14:52:16',1);
-INSERT INTO `changelog` VALUES (91,60,'Updating the ENCODE excluded regions','Update of the ENCODE excluded regions',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',9335,'2010-08-25 14:44:25',9335,'2010-08-26 17:03:46',1);
-INSERT INTO `changelog` VALUES (92,60,'API and schema change','<p>schema change for ensembl genomes to store the population size for each frequency calculation</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2010-08-25 16:16:39',3,'2010-10-06 12:06:41',1);
-INSERT INTO `changelog` VALUES (93,60,'Fix duplicate transcript attributes','<p>Duplicate transcript attributes removed</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2010-08-31 09:48:23',5132,'2010-09-01 17:09:03',1);
-INSERT INTO `changelog` VALUES (94,60,'Translations removed for retrotransposed transcripts',NULL,NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',97245,'2010-09-01 13:30:12',97245,'2010-09-01 13:40:43',1);
-INSERT INTO `changelog` VALUES (95,60,'homo_sapiens rnaseq data','<p>Rnaseq data from transcriptome sequencing done by illumina on human tissues will be provided in a stand-alone database, ie no mart / compara relationships.</p>\r\n<p> </p>\r\n<p>Core, web and releaes coordinatoer has been informed.</p>','Rnaseq data from transcriptome sequencing done by illumina on human tissues will be provided in a stand-alone database, ie no mart / compara relationships.\r\n\r\n\r\nCore, web and releaes coordinatoer has been informed. ','declared','Genebuild','N','N','N','N','N','N','N','N/A',1011,'2010-09-06 15:12:14',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (96,60,'Synteny','<p>H.sap-C.jac</p>\r\n<p>H.sap-O.cun</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',49918,'2010-09-07 11:34:08',49918,'2010-11-05 10:55:16',1);
-INSERT INTO `changelog` VALUES (97,60,'Schema patch: probe_feature.cigar_line','<p>patch_59_60_d.sql The probe_feature table has been patched to change the cigar_line field to a varchar from a free text field.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',1273,'2010-09-08 17:12:02',1273,'2010-11-05 14:30:42',1);
-INSERT INTO `changelog` VALUES (98,60,'Schema patch: regulatory_attribute.attribute_table_name','<p>patch_59_60_e.sql The regulatory_attribute table has been modified to allow \'motif\' as an attribute_feature_table.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',1273,'2010-09-09 11:24:36',1273,'2010-11-05 14:31:16',1);
-INSERT INTO `changelog` VALUES (99,60,'Large scale changes to webcode','<p>There are a number of changes to how web pages are configured and rendered which will affect plugin developers, most notably to EnsEMBL::Web::Configuration and EnsEMBL::Web::Document::HTML modules, and $SiteDefs::OBJECT_TO_SCRIPT</p><p>See <a href=\"/info/docs/webcode/changes_60.html\">here</a> for full details.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2010-10-01 16:01:45',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (100,60,'Autocomplete Gene searching on Location pages','<p>The navigation bar on location pages has been changed. Locations can now be typed in one input box, rather than three, and there is a new input to search for genes.</p>\r\n<p>This new box features an autocomplete dropdown for all genes with xref display labels, and will take you to the <strong>location</strong> of the gene you searched for.</p>','Fixed some of Simon\'s typos :)','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2010-10-22 15:48:08',2,'2010-11-05 12:15:27',1);
-INSERT INTO `changelog` VALUES (101,60,'History and Bookmarks in tabs','<p>When you are logged in, recent browsing history is stored on dropdowns accessible from the tabs in the header of the website (up to 5 links per tab). Up to 5 bookmarks are also available from these dropdowns, ordered by most frequently used.</p>\r\n<p> </p>\r\n<p>There is also a dropdown from the species tab, providing quick access to all species home pages. This is available even if you are not logged in.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2010-10-22 15:53:30',2,'2010-11-05 12:16:41',1);
-INSERT INTO `changelog` VALUES (102,60,'Gene Ontology view','<p>The Gene Ontology page on the Transcript page has changed. Instead there is now a <strong>Gene Ontology</strong> sub-menu with an <strong>Ontology Image</strong> and an <strong>Ontology Table</strong>.</p>\r\n<p>The image visualises the term graph of Go terms and the terms closest in the goslim and goa subset for cellular_component, biological_process and molecular_function.</p>\r\n<p>The table lists the go terms for forcellular_component, biological_process and molecular_function and thier closes term(s) in the goslim and goa subset.</p>\r\n<p> </p>\r\n<p>Both new pages make use of the Ontology API, and the Ontology image uses EnsEMBL::Web::Tools::OntologyVisualisation. <strong>In principle this could be used with any OBO ontology</strong>.</p>\r\n<p> </p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',101273,'2010-10-26 14:49:52',2,'2010-11-05 12:18:15',1);
-INSERT INTO `changelog` VALUES (103,60,'Transcript xrefs (external references) on gene page','<p>For genes, on the external references page, we now list an additional table with the all xrefs (external references) of all transcripts of the gene. As this can be a large number, a subset is show by default. this defaults can be changed using the Configure this page link.</p>',NULL,'declared','Web','N','N','N','N','N','N','N','N/A',101273,'2010-10-26 14:54:25',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (104,60,'Download as CSV','<p>Pages with tabulated data now have a \"Download view as CSV\" button at the bottom of the left hand menu. These files can be opened in Excel or other spreadsheet programs.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2010-10-27 12:53:44',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (105,60,'Upgrade to Gene - Variation Table page','<p>The Variation Table page has been redesigned to cope with the large amounts of data it can display.</p>\r\n<p>Initially you will see a summary table of available consequence types, and clicking on the \"Show\" links here will display additional tables with information about the relevant variations.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2010-11-02 16:04:26',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (106,60,'RNA-Seq data on location views','<p>RNA-seq data supporting the introns for RNA Seq genes can be rendered with the height of the features scaled according to the read coverage (upto a maximum of 50).</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',161,'2010-11-04 15:38:04',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (112,60,'New web page - Multi/GeneTree','<p>In order that external sites can link directly to Ensembl on a gene tree stable ID, we have created a new view that does just that. It uses the same image code as the genetree for a specific gene, but with all nodes expanded.</p>\r\n<p>Sample link: http://www.ensembl.org/Multi/GeneTree/Image?gt=ENSGT00590000083062</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2010-11-05 12:35:40',2,'2010-11-05 12:38:09',1);
-INSERT INTO `changelog` VALUES (113,60,'Assembly and genebuild information on archive links','<p>On species-specific pages, the \"View in archive site\" panel (accessible from the footer of every page) now shows assembly and genebuild information for each archive, to make it easier to choose the right archive.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2010-11-05 12:41:04',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (114,60,'Structural Variation tab','<p>Structural variations are now displayed in their own <a href=\"http://www.ensembl.org/Homo_sapiens/StructuralVariation/Summary?sv=nsv455827\">tab.</a>Currently this dispays a context iamge and tables of overlapping features. The number of available view for this feature type will be extended in release 61</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',121,'2010-11-05 13:03:27',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (115,61,'C.elegans WS220','<p>The data on this site is a direct import of the WormBase WS220 frozen dataset. Included are annotated operons, genes, transcripts and CDSs as well as RNAi and BLAST/BLAT homology data. Information about the location of available fosmid clones is also included. In addition Affymetrix and Agilent cross references for C.elegans expression arrays have been added.<br />The WS220 dataset is the anniversary frozen release of WormBase C.elegans data. All data used in the frozen releases is available from the WormBase FTP site and links to permanent websites can be found on the WormBase home page.<br />We have included C.elegans in the Ensembl system to allow people to access the data through the Ensembl user interface (both for visualisation and data mining) and to provide cross-species integration through our comparative genomics resources (such as homologous gene links and protein family pages).</p>','Need to sort out the affy_mapping with Nathan/Dan.','declared','Wormbase','Y','Y','Y','N','Y','Y','N','new',NULL,NULL,14179,'2010-11-25 14:36:51',1);
-INSERT INTO `changelog` VALUES (116,61,'Ensembl Marts for release 61','<p>Full build of all 7 marts for all species.</p>',NULL,'handed_over','Mart','N','N','N','N','N','N','N','N/A',25629,'2010-11-09 16:01:53',25629,'2011-01-27 10:47:42',1);
-INSERT INTO `changelog` VALUES (117,61,'77 Human ChIP-Seq datasets added','<p>New datasets from ENCODE and the Epigenomics Roadmap were added, which complement existing cell types. A new cell type, K562b was created. 2 sets already in the database, previously associated to K562, were corrected, being now associated to K562b. There is no regulatory build for K562b due the scarcity of data specific for this cell line, which is a variant of K562.</p>','Import post-poned due to concentration on speed of displays and other urgent development','postponed','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2010-11-09 16:35:51',1273,'2010-11-10 14:03:01',1);
-INSERT INTO `changelog` VALUES (119,61,'Human cDNA update','<p>Updated set of cDNA alignments to the human genome.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',14183,'2010-11-10 13:51:16',14183,'2010-11-30 17:12:59',1);
-INSERT INTO `changelog` VALUES (120,61,'seq region synonyms','<p>New table seq_region_synonym added to allow multiple names for sequence regions.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2010-11-10 13:55:31',23,'2011-01-19 14:41:41',1);
-INSERT INTO `changelog` VALUES (121,61,'external database references','<p>Human, mouse, rat and tree shrew will be updated.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2010-11-10 13:57:26',23,'2011-01-19 14:43:31',1);
-INSERT INTO `changelog` VALUES (122,61,'Array Mapping','<p>Array mapping was updated on all species which have had an update to their genome assemblies or gene builds. The probe/set to transcript xrefs were recalculated across all species.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-11-10 14:05:40',1273,'2011-01-28 16:59:00',1);
-INSERT INTO `changelog` VALUES (123,61,'Mouse Regulatory Build','<p>The mouse RegulatoryBuild was re-run to re-introduce some data which had been omitted in the previous build.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2010-11-10 14:08:24',100304,'2011-01-19 14:39:42',1);
-INSERT INTO `changelog` VALUES (124,61,'Haplotype correction','<p>Correction of an error that added one extra N to the end of the alternative versions of the chromosomes for five of the haplotypes. The altered alternative chromosomes are: HSCHR6_MHC_MANN, HSCHR6_MHC_MCF, HSCHR6_MHC_SSTO, HSCHR4_1 and HSCHR17_1.</p>','This will be updated in all databases containing the human assembly (core, otherfeatures, cdna and rnaseq).','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',14183,'2010-11-10 14:20:26',14183,'2010-12-06 13:25:35',1);
-INSERT INTO `changelog` VALUES (125,61,'Zebrafish Havana merge','<p>A merge of the zebrafish core gene set with Havana manual annotation. The core gene set has been altered to include missing genes that were lost in e60 due to a problem in gene clustering.</p>',NULL,'handed_over','Genebuild','N','Y','N','Y','Y','N','N','new',29,'2010-11-11 09:39:37',29,'2011-01-07 13:58:11',1);
-INSERT INTO `changelog` VALUES (126,61,'GENCODE gene set update','<pre>GENCODE gene set update (release 6)<br /><br />Update to the Ensembl/Havana GENCODE gene set using the latest Vega gene<br />set</pre>\r\n<p> </p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',9335,'2010-11-11 09:43:42',9335,'2011-01-19 15:23:52',1);
-INSERT INTO `changelog` VALUES (127,61,'GO term and gene name projections','<p>Gene display names and GO terms will be projected from high-coverage species to those with lower coverage.</p>','All species EXCEPT: \r\n\r\nC. elegans\r\nC. intestinalis\r\nC. savignyi\r\nFly\r\nYeast','handed_over','Core','N','N','N','N','N','N','N','patched',36,'2010-11-11 13:21:59',25629,'2010-12-10 16:56:50',1);
-INSERT INTO `changelog` VALUES (130,61,'Ontology database','<p>The Ensembl Ontology database will as usual be populated with the latest available versions of the</p>\r\n<ul>\r\n<li>Gene Ontology (GO)</li>\r\n<li>Sequence Ontology (SO)</li>\r\n<li>Experimental Factor Ontology (EFO)</li>\r\n</ul>','The EFO ontology will be included if we\'re able to get an OBO file from them in time (we didn\'t).','handed_over','Core','N','N','N','N','N','N','N','new',896,'2010-11-11 14:08:28',896,'2010-12-02 15:05:28',1);
-INSERT INTO `changelog` VALUES (131,61,'Data','<p>- import dbSNP 132 (human), zebrafinch, Tetraodon and new variation databases for cat, opossum</p>\r\n<p>- import dbSNP for further species if available in time (mouse, rat, zebrafish)</p>\r\n<p>- import new release of HGMD database</p>\r\n<p>- corrections to Affymetrix CNV probe data</p>\r\n<p>- import PorcineSNP60 BeadChip</p>\r\n<p>- update of zebrafish variation consequences for new gene build</p>\r\n<p>- variations will now be flagged and retained instead of failed and deleted for species with a new import of dbSNP</p>\r\n<p>- produce GVF file dumps of all variants by species</p>\r\n<p><br />- for Tetraodon, the Ensembl-assigned variation names (\'ENSTNISNP...\') used prior to release 61 have been replaced with the dbSNP-assigned rsIds. If the<br />mapping between the Ensembl and rsIDs is required, there is a tab-separated file available for download on the ftp-site:<br /> ftp://ftp.ebi.ac.uk/pub/software/ensembl/snp/tetraodon/Tetraodon_Ensembl_SNP_id_to_dbSNP_rsid.txt.gz.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',96712,'2010-11-11 14:59:04',3,'2011-01-14 14:59:34',1);
-INSERT INTO `changelog` VALUES (132,61,'Updates to mouse and human Vega annotation','<p>The Vega annotation for both human and mouse has been updated. This matches the annotation presented in Vega release 41.</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2010-11-11 18:07:21',161,'2011-01-28 16:54:52',1);
-INSERT INTO `changelog` VALUES (133,61,'new rnaseq database','<p>I will provide a new databases which consists of the core tables ; the data will data from the human bodymap project ( rnasesq data ). This is a new database which has not been released before. This was originally planned for e60.</p>','I will provide a new databases which consists of the core tables ; the data will data from the human bodymap project ( rnasesq data ). This is a new database which has not been released before. This was originally planned for e60.','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',1011,'2010-11-12 13:37:35',5132,'2011-01-07 14:02:14',1);
-INSERT INTO `changelog` VALUES (134,61,'mouse cDNA update','<p>mouse cDNA update</p>','mouse cDNA update - performed by Thibaut','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',1011,'2010-11-12 13:42:18',101214,'2010-12-06 13:15:49',1);
-INSERT INTO `changelog` VALUES (135,61,'Families','<p>Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.<br />   * Clustering by MCL <br />   * Multiple Sequence Alignments with MAFFT<br />   * Family stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-12 15:37:40',22288,'2011-01-07 12:35:51',1);
-INSERT INTO `changelog` VALUES (136,61,'Gene Homologies','<p>GeneTrees with new/updated genebuilds and assemblies<br />   * Updated build of ncRNA trees<br />   * Clustering using hcluster_sg   <br />   * Multiple Sequence Alignments using consistency-based MCoffee meta-aligner<br />   * Homology inference including the recent \'possible_ortholog\' type and \'putative gene split\' and <br />     \'contiguous gene split\' exceptions<br />   * Pairwise gene-based dN/dS calculations for high coverage species pairs only<br />   * GeneTree stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',NULL,NULL,22288,'2011-01-07 12:37:09',1);
-INSERT INTO `changelog` VALUES (137,61,'Zebrafish Vega annotation','<p>Manual annotation of zebrafish from Havana is now present in Ensembl. This represetns the annotation presented in Vega release 40</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2010-11-12 17:20:12',161,'2010-11-23 11:15:18',1);
-INSERT INTO `changelog` VALUES (138,61,'Mouse gene set update','<p>A merge of Ensembl core gene set and Vega manual annotation.</p>\r\n<p>The core gene set has been improved by incorporating new data resources which had become available since the last NCBIM37 genebuild (April 2007), resulting in the correction of existing gene models and the recovery of new mouse genes with human orthologues.</p>\r\n<p>A new otherfeatures database is also available.</p>\r\n<p>RepeatMask data have been updated by re-running RepeatMasker with options \"-nolow -s -species mouse\".</p>',NULL,'handed_over','Genebuild','N','Y','Y','Y','Y','N','N','new',97238,'2010-11-13 16:21:57',97238,'2010-11-25 13:25:34',1);
-INSERT INTO `changelog` VALUES (139,61,'New assembly for lizard','<p>A new assembly for lizard</p>',NULL,'handed_over','Genebuild','Y','Y','Y','N','Y','N','N','new',97245,'2010-11-15 09:07:00',97245,'2010-11-18 15:31:31',1);
-INSERT INTO `changelog` VALUES (140,61,'Turkey','<p>The first genebuild for turkey</p>',NULL,'handed_over','Genebuild','Y','Y','Y','N','Y','N','N','new',97245,'2010-11-15 09:43:22',97245,'2010-11-25 14:29:34',1);
-INSERT INTO `changelog` VALUES (141,61,'New Canonical Transcript definition','<p>For previous releases, the canonical transcript of a gene has been set to the transcript with the longest translation (for coding genes) or to the transcript with the longest mRNA (for noncoding genes). From release 61, the canonical transcript for human and mouse will now be set to the longest CCDS transcript. Where no CCDS transcript exists for the gene, the longest Ensembl-HAVANA merge transcript will be used.</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','N/A',5132,'2010-11-15 09:58:12',5132,'2011-01-07 14:03:10',1);
-INSERT INTO `changelog` VALUES (142,61,'Pairwise Alignments','<p>Human - Lizard tBlat - net</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',NULL,NULL,22288,'2011-01-07 12:38:19',1);
-INSERT INTO `changelog` VALUES (143,61,'Pairwise Alignments','<p>Human - Turkey tBlat net</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-15 11:51:11',22288,'2011-01-07 12:43:33',1);
-INSERT INTO `changelog` VALUES (144,61,'Pairwise Alignments','<p>Turkey - Chicken Lastz</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-15 11:52:04',22288,'2011-01-10 09:47:15',1);
-INSERT INTO `changelog` VALUES (145,61,'Pairwise Alignments','<p>Lizard - Chicken Lastz</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-15 11:53:04',22288,'2011-01-10 09:45:52',1);
-INSERT INTO `changelog` VALUES (146,61,'Pairwise Alignments','<p>Dog - Horse Lastz</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-15 11:53:47',22288,'2011-01-10 09:46:16',1);
-INSERT INTO `changelog` VALUES (147,61,'Pairwise Alignments','<p>**Removing chicken - zebrafinch tBlat</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-15 11:55:43',22288,'2011-01-10 09:52:28',1);
-INSERT INTO `changelog` VALUES (148,61,'Multiple alignments','<p>Chicken - Turkey -Zebrafinch EPO multiple alignment</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2010-11-15 12:30:36',22288,'2011-01-10 09:53:01',1);
-INSERT INTO `changelog` VALUES (150,61,'Removal of ambiguous bases from human DNA sequence','<p>Ambiguous bases have been replaced with \'N\' for the following two human contigs:</p>\r\n<ul>\r\n<li>contig::AF152363.1:1:185763:1. This contig held 28 ambiguous bases: S(4), W(6), M(5), K(4), R(5), Y(4).</li>\r\n<li>contig::AF152364.1:1:170452:1. This contig held 4 ambiguous bases: S(1), W(1), Y(1), K(1).</li>\r\n</ul>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2010-11-15 13:39:50',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (156,61,'Updated CCDS','<p>Updated CCDS databases for Human and Mouse. Populates other_features with new gene models and serves data for CCDS Public Note DAS track.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',102717,'2010-11-19 11:11:15',97238,'2011-01-19 14:40:13',1);
-INSERT INTO `changelog` VALUES (157,61,'embl and genbank dumps','<p>Onlt the reference sequence will be dumped in the main directory for embl and genbank. Unique non-reference regions(haplotype/par regions) will now be dumped in a subdirectory and only contain the unique regions.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',NULL,NULL,23,'2011-01-19 14:45:13',1);
-INSERT INTO `changelog` VALUES (159,61,'Chromosome and haplotype synonyms','<p>Addition of synonyms for the human chromosomes and haplotypes in the seq_region_synonym tables of the human databases.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',14183,'2010-12-06 13:29:14',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (162,61,'Schema and API changes','<p>- import dbSNP 132 (human including 1000 genomes data, zebrafinch) and also new variation species (cat, opossum, Tetraodon)<br />- import new release of HGMD database<br />- import of new Cosmic (somatic mutation) data<br />- import Illumina PorcineSNP60 BeadChip for pig<br />- import OMIM, NHGRI and UniProt phenotype data for variants<br />- import new DGVa data sets for structural variants<br />- import new variants submitted using LRG sequences that have been accessioned by dbSNP<br />- move CNV probe data to structural variation table<br />- update of zebrafish and mouse variation consequences for new gene build<br />- produce GVF file dumps of all variants and their consequence by species<br />- variants from 1kG unique to Jan09 submission to be flagged as \"withdrawn by 1000 genomes\"<br />- new set for OMIM data, failed variants<br />- split InDel variation class into insertions and deletions</p><p>- For speed purposes, store the variation set membership of each variation feature in the variation_feature table</p>\r\n<p><br />API fix: <br />to correct TranscriptAlleles.pm translated transcript sequence to include the * stop codon at the end of the string so that STOP_LOSTs are not missed.<br /><br /></p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2010-12-13 09:44:05',3,'2011-01-07 12:07:17',1);
-INSERT INTO `changelog` VALUES (164,61,'19-way pecan multiple alignment','<p>Added turkey + Rabbit + Lizard genomes</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-01-10 10:46:43',22288,'2011-01-19 14:56:07',1);
-INSERT INTO `changelog` VALUES (165,61,'Favourite tracks','<p>You can now use the star icon in the configuration panel (accessed via the Configure this page button below the left navigation menu) to mark tracks as favourites.</p>\r\n<p>These can then be displayed together by clicking the \'Favourite tracks\' link in the panel\'s navigation menu.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-01-19 14:50:33',97803,'2011-01-19 14:52:01',1);
-INSERT INTO `changelog` VALUES (166,61,'***IMPORTANT FOR DEVELOPERS*** Schema change to session_record table','<p>There has been a schema change to the session_record table in the ensembl_web_user_db database.</p>\r\n<p> </p>\r\n<p>As we do not provide dumps of this database, you MUST run the script /utils/update_session_record.pl when updating to the new code for this release, otherwise track configuration will no longer be stored correctly. This script both alters the table and updates all existing configurations to work with the new code.</p>\r\n<p> </p>\r\n<p>Further changes to this table will probably be coming over the next few releases. You will be notified here in cases where an action is required.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-01-19 15:00:41',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (167,61,'New popups on images','<p>Configurable tracks now generate a popup when hovering over the track name. This popup provides an easy way to change the track\'s renderer or remove it from the image without having to go to the configuration panel. The popup also provides information about the track.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-01-19 15:04:55',97803,'2011-02-02 10:17:57',1);
-INSERT INTO `changelog` VALUES (169,61,'\'Did you know...\' box is back','<p>The \'Did you know\' box on the home page is back. It displays tweets of ensembl. This has been implemented with the New Twitter API. New cpan module installed Net::Twitter.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2011-01-31 10:07:34',99923,'2011-01-31 10:08:08',1);
-INSERT INTO `changelog` VALUES (179,61,'Static server','<p>Ensembl can now serve static files - images, css and javascript - from a different URL, specified in SiteDefs as $ENSEMBL_STATIC_SERVER.</p>\r\n<p>This change reduces server load as cookies will not be registered for the static domain.</p>\r\n<p>If no ENSEMBL_STATIC_SERVER variable is set, the site will behave as it did previously.</p>\r\n<p> </p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-02-02 10:17:13',102019,'2011-02-02 10:31:50',1);
-INSERT INTO `changelog` VALUES (181,61,'Changes to ZMenu plugins','<p>ZMenu plugins now work in the same way as the rest of the code.</p>\r\n<p>Previously all modules matching the required namespace would be called, starting from the most important plugin and ending with the core code.</p>\r\n<p>Now only the first matching namespace will be used, and as a result plugin code should be changed to call $self->SUPER::content in the content function where required.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-02-02 10:20:13',102019,'2011-02-02 10:25:15',1);
-INSERT INTO `changelog` VALUES (185,62,'Patch for panda','Transcript supporting features added for pseudogenes',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',97245,'2011-02-04 10:52:56',97245,'2011-02-14 16:09:17',1);
-INSERT INTO `changelog` VALUES (186,62,'Patch for rabbit','Geneset re-clustered\r\nTranscript supporting features added for pseudogenes\r\nAssembly updated to match the official ncbi one','The underlying contig sequences have not changed and the sequence of the toplevel sequences has not changed either\r\nBut, the rank of some sequences has changed','handed_over','Genebuild','Y','Y','N','N','N','N','N','new',97245,'2011-02-04 11:02:50',97245,'2011-02-14 16:10:02',1);
-INSERT INTO `changelog` VALUES (187,62,'Patch for marmoset','Deprecated contig sequences removed\r\nRaw-computes re-run\r\nGeneset re-clustered\r\nMapping added\r\nTranscript supporting features for pseudogenes added\r\nNew seq region synonyms',NULL,'handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',97245,'2011-02-04 11:07:47',97245,'2011-02-14 16:09:40',1);
-INSERT INTO `changelog` VALUES (188,62,'Rerun Xrefs pipeline for Yeast','Update the external_db table, and rerun the xrefs pipeline.','Arnaud Kerhornou, arnaud@ebi.ac.uk is the person to contact.','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',101255,'2011-02-04 11:32:44',101255,'2011-03-09 17:10:33',1);
-INSERT INTO `changelog` VALUES (189,62,'Human Vega annotation','Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 42','Vega 42 has yet to be released (but will be released before Ensembl)','handed_over','Genebuild','N','Y','N','N','N','N','N','new',101273,'2011-02-04 11:52:12',101273,'2011-02-21 15:30:32',1);
-INSERT INTO `changelog` VALUES (190,62,'Rebuild otherfeatures database for Yeast.','Rebuild otherfeatures database, cleaning up long EST alignments.','Contact: arnaud@ebi.ac.uk\r\n\r\nRemoved too long EST alignments.','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',101255,'2011-02-07 11:08:35',101255,'2011-03-09 17:09:50',1);
-INSERT INTO `changelog` VALUES (191,62,'Patch for mouse','Patched the mouse Ensembl-Havana merged gene set to maintain its consistency with the latest CCDS gene set (as of 9 February 2011).',NULL,'handed_over','Genebuild','N','Y','N','Y','Y','N','N','patched',97238,'2011-02-07 12:00:54',97238,'2011-02-18 15:58:32',1);
-INSERT INTO `changelog` VALUES (192,62,'patch_61_62_a Update meta schema version','meta schema_version has be updated to 62',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:04:07',1273,'2011-03-09 10:09:02',1);
-INSERT INTO `changelog` VALUES (193,62,'patch_61_62_b interdb_stable_id','A interdb_stable_id field has been added to the motif_feature and external_feature tables. NOTE: This is not an \'Ensembl stable ID\', and will only be used internally to enable inter-DB linking between the variation and funcgen schemas. These are not guaranteed to be stable between Ensembl releases.',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:07:54',1273,'2011-03-09 11:00:34',1);
-INSERT INTO `changelog` VALUES (194,62,'patch_61_62_c feature_type Sequence Ontology fields','so_name and so_accession will be added to the feature_type table to enable display of Sequence Ontology information and linking to the ensembl_ontology DB',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:09:58',1273,'2011-03-09 11:00:52',1);
-INSERT INTO `changelog` VALUES (195,62,'ResultFeature DBFile Collections','Where possible data from the result_feature table has been moved outside of the database to indexed binary \'.col\' files. The ResultFeatureAdaptor now uses the new core DBFile::CollectionAdaptor and DBFile::FileAdaptor to access these data directly.',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:17:32',1273,'2011-03-09 11:05:39',1);
-INSERT INTO `changelog` VALUES (196,62,'Bio::EnsEMBL::DBFile::FileAdaptor','A new base class for accessing data from flat files',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:26:05',1273,'2011-02-25 15:52:42',1);
-INSERT INTO `changelog` VALUES (197,62,'Bio::EnsEMBL::DBFile::CollectionAdaptor','A new class to access Collection Feature data stored in flat files.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:30:14',1273,'2011-02-25 15:53:15',1);
-INSERT INTO `changelog` VALUES (198,62,'Array Mapping','<p>Genomic and transcript alignments and transcript xref annotation has been re-run for all species with new genome assemblies or genebuilds.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 11:33:29',1273,'2011-04-04 14:26:14',1);
-INSERT INTO `changelog` VALUES (199,62,'patch_61_62_a: Schema version patch','Patch file patch_61_62_a.sql, updates the schema version of a core database to 62.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',896,'2011-02-08 11:37:45',896,'2011-02-16 10:50:55',1);
-INSERT INTO `changelog` VALUES (200,62,'Ontology database','Database ensembl_ontology_62 with latest available GO, SO, and EFO ontologies.\r\n\r\nSynonyms will now be included in a new \'synonym\' table.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',896,'2011-02-08 11:39:04',103537,'2011-02-15 16:44:21',1);
-INSERT INTO `changelog` VALUES (201,62,'New Array Imports','<p>New Illumina Infinium arrays: HumanMethylation27K HumanMethylation450K New Rat array: Phalanx OneArray</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-08 13:24:22',1273,'2011-04-04 14:26:47',1);
-INSERT INTO `changelog` VALUES (202,62,'Schema diagrams for online documentation','Schema diagrams for online for core database documentation.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-02-08 13:35:56',103537,'2011-03-07 15:12:43',1);
-INSERT INTO `changelog` VALUES (203,62,'patch_61_62_b: synonym field extension','Patch file patch_61_62_b.sql, extends field synonym in external_synonym table to 100 chars.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-02-08 13:41:11',896,'2011-02-16 10:51:18',1);
-INSERT INTO `changelog` VALUES (204,62,'patch_61_62_c: index for db_name, db_release','Patch file patch_61_62_c.sql adds unique index to db_name, db_release fields in external_db table.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-02-08 13:45:02',103537,'2011-02-28 16:20:08',1);
-INSERT INTO `changelog` VALUES (205,62,'Human otherfeatures','Removed EST alignments with hcoverage <90 and perc_ident <94.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2011-02-08 21:05:36',5132,'2011-02-16 13:04:28',1);
-INSERT INTO `changelog` VALUES (206,62,'GENCODE gene set update (release 7)','Update to the Ensembl/Havana GENCODE gene set based on a complete re-annotation of the Ensembl gene set and combined with the latest Vega gene set',NULL,'handed_over','Genebuild','N','Y','N','Y','N','N','N','new',9335,'2011-02-09 10:09:18',9335,'2011-02-23 09:39:02',1);
-INSERT INTO `changelog` VALUES (207,62,'Human cDNA update','New cDNA db for human.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',14183,'2011-02-09 10:33:01',14183,'2011-02-23 09:20:36',1);
-INSERT INTO `changelog` VALUES (208,62,'GRCh37.p3','Adding the third patch release for the human assembly. This alters the assembly information in all human databases.',NULL,'handed_over','Genebuild','N','N','Y','N','N','N','N','patched',14183,'2011-02-09 10:34:57',14183,'2011-02-18 17:55:08',1);
-INSERT INTO `changelog` VALUES (209,62,'GRCh37.p3 annotation','Annotation of the patches in the other features db.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',14183,'2011-02-09 10:36:15',14183,'2011-03-07 09:21:23',1);
-INSERT INTO `changelog` VALUES (210,62,'Patch_61_62_d: Experimental Group Description','<p>This change serves to support a better annotation of data sources.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',100304,'2011-02-09 10:37:10',100304,'2011-04-04 14:14:24',1);
-INSERT INTO `changelog` VALUES (211,62,'Mart databases','<p>News for release 62:<br />________________<br /><br />Ensembl Genes 62:<br /><br />Addition of new species Nomascus leucogenys (Gibbon)<br />Xenopus tropicalis new assembly (JGI 4.2)<br />Human updated to GRCh37.p3<br />Pongo pygmaeus has been renamed to Pongo abelii<br />Gene Ontology Filter and Attribute section has been modified and all three domains have now been merged into one. <br />Error reported by users regarding broken homolog attributes between C. elegans and C. intestinalis has been fixed.<br />Exon ID filter in transcript event attributes has been removed as this was causing confusion for users.<br />Germline and Somatic variation information attribute sections now contain \"Consequence specific allele\" attribute.<br /><br />Ensembl Variation 62:<br /><br />Pongo pygmaeus has been renamed to Pongo abelii<br />SIFT and PolyPhen filters and attributes added<br />Variation->Gene Associated Information->Consequence specific allele attribute added <br />Variation Set filters now multi select<br />General variation filters->Filter by variation ID (Users can now filter variants from multiple sources e.g. rs123, CM000001)<br /><br /></p>',NULL,'handed_over','Mart','N','N','N','N','N','N','N','N/A',25629,'2011-02-09 10:49:20',25629,'2011-04-01 14:30:04',1);
-INSERT INTO `changelog` VALUES (212,62,'Update of Human functional genomics data','<p>New datasets from ENCODE and the Epigenomics Roadmap, covering existing cell lines. The Regulatory Build was rerun for cell lines with new data.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-02-09 10:51:58',100304,'2011-04-04 14:06:45',1);
-INSERT INTO `changelog` VALUES (213,62,'Xrefs','Update external database references.','Ian is away on holiday at the moment and as he does the xref mapping, I am not sure what species he is mapping for 62 or what changes will be made. Ian to modify this declaration when he returns.','handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-02-09 11:03:34',23,'2011-03-07 10:35:12',1);
-INSERT INTO `changelog` VALUES (214,61,'Test','Test',NULL,'declared','Web','N','N','N','N','N','N','N','N/A',102019,'2011-02-09 11:04:36',102019,'2011-02-09 12:43:43',1);
-INSERT INTO `changelog` VALUES (215,62,'xref projection','Project GO ids and gene names to species. Make alterations to zebrafish projections.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-02-09 11:08:39',25629,'2011-03-10 08:31:38',1);
-INSERT INTO `changelog` VALUES (216,62,'EMBL/Genbank dumps','<p>EMBL & Genbank dumps for all species</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-02-09 11:25:48',25629,'2011-04-01 14:00:10',1);
-INSERT INTO `changelog` VALUES (217,62,'patch_61_62_d: remove field display_label_linkable','Patch file patch_61_62_d.sql removes field display_label_linkable from table external_db.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-02-09 12:30:26',896,'2011-02-16 10:52:31',1);
-INSERT INTO `changelog` VALUES (218,62,'new variation saccharomyces_cerevisiae database','<p>Provide the variation saccharomyces_cerevisiae database</p>','contact: arnaud@ebi.ac.uk','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',101255,'2011-02-09 12:47:20',101255,'2011-03-18 15:45:14',1);
-INSERT INTO `changelog` VALUES (219,62,'New funcgen saccharomyces_cerevisiae database','funcgen saccharomyces_cerevisiae database built by EG Team on 61 schema, and patched to 62 subsequently.','contact: arnaud@ebi.ac.uk','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',101255,'2011-02-09 12:47:55',101255,'2011-03-09 17:05:00',1);
-INSERT INTO `changelog` VALUES (220,62,'Import of LRG sequences','Newly published LRG sequences will be imported',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',99616,'2011-02-09 13:16:45',99616,'2011-03-08 13:32:07',1);
-INSERT INTO `changelog` VALUES (221,62,'Gibbon build','First release of gene build for Gibbon, Nomascus leucogenys (Northern white-cheeked gibbon). Assembly: Nleu1.0.','New species.','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',102717,'2011-02-09 14:39:49',102717,'2011-02-23 15:08:34',1);
-INSERT INTO `changelog` VALUES (222,62,'Ontology API','Addition of fetch_all_by_name() method to the OntologyTermAdaptor to fetch ontology terms by their names or synonyms.\r\n\r\nAdditional synonym() method for OntologyTerm objects to get their synonyms.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',896,'2011-02-09 14:53:25',896,'2011-02-16 10:53:31',1);
-INSERT INTO `changelog` VALUES (223,62,'Zebrafish WGS/clone assembly track','Added a WGS/clone assembly track.','This only affects the misc features tables','handed_over','Genebuild','N','N','N','N','N','N','N','patched',29,'2011-02-09 14:58:17',29,'2011-03-07 17:33:59',1);
-INSERT INTO `changelog` VALUES (224,62,'Flagging obsolete Uniprot proteins','Flagging Transcript attribute where the Uniprot evidence was removed',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',101214,'2011-02-09 17:17:26',101214,'2011-03-04 15:50:26',1);
-INSERT INTO `changelog` VALUES (225,62,'Flagging obsolete Ensembl proteins','Flagging Transcript attribute where the evidence was removed from 2x genomes','Finally we ran it against all species because almost all of them have Ensembl human proteins as evidence','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',101214,'2011-02-09 17:27:08',101214,'2011-03-10 12:02:10',1);
-INSERT INTO `changelog` VALUES (226,62,'Mouse RefSeq import','RefSeq annotations imported into the mouse otherfeatures database',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2011-02-10 09:28:00',5132,'2011-02-18 09:09:07',1);
-INSERT INTO `changelog` VALUES (227,62,'Xenopus tropicalis new assembly 4.2','New assembly of Xenopus tropicalis version 4.2','Should be on time','handed_over','Genebuild','Y','Y','N','Y','N','N','N','new',101214,'2011-02-10 10:17:18',101214,'2011-02-22 14:25:59',1);
-INSERT INTO `changelog` VALUES (228,62,'Human Body Map missing liver','Add the liver models',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',101214,'2011-02-10 10:18:58',101214,'2011-03-04 15:51:32',1);
-INSERT INTO `changelog` VALUES (229,62,'Mouse cDNA update','New cDNA db for mouse. ens-staging2: mus_musculus_cdna_62_37o',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',102717,'2011-02-10 11:15:39',102717,'2011-03-08 09:12:00',1);
-INSERT INTO `changelog` VALUES (230,62,'Updated human otherfeatures db: new CCDS import','Update to CCDS set for human',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',102717,'2011-02-10 11:20:19',102717,'2011-03-08 13:51:01',1);
-INSERT INTO `changelog` VALUES (231,62,'Updated mouse otherfeatures db: New CCDS import','Update to CCDS set for mouse',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',102717,'2011-02-10 11:21:35',5132,'2011-03-11 16:22:52',1);
-INSERT INTO `changelog` VALUES (232,62,'nada','ceci n\'est pas une declaration',NULL,'cancelled','Variation','N','N','N','N','N','N','N','N/A',3,'2011-02-10 14:27:32',3,'2011-03-10 16:36:05',1);
-INSERT INTO `changelog` VALUES (233,62,'New variation consequences','New variation consequences due to a schema change linking consequences to allele and transcript rather than just to a variation and transcript',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 14:50:05',99616,'2011-03-10 13:59:47',1);
-INSERT INTO `changelog` VALUES (234,62,'HGVS coordinates stored in database','HGVS coordinates for variant alleles will be pre-calculated and stored in the database. These were previously calculated on the fly.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 14:52:38',99616,'2011-03-10 14:00:57',1);
-INSERT INTO `changelog` VALUES (235,62,'New variation database','<p>The human variation database will be built fresh from dbSNP release 132 due to data updates by dbSNP.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','new',99616,'2011-02-10 14:56:43',99616,'2011-03-21 10:22:04',1);
-INSERT INTO `changelog` VALUES (236,62,'Data import/update from external sources','<p>Allele frequencies from 1000 Genomes Project. Variation submissions on LRGs from UniProt. Structural variation data from DGVa. Somatic mutation data from Cosmic. Variation phenotype data from OMIM, NHGRI, UniProt and EGA. Variation synonyms from UniProt.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 15:03:00',99616,'2011-03-21 10:23:31',1);
-INSERT INTO `changelog` VALUES (237,62,'New variation database','Fresh build from dbSNP 132.',NULL,'cancelled','Variation','N','N','N','N','N','N','N','new',99616,'2011-02-10 15:05:05',99616,'2011-03-10 14:01:23',1);
-INSERT INTO `changelog` VALUES (238,62,'Data import/update from external sources','Structural variation data from DGVa.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 15:07:44',99616,'2011-03-10 14:15:47',1);
-INSERT INTO `changelog` VALUES (239,62,'patch_61_62_a: Meta schema version','Meta schema version update',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:10:52',99616,'2011-03-10 14:02:09',1);
-INSERT INTO `changelog` VALUES (240,62,'patch_61_62_b: Alter failed_variation','Drop the subsnp_id column from failed_variation',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 15:23:25',99616,'2011-03-10 14:16:12',1);
-INSERT INTO `changelog` VALUES (241,62,'patch_61_62_c: Introduce failed_allele table','Add a table to store failed alleles',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 15:25:12',99616,'2011-03-10 14:22:05',1);
-INSERT INTO `changelog` VALUES (242,62,'patch_61_62_d: Add type column to source table','Introduce a type column (enum) to indicate the type of a source',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',99616,'2011-02-10 15:26:46',99616,'2011-03-10 14:20:55',1);
-INSERT INTO `changelog` VALUES (243,62,'patch: Table to store study data','A new table to store description of studies will be introduced and foreign keys to this table will be introduced in variation_annotation and structural_variation tables.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:30:04',99616,'2011-03-10 14:03:33',1);
-INSERT INTO `changelog` VALUES (244,62,'patch: Rationalize data type for allele columns','The data type of allele columns in e.g. allele, variation and variation_feature will be harmonized to use varchar.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:41:40',99616,'2011-03-10 14:22:35',1);
-INSERT INTO `changelog` VALUES (245,62,'patch: Table to store supporting structural variations','A new table to store supporting structural variations will be introduced',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:50:04',99616,'2011-03-10 14:17:03',1);
-INSERT INTO `changelog` VALUES (246,62,'BLAT patch','<p>for aesthetic reasons, we will flip the strand of paired 3\'-ESTs</p>','the DNA-align-features were patched for display reasons','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','patched',14179,'2011-02-10 15:50:54',14179,'2011-04-04 14:14:05',1);
-INSERT INTO `changelog` VALUES (247,62,'patch: Table to store variation consequences on regulatory regions','A table to support storing variation consequences on regulatory regions will be introduced',NULL,'cancelled','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:51:50',99616,'2011-03-10 14:23:57',1);
-INSERT INTO `changelog` VALUES (248,62,'patch: Re-design of the transcript_variation table','Variation consequences will be stored by allele instead of by variation. The transcript_variation table will be modified to accommodate this. In addition, HGVS coordinates will be stored as well.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:54:50',99616,'2011-03-10 14:19:03',1);
-INSERT INTO `changelog` VALUES (249,62,'patch: Drop somatic column from source table','The somatic column will be dropped from source and instead introduced in the variation table.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:56:25',99616,'2011-03-10 14:06:11',1);
-INSERT INTO `changelog` VALUES (250,62,'API changes','<p>The API will be updated to accommodate schema patches.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 15:58:35',99616,'2011-04-12 09:39:42',1);
-INSERT INTO `changelog` VALUES (251,62,'Families','Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.\r\n * Clustering by MCL\r\n * Multiple Sequence Alignments with MAFFT\r\n * Family stable ID mapping',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-02-10 16:01:21',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (252,62,'SIFT and PolyPhen consequences','<p>Non-synonymous coding consequences evaluated by SIFT and PolyPhen will be calculated</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-10 16:01:24',99616,'2011-03-21 10:22:55',1);
-INSERT INTO `changelog` VALUES (253,62,'Gene Homologies','GeneTrees (protein-coding) with new/updated genebuilds and assemblies\r\n * Clustering using hcluster_sg\r\n * Multiple sequence alignments using MCoffee\r\n * Phylogenetic reconstruction using TreeBeST\r\n * Homology inference including the recent \'possible_ortholog\',\r\n\'putative gene split\' and \'contiguous gene split\' exceptions\r\n * Pairwise gene-based dN/dS scores for high coverage species\r\npairs only\r\n * GeneTree stable ID mapping',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-02-10 16:04:30',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (254,62,'GeneTrees (ncRNA) with new/updated genebuilds and assemblies','* Classification based on RFAM model\r\n * Multiple sequence alignments with infernal\r\n * Phylogenetic reconstruction using RaxML\r\n * Additional multiple sequence alignments with Prank (w/ genomic flanks)\r\n * Additional phylogenetic reconstruction using PhyML and NJ\r\n * Phylogenetic tree merging using TreeBeST\r\n * Homology inference',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-02-10 16:05:38',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (255,62,'Pairwise Alignments','* Non-reference alignments for human vs high coverage blastz-net\r\n * human vs gibbon lastz.\r\n * human vs marmoset lastz\r\n * human vs rabbit lastz\r\n * xenopus vs mouse tblat-net\r\n * xenopus vs chicken tblat-net\r\n * xenopus vs tetraodon tblat-net\r\n * xenopus vs human tblat-net\r\n * xenopus vs danio tblat-net',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-02-10 16:06:54',22288,'2011-03-16 10:05:44',1);
-INSERT INTO `changelog` VALUES (256,62,'Multiple alignments','* update 6way-primate-epo alignments to incorporate new marmoset seq_region names\r\n * update 12way-mammal-epo alignments to incorporate new marmoset seq_region names\r\n * update 19way-amniota-pecan alignments to incorporate new marmoset seq_region names\r\n * 35way-mammal low-coverage-epo alignments (addition of gibbon and new marmoset seq_region names)',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-02-10 16:08:58',22288,'2011-03-16 10:06:12',1);
-INSERT INTO `changelog` VALUES (257,62,'patch_61_62_e Addition of dbfile_registry table','<p>A dbfile_registry table has been added to store the filepaths of result feature collection (.col) files</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-11 11:53:22',100304,'2011-04-04 14:15:28',1);
-INSERT INTO `changelog` VALUES (258,62,'Binding Matrix: simpler representation of matrix frequencies','<p>This change intends to make the representation simpler, towards something that can applied to different formats.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-02-11 13:04:43',100304,'2011-04-04 14:05:35',1);
-INSERT INTO `changelog` VALUES (259,62,'xrefs','Update human external database references.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2011-02-14 16:14:35',23,'2011-03-07 10:35:38',1);
-INSERT INTO `changelog` VALUES (260,62,'xrefs','Update external database references',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2011-02-14 16:16:39',23,'2011-03-07 10:36:23',1);
-INSERT INTO `changelog` VALUES (261,62,'schema changes','* meta.meta_value has been extended to TEXT (previously it was VARCHAR) and the corresponding indexes have been fixed.\r\n\r\n* analysis.module has been extended to VARCHAR(255) - previously it was VARCHAR(80)\r\n\r\n* mapping_session.prefix column has been added to allow EnsEmblGenomes to track their different types of stable_ids',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',22288,'2011-02-17 10:34:34',22288,'2011-03-16 10:06:35',1);
-INSERT INTO `changelog` VALUES (262,62,'PolIII Transcription Associated Regulatory Features','<p>The Regulatory Build now also annotates Regulatory Features associated to PolIII Transcription.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-02-22 09:15:47',100304,'2011-04-04 14:07:16',1);
-INSERT INTO `changelog` VALUES (263,62,'Support for BigWig format','<p>In addition to BAM format, the Ensembl website now supports attachment of BigWig data via URL. Click on \"Manage Your Data\" then select \"Attach Remote File\" from the lefthand menu.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2011-02-22 15:54:52',2,'2011-04-13 16:36:04',1);
-INSERT INTO `changelog` VALUES (264,62,'Export data on structural variation','<p>Enabling data to be exported for the variation page. (same functionalities as on location, gene and transcript)</p>',NULL,'postponed','Web','N','N','N','N','N','N','N','N/A',99923,'2011-02-22 16:06:58',99923,'2011-04-12 13:57:42',1);
-INSERT INTO `changelog` VALUES (265,62,'Export on Karyotype','<p>Will try to get the karyotype exported to PDF and other formats. Export button just below the karyotype image</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2011-02-22 16:07:45',99923,'2011-04-12 13:59:35',1);
-INSERT INTO `changelog` VALUES (266,62,'BED Format export','<p>Adding BED format to the export functionality on location, genes, transcript and variation.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2011-02-22 16:10:01',99923,'2011-04-12 13:59:49',1);
-INSERT INTO `changelog` VALUES (267,62,'Highlighting row in feature table for variation','<p>When clicking on a SNP on the karyotype for phenotype, the corresponding row (variation) is highlighted in the feature table</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2011-02-22 16:11:01',99923,'2011-04-12 14:00:07',1);
-INSERT INTO `changelog` VALUES (268,62,'Add a variation set for variations flagged as failed','Variations that have been flagged as failed will be grouped in a variation set named \'Failed variations\'',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-02-23 12:38:27',99616,'2011-03-10 14:06:36',1);
-INSERT INTO `changelog` VALUES (269,62,'Mouse RegBuild update','<p>The Mouse RegulatoryBuild has been rerun to include some MotifFeatures which we re previously being excluded. Input data sets remained the same, hence structures are unaffected.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-25 15:45:34',100304,'2011-04-04 14:08:37',1);
-INSERT INTO `changelog` VALUES (270,62,'patch_61_62_f regulatory_feature.fset_seq_region_idx','<p>A new regulatory_feature unique index has replaced two older indexes.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-25 15:51:49',100304,'2011-04-04 14:12:26',1);
-INSERT INTO `changelog` VALUES (271,62,'Core schema patches','<p>Core schema patches have been propagated to the funcgen schema where appropriate i.e. patch_61_62_g - synonym_field_extension patch_61_62_h - external_db.db_name_idx patch_61_62_i - drop_external_db.display_label_linkable</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-02-25 16:57:49',100304,'2011-04-04 14:13:13',1);
-INSERT INTO `changelog` VALUES (272,62,'Line numbers on exon view','Line numbering can now be added to exon sequence when configuring the exon view page',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-03-04 09:15:44',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (273,62,'Resizable control panel','The control panel which appears for page configurations, exports, etc. can now be resized and moved around the page',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-03-04 09:17:35',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (274,62,'patch_61_62_j - extend meta.meta_key','Extended the length of the meta_key field to handle longer values',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-03-04 10:06:53',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (275,62,'Searchable content','<p>The ensembl search now includes content from the Help database and from static content pages, for example species homepages.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',161,'2011-03-10 16:10:18',161,'2011-04-12 14:00:38',1);
-INSERT INTO `changelog` VALUES (283,62,'Supporting Evidence','<p>Supporting Evidence View, ie the view that shows the alignments of transcripts/exons and evidence, is now configurable.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',161,'2011-04-12 14:07:23',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (284,63,'BioMart 63 databases','<p>Ensembl Genes 63:</p>\r\n<p>Updated to new Microbat assembly Myoluc2.0</p>\r\n<p>Updated to new Yeast assembly EF3</p>\r\n<p>Added a new Exon ID filter to the GENE->Limit to genes filter. <br />Reinstated the protein allele attribute in the Variation->GERMLINE VARIATION INFORMATION attribute section.<br />The PRIDE team have collaborated with us to reinstate the linking between the Ensembl Gene mart and the PRIDE mart.<br />The Exon ID was removed from the Transcript Event attribute section as this was misleading.<br />The text (bp) was removed from the GO attributes.<br />Gene and transcript biotype attributes have been added to the Sequence attribute section.<br />The HGNC symbol link has been updated.<br />The following external references are now stored on gene IDs: EntrezGene, WikiGene, RFAM, MIM, MIM_GENE, MIM_MORBID, miRBase, UniGene, Uniprot_genename, DBASS3, DBASS5</p>\r\n<p><br /> Ensembl Variation 63:</p>\r\n<p>Updated mouse to dbSNP 132<br />Phenotypes in the GENERAL VARIATION FILTERS->Phenotype filter drop down have had all commas removed as this caused problems for the biomart code which resulted in incorrect filtering.<br />Peptide shift attribute has been reinstated in the Variation->GENE ASSOCIATED INFORMATION attribute section.<br />The Variation->SEQUENCE VARIATION->Variation annotation attribute section has been renamed Phenotype annotation<br />Variation ID attribute has been renamed Variation Name<br /><br /><br />Ensembl Regulation 63:<br /><br />\"Is projected\" attribute added to the Regulatory features.<br />Annotated features have now been renamed to Regulatory Evidence<br />Useful text information on how to use the filters and attributes for this mart has been added to the top of the filter panel and the top of the attribute panel on the interface. <br /><br />Vega 43:<br /><br />Human and Danio manual annotation has been updated to represent the annotation presented in Vega release 43.</p>','','handed_over','Mart','N','N','N','N','N','N','N','N/A',25629,'2011-04-21 09:21:42',25629,'2011-06-24 09:16:35',1);
-INSERT INTO `changelog` VALUES (285,63,'xref projection','<p>Project GO ids and gene names to species. Make alterations to zebrafish projections.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-04-21 09:49:10',25629,'2011-06-03 10:43:20',1);
-INSERT INTO `changelog` VALUES (286,63,'EMBL & Genbank dumps','<p>EMBL & Genbank dumps for all species</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-04-21 09:49:33',25629,'2011-06-20 12:13:16',1);
-INSERT INTO `changelog` VALUES (287,63,'New core database for Yeast','<p>New core database for Saccharomyces cerevisiae to reflect the new assembly and genebuild from SGD</p>','contact: hpedro@ebi.ac.uk\r\nAlready built and live in EnsemblGenomes website, so it will just need patching to 63.','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',103312,'2011-04-21 10:45:53',103312,'2011-05-05 11:13:19',1);
-INSERT INTO `changelog` VALUES (288,63,'New otherfeatures database for Yeast','<p>Rebuilt otherfeatures database with new EST alignments reflecting the new assembly from SGD.</p>','Contact: Helder Pedro hpedro@ebi.ac.uk\r\nAlready built as a 62 schema, just needs patching to 63.','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',103312,'2011-04-21 10:51:49',103312,'2011-05-05 11:13:51',1);
-INSERT INTO `changelog` VALUES (289,63,'New funcgen database for Yeast','<p>New functional genomics database for Yeast with new probe mapping to reflect the assembly update from SGD.</p>','Contact: Helder Pedro hpedro@ebi.ac.uk\r\nAlready built, needs patching to 63','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',103312,'2011-04-21 10:57:04',101255,'2011-05-26 18:33:21',1);
-INSERT INTO `changelog` VALUES (290,63,'New variation database for Yeast','<p>New variation database for Yeast with mapped variation features to reflect the latest assembly from SGD.</p>','Contact: Helder Pedro hpedro@ebi.ac.uk\r\nAlready done as a 62 schema, needs patching to 63','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',103312,'2011-04-21 11:02:45',101255,'2011-05-31 09:23:59',1);
-INSERT INTO `changelog` VALUES (291,63,'New microbat assembly','<p>A full gene annotation on the new high coverage microbat assembly, Myoluc2.0</p>','','handed_over','Genebuild','Y','Y','Y','N','Y','N','N','new',97245,'2011-04-21 13:21:25',97245,'2011-05-09 13:05:40',1);
-INSERT INTO `changelog` VALUES (292,63,'Removed duplicated dna in panda','<p>Scaffold dna sequences removed from the dna table</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',97245,'2011-04-21 13:22:20',97245,'2011-05-09 10:20:55',1);
-INSERT INTO `changelog` VALUES (293,63,'Rabbit xrefs','<p>Missing xrefs added for ncRNAs</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',97245,'2011-04-21 16:19:21',97245,'2011-05-09 10:20:30',1);
-INSERT INTO `changelog` VALUES (294,63,'Human Vega annotation','<p>Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 43. Annotation by Havana of chromosome 12 has been completed and that of chromosome 14 is nearly finished.</p>\r\n<p> </p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2011-04-26 12:21:29',100304,'2011-05-26 15:37:58',1);
-INSERT INTO `changelog` VALUES (295,63,'Zebrafish Vega annotation','<p>Manual annotation of zebrafish from Havana has been updated. This represents the annotation presented in Vega release 43. There is an increase of about 50Mb of annotated sequence, with an extra 1300 annotated loci.</p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2011-04-26 12:22:49',100304,'2011-05-26 15:38:48',1);
-INSERT INTO `changelog` VALUES (296,63,'GRCh37.p4','<p>GRCh37.p4 added to the human databases.</p>','This adds the sequence and assembly data associated with GRCh37.p4 to the human databases.','postponed','Genebuild','Y','N','Y','N','N','N','N','N/A',14183,'2011-04-26 13:20:38',14183,'2011-05-10 10:54:54',1);
-INSERT INTO `changelog` VALUES (297,63,'GRCh37.p4 annotation','<p>Gene annotation of the patches in the otherfeatures db.</p>','Addition of assembly patch gene annotation using a \'light-weight\' annotation strategy, instead of the full genebuild process.','postponed','Genebuild','N','N','N','Y','N','N','N','patched',14183,'2011-04-26 13:25:03',14183,'2011-05-10 10:55:46',1);
-INSERT INTO `changelog` VALUES (298,63,'Human cDNA update','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 13px;\">The latest set of cDNAs for human (as of 05/May/2011) from the <br />European Nucleotide Archive and NCBI RefSeq were aligned to the <br />current genome using <a style=\"color: #3366bb;\" title=\"Exonerate\" href=\"http://www.ebi.ac.uk/~guy/exonerate/\" target=\"_blank\">Exonerate</a>. There are 1104 new cDNA alignments for Ensembl 63</span></p>\r\n<p> </p>','','handed_over','Genebuild','N','N','N','N','N','N','N','new',14183,'2011-04-26 13:27:02',100304,'2011-05-26 10:30:35',1);
-INSERT INTO `changelog` VALUES (299,63,'Update schema version','<p> </p>\r\n<p># Description:</p>\r\n<p># Update schema_version in meta table to 63.</p>\r\n<p> </p>\r\n<p>UPDATE meta SET meta_value=\'63\' WHERE meta_key=\'schema_version\';</p>\r\n<p> </p>\r\n<p># Patch identifier</p>\r\n<p>INSERT INTO meta (species_id, meta_key, meta_value)</p>\r\n<p> VALUES (NULL, \'patch\', \'patch_62_63_a.sql|schema_version\');</p>\r\n<p> </p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-04-28 10:05:44',103537,'2011-05-19 12:47:30',1);
-INSERT INTO `changelog` VALUES (300,63,'Indexing changes for core database.','<p> </p>\r\n<p>Change stable Id version to not null, default 1 in exon_stable_id, gene_stable_id, transcript_stable_id, translation_stable_id, gene_archive.</p>\r\n<p>Create unique index on stable_id and verision for gene_archive.</p>\r\n<p>Create a unique index for table umapped_object. </p>\r\n<p> </p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-04-28 10:11:21',103537,'2011-05-19 12:48:49',1);
-INSERT INTO `changelog` VALUES (301,63,'Remove field dbprimary_acc_linkable from external_db table.','<p>Remove field dbprimary_acc_linkable from external_db table.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-04-28 10:12:13',103537,'2011-05-19 12:49:19',1);
-INSERT INTO `changelog` VALUES (302,63,'Mouse cDNA update','<p>The latest set of cDNAs for mouse (as of 05/May/2011) from the <br />European Nucleotide Archive and NCBI RefSeq were aligned to the <br />current genome using <a title=\"Exonerate\" href=\"http://www.ebi.ac.uk/~guy/exonerate/\" target=\"_blank\">Exonerate</a>. There are 1009 new cDNA alignments for Ensembl 63.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',102717,'2011-04-28 13:32:23',102717,'2011-05-18 12:48:48',1);
-INSERT INTO `changelog` VALUES (303,63,'New rhesus macaque variation database','<p>Based on dbSNP 131</p>','Postponed until a dbSNP build with more complete clustering is available.','postponed','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-05-03 09:51:03',99616,'2011-05-16 10:18:49',1);
-INSERT INTO `changelog` VALUES (304,63,'New Cow Assembly','<p>The first genebuild on cow assembly UMD3.1.</p>','Cow will now be available for the next release (64).','postponed','Genebuild','Y','Y','Y','Y','Y','N','N','new',97238,'2011-05-03 10:02:32',97238,'2011-05-09 09:59:22',1);
-INSERT INTO `changelog` VALUES (305,63,'Update to Ensembl-Havana GENCODE gene set (release 8)','<p>Update to Ensembl-Havana GENCODE gene set (release 8) - this is based on updated Ensembl gene set and latest Havana gene annotation.</p>','The database will contains the latest GRC patches (p4) declared by Susan.','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','new',9335,'2011-05-03 10:04:27',9335,'2011-05-23 16:13:51',1);
-INSERT INTO `changelog` VALUES (306,63,'Updates to human phenotype associations','<p>OMIM, UniProt, NHGRI GWAS catalog, HGMD mutations, COSMIC</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-05-03 10:07:23',99616,'2011-06-03 14:22:06',1);
-INSERT INTO `changelog` VALUES (307,63,'New mouse variation database','<p>Based on dbSNP 132</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-05-03 10:11:08',99616,'2011-06-03 14:22:34',1);
-INSERT INTO `changelog` VALUES (308,63,'Import of new LRGs','','','handed_over','Core','N','N','N','N','N','N','N','N/A',99616,'2011-05-03 10:11:55',99616,'2011-06-03 14:27:02',1);
-INSERT INTO `changelog` VALUES (309,63,'Updated Regulation API Tutorial','','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 11:32:53',100304,'2011-05-31 10:51:00',1);
-INSERT INTO `changelog` VALUES (310,63,'Add attrib_id column to variation_set','<p>An attrib_id column is added to variation_set in order to be able to provide general and human-friendly names to variation sets without breaking the web display.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-05-03 13:25:55',99616,'2011-06-03 14:22:59',1);
-INSERT INTO `changelog` VALUES (311,63,'Update structural variation data from DGVa','<p>Update done only for Human, Mouse, Pig and Dog.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-05-03 13:27:14',102503,'2011-06-08 13:14:38',1);
-INSERT INTO `changelog` VALUES (312,63,'Flagging obsolete Uniprot proteins','<p>Flag the obsolete proteins in Uniprot used as supporting evidence. 122 proteins used as evidence were flagged as obsolete for this release.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',101214,'2011-05-03 13:30:10',100304,'2011-06-14 10:11:30',1);
-INSERT INTO `changelog` VALUES (313,63,'Flagging obsolete Ensembl proteins','<p>Flag obsolete human Ensembl proteins used as supporting evidence for other species. 364 proteins used as evidence were flagged as obsolete.</p>','Except the human...','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',101214,'2011-05-03 13:32:42',100304,'2011-06-14 10:13:27',1);
-INSERT INTO `changelog` VALUES (314,63,'patch_62_63_a - Schema Version','<p>This patch updates the schema version</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-05-03 13:41:20',1273,'2011-05-24 10:08:55',1);
-INSERT INTO `changelog` VALUES (315,63,'patch_62_63_b - binding_matrix.analysis_id','<p>This patch updates the the analysis_id field of the binding_matrix tables to a smallint</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-05-03 13:43:35',1273,'2011-05-24 10:09:13',1);
-INSERT INTO `changelog` VALUES (316,63,'Removal of lowercase letter at the end of all database names','<p>For release 63 it has been decided to remove the lowercase letter at the end of all database names as it is confusing for users and provides little meaning about actual data changes.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-05-03 13:45:25',25629,'2011-06-03 10:44:05',1);
-INSERT INTO `changelog` VALUES (317,63,'MicroArray Mapping','<p>Mapping of expression arrays to Ensembl Transcripts has been updated for Human, Mouse, Rat and Zebrafish. We also included an updated version of the Phalanx OneArray for Rat.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-05-03 13:49:55',100304,'2011-06-22 12:53:04',1);
-INSERT INTO `changelog` VALUES (318,63,'RegulatoryFeatureAdaptor::fetch_all','<p>The base fetch_all method has been over-ridden for the RegulatoryFeatureAdaptor, this now defaults to returning only the MultiCell RegulatoryFeatures, as the other generic methods do.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-05-03 13:58:56',1273,'2011-05-25 12:31:55',1);
-INSERT INTO `changelog` VALUES (319,63,'Update xrefs for core databases','<p>Update xrefs for Human, Mouse, Rat, Pig, Macaque, Chimp, Orangutan, Fugu and Stickleback.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-05-03 14:00:03',23,'2011-05-26 11:56:39',1);
-INSERT INTO `changelog` VALUES (320,63,'Logic name update','<p>Whenever possible, logic names updated to be consistent across all databases</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',97245,'2011-05-03 14:19:14',97245,'2011-06-03 11:02:34',1);
-INSERT INTO `changelog` VALUES (321,63,'ResultFeatureAdaptor method over-rides','<p>Where appropriate some of the base feature adaptor methods have been over-riden, this prevents some API errors due to the nature of the ResultFeature storage </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-05-03 14:06:41',1273,'2011-06-03 16:01:13',1);
-INSERT INTO `changelog` VALUES (322,63,'Added Motif Features for Missing Jaspar Matrices','<p>Motif Features were added for the following Jaspar Matrices: </p>\r\n<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">E2F1: MA0024.1 (2315 sites)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">NFKB: MA0105.1 (2040)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BHLHE40: PB0111.1 (46); PB0007.1 (276)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Nrsf: MA0138.1 (4321)</li>\r\n</ul>\r\n<p> </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 15:16:41',100304,'2011-05-31 10:45:44',1);
-INSERT INTO `changelog` VALUES (323,63,'API web documentation overhaul','<p>Replace PDoc system with Doxygen + Perl Filter to produce API reference web pages.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103988,'2011-05-03 15:26:45',103988,'2011-06-28 15:30:37',1);
-INSERT INTO `changelog` VALUES (324,63,'Changed Motif Features score to [0-1] relative affinity scale','<p>Instead of showing the absolute score from the MOODs software, we now display a [0-1] linear relative value between the maximum (1) and minimum (0) score. This is to make it coherent with the API BindingMatrix::relative_affinity function and to make it easier for the user to interpret the score. </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 15:27:26',100304,'2011-05-31 10:50:08',1);
-INSERT INTO `changelog` VALUES (325,63,'patch_62_64_c : Added binding_matrix.threshold','<p>A new threshold float field was added to the Binding Matrix to store the minimum score for Motif Features from each matrix (patch_62_63_c).</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 15:32:00',1273,'2011-05-25 12:11:33',1);
-INSERT INTO `changelog` VALUES (326,63,'Added species-specific thresholds to Binding Matrices','<p>Added to each Binding Matrix the lowest score for Motif Features belonging to that matrix and that species. This will make it easier for people using the API to know if the potential binding affinity for a given sequence goes above the currently used threshold (ie would be classified as a binding site). </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 15:41:13',100304,'2011-05-31 10:53:57',1);
-INSERT INTO `changelog` VALUES (327,63,'Schema changes','<p># structural variation schema changes:</p>\r\n<p>- Change the columns name from bound_start to inner_start and bound_end to inner_end</p>\r\n<p>- Add a column for validation status</p>\r\n<p>- Change the column class to class_attrib_id, using more detailled SO terms.</p>\r\n<p><br /># moved failed descriptions into attribute table <-- Postponed</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-05-03 15:58:42',99616,'2011-06-03 14:24:03',1);
-INSERT INTO `changelog` VALUES (328,63,'Cleaned Regulatory Regions in chromosomal boundaries','<p>In some rare cases, regulatory regions can pass the boundaries of sequence regions (chromosomes or scaffolds). These cases will be removed as they are likely to be artifactual. For release 63, 18 mouse regulatory features were removed.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 15:59:00',100304,'2011-05-31 10:54:38',1);
-INSERT INTO `changelog` VALUES (329,63,'LRG data','<p>import LRG variant data</p>\r\n<p>add LRG consequences to the database</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-05-03 16:01:34',99616,'2011-06-03 14:24:25',1);
-INSERT INTO `changelog` VALUES (330,63,'Update of Regulation Metadata','<p>CTCF is now classified generically as a \"Transcription Factor\" instead of \"Insulator\"</p>\r\n<ul>\r\n</ul>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-05-03 16:01:50',100304,'2011-05-31 10:49:27',1);
-INSERT INTO `changelog` VALUES (331,63,'New individual genotypes','<p>Individual genotypes from Penn State University:</p>\r\n<ul>\r\n<li>Han Chinese Individual (YanHuang Project)</li>\r\n<li>Seong-Jin Kim (SJK, GUMS/KOBIC)</li>\r\n<li>Anonymous Irish Male</li>\r\n<li>Individual from the Extinct Palaeo-Eskimo Saqqaq (Saqqaq Genome Project)</li>\r\n<li>Individual from the Extinct Palaeo-Eskimo Saqqaq, high confidence SNPs (Saqqaq Genome Project)</li>\r\n<li>Anonymous Korean individual, AK1 (Genomic Medicine Institute) : Individual genotype</li>\r\n<li>Misha Angrist (Personal Genome Project)</li>\r\n<li>Henry Louis Gates Jr (Personal Genome Project) </li>\r\n<li>Henry Louis Gates Sr (Personal Genome Project) </li>\r\n<li>Rosalynn Gill (Personal Genome Project)</li>\r\n<li>Marjolein Kriek (Leiden University Medical Centre)</li>\r\n<li>Stephen Quake (Stanford)</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',102503,'2011-05-03 16:03:37',99616,'2011-06-03 14:24:58',1);
-INSERT INTO `changelog` VALUES (332,63,'xref sources to be moved to gene level','<p>The following External database sources have been moved up to the Gene level :-</p>\r\n<p>DBASS3, DBASS5, EntrezGene, miRBase, RFAM, UniGene, Uniprot_genename, WikiGene, MIM_GENE and MIM_MORBID.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2011-05-04 13:20:54',23,'2011-05-26 11:57:49',1);
-INSERT INTO `changelog` VALUES (333,63,'pairwise alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<div><span style=\"font-size: small;\"><span style=\"font-size: 13px; line-height: 17px;\"><br /></span></span></div>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs marmoset lastz</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs microbat lastz</li>\r\n</ul>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:13:42',98792,'2011-06-08 13:35:42',1);
-INSERT INTO `changelog` VALUES (334,63,'multiple alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">6way-primate-epo alignments to incorporate new marmoset</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">12way-mammal-epo alignments to incorporate new marmoset</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">19way-amniota-pecan alignments to incorporate new marmoset</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">35way-mammal low-coverage-epo alignments ( new marmoset and microbat )</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">5way-fish (new mappings with HMM derived anchors)</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:14:43',98792,'2011-06-08 13:34:46',1);
-INSERT INTO `changelog` VALUES (335,63,'syntenies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human marmoset synteny</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:15:23',98792,'2011-06-08 13:36:21',1);
-INSERT INTO `changelog` VALUES (336,63,'ProteinTrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<p style=\"font-size: 10pt; line-height: 13pt; color: #000000; font-weight: normal; margin-top: 10px; margin-right: 0px; margin-bottom: 10px; margin-left: 0px; padding: 0px;\">GeneTrees (protein-coding) with new/updated genebuilds and assemblies</p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering using hcluster_sg</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments using MCoffee, without the exon-disaligner module (AKA decaf)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference including the recent \'possible_ortholog\',\'putative gene split\' and \'contiguous gene split\' exceptions</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Pairwise gene-based dN/dS scores for high coverage species pairs only</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">GeneTree stable ID mapping</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:16:31',98792,'2011-06-08 13:38:07',1);
-INSERT INTO `changelog` VALUES (337,63,'ncRNAtrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Classification based on RFAM model</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments with infernal</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using RaxML</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional multiple sequence alignments with Prank (w/ genomic flanks)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional phylogenetic reconstruction using PhyML and NJ</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic tree merging using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:17:17',98792,'2011-06-08 13:40:49',1);
-INSERT INTO `changelog` VALUES (338,63,'families','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering by MCL</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple Sequence Alignments with MAFFT</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Family stable ID mapping</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:17:51',98792,'2011-06-08 13:41:49',1);
-INSERT INTO `changelog` VALUES (339,63,'data dumps','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 19 way PECAN multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 19 way GERP constrained elements</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 12 way EPO multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 6 way EPO primate multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 5 way fish EPO alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 5 way fish EPO alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ProteinTrees</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ncRNAtrees</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:18:51',98792,'2011-06-20 12:44:32',1);
-INSERT INTO `changelog` VALUES (340,63,'schema changes','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ol style=\"font-size: 10pt; line-height: 13pt; list-style-type: decimal;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">The linking table \'species_set\' is renamed into \'species_set_genome_db\'</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">There will be a new, \"header\" table called \'species_set\' for which \'species_set_id\' will be [obviously, unique] primary key.</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">species_set.species_set_id will become a foreign key for species_set_genome_db.species_set_id</li>\r\n</ol>\r\n<p> </p>','','postponed','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-05-04 15:20:06',98792,'2011-06-08 13:37:22',1);
-INSERT INTO `changelog` VALUES (341,63,'Zebrafish Vega merge','<p>A new Vega gene set has been merged with the Ensembl geneset from release 61.</p>','','handed_over','Genebuild','N','Y','N','Y','N','N','N','new',29,'2011-05-05 08:57:49',29,'2011-05-19 13:06:48',1);
-INSERT INTO `changelog` VALUES (342,63,'update variation consequences','<p>update variation consequences on human, zebrafish and cow due to new gene sets</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-05-05 16:08:12',99616,'2011-06-03 14:25:24',1);
-INSERT INTO `changelog` VALUES (343,63,'Uploading zipped files','<p>Upload of custom data (BED, GFF, etc) now supports both .zip and .gz formats seamlessly. Files are unzipped during uploading and stored on our servers in uncompressed format.</p>','Needs testing with a few different formats!','handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2011-05-09 13:26:47',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (344,62,'Test','<p>Link test</p>\r\n<p><a title=\"Ensembl\" href=\"http://www.ensembl.org\">Ensembl</a></p>','Test','declared','Web','N','N','N','N','N','N','N','N/A',102019,'2011-05-18 12:25:17',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (345,63,'Lucene plugin','<p>Our plugin for the Lucene search engine has been made public. Please note that this is only the web interface - it requires a Lucene web service to connect to. We intend to provide instructions on how to set up your own Lucene server in a future release.</p>\r\n<p>The main web code for simple text-based searching (UniSearch) has also been refactored, and old code removed. This should make it much easier to develop additional plugins for other search engines - see the lucene plugin for the modules you will need to create.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,'2011-05-19 09:17:20',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (346,63,'Update ancestral alleles','<p>Update of the ancestral allele annotation for variations to primarily use data from the Ensembl Compara Ortheus calls. The ancestral allele data source priority is::</p>\r\n<p>1. Compara high confidence</p>\r\n<p>2. Compara low confidence</p>\r\n<p>3. Ancestral allele calls reported by Dr Jim Mullikin (http://www.ncbi.nlm.nih.gov/books/NBK44409/)</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',99616,'2011-05-24 15:31:54',99616,'2011-06-03 14:25:42',1);
-INSERT INTO `changelog` VALUES (347,63,'ResultFeatureAdaptor ExperimentalChip support removed','<p>Support for ResultFeatures originating from ExperimentalChips (i.e. array experiments) has been removed.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-05-25 12:34:43',1273,'2011-06-03 16:01:35',1);
-INSERT INTO `changelog` VALUES (348,63,'Update to CCDS and RefSeq models in human otherfeatures database','<p>Imported CCDS models into human otherfeatures databases. (CCDS Data freeze 9 February 2011).</p>\r\n<p>Imported RefSeq models into human otherfeatures database.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2011-05-25 13:34:51',5132,'2011-06-02 13:39:46',1);
-INSERT INTO `changelog` VALUES (349,63,'Sortable tracks on images','<p>Tracks on <strong>Region in detail</strong> and <strong>Region overview</strong> pages can now be reordered by dragging them to a new position on the image.</p>\r\n<p>There is also an interface for this in the control panel, which is available on the following additional views:</p>\r\n<ul>\r\n<li>Location: Alignments (image), Multi-species view</li>\r\n<li>Gene: Summary, Regulation</li>\r\n<li>Regulation: Feature context</li>\r\n<li>Variation: Genomic context</li>\r\n</ul>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-05-31 08:27:34',97803,'2011-05-31 08:28:12',1);
-INSERT INTO `changelog` VALUES (350,63,'Favourite tracks saved across all configurations','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 12px;\">If you make a track your favourite on one page, it will be marked as a favourite on all pages where it appears.</span></p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-05-31 08:28:59',97803,'2011-05-31 08:33:45',1);
-INSERT INTO `changelog` VALUES (351,63,'Download genotype information as CSV','<p>The download view as csv has been enabled for the individual genotype information. The tables can now be downloaded as CSV format.</p>\r\n<p>http://www.ensembl.org/Homo_sapiens/Variation/Individual?r=9:22125003-22126003;v=rs1333049;vdb=variation;vf=19660490</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2011-05-31 08:32:51',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (352,63,'Tracks on location based Multi-species and Alignments (image) views are now configurable on a species by species basis','<p>There is now a dropdown with a species list in the configuration panel for these pages. Only tracks for the selected species will be displayed, to make configuration easier.</p>\r\n<p> </p>\r\n<p>On Multi-species view, there is an <strong>All species</strong> option, which contains options for which alignments to show.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-05-31 08:32:58',97803,'2011-05-31 08:33:23',1);
-INSERT INTO `changelog` VALUES (353,63,'Species selection on Multi-species view is saved','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 12px;\">Your choice of secondary species is saved for each primary species so that when you come back to the site you don\'t have to make the selection again.</span></p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-05-31 08:34:20',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (354,63,'New style popup menus on images','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 12px;\">The menus which appear when you click on tracks on images (e.g. Region in detail) have been redesigned.</span></p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-05-31 08:34:53',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (355,63,'New style regulation configuration matrix','<p>The <strong>Evidence types</strong> matrix has been redesigned so that it fits more easily in the configuration panel.</p>\r\n<p> </p>\r\n<p>The checkboxes have been replaced with a grid, with colours indicating the status of the options - light blue for off, dark blue for on, grey for unavailable.</p>\r\n<p> </p>\r\n<p>Options can be changed by clicking on the grid, and there is also the ability to select or deselect all options in a column or row from a menu which appears when hovering over the labels for that column or row.</p>\r\n<p> </p>\r\n<p>Additionally, selection can be performed by holding down the left mouse button and dragging over the grid, but note that this performs a toggle operation, so any options in your selection which were on will be turned off, and vice versa. (This functionality is not available in IE 8 and older.)</p>\r\n<p> </p>\r\n<p>Finally, there is a filter input, allowing for quick identification of required options.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-05-31 08:43:46',97803,'2011-05-31 14:31:57',1);
-INSERT INTO `changelog` VALUES (356,63,'Download as CSV button on tables','<p>Most tables on the site now have a button to download the data as a CSV file in the table header (to the right of the filter).</p>\r\n<p> </p>\r\n<p>If you hover over the button you will get a popup with options to download the entire table, or just the data visible at the time. Clicking on the button without waiting for this popup will download the visible data.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-06-02 10:03:53',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (357,63,'Pie graphs to display alleles frequencies by population','<p>Web display: Add pie graphs in the Variation -> Population genetics pages, for the 1000 genomes populations</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',102503,'2011-06-02 14:32:01',99616,'2011-06-03 14:26:11',1);
-INSERT INTO `changelog` VALUES (358,63,'Probe features in gff export','<p>Probe features are now included in the export for GFF Format.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',99923,'2011-06-06 16:14:06',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (359,63,'CAGE-defined TSS (K562)','<p>CAGE-defined transcription start sites for K562 cell line imported into the human otherfeatures database. Data provided by Riken as part of the ENCODE collaboration. Data from additional cell lines expected in due course.</p>','','cancelled','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2011-06-09 10:49:20',5132,'2011-06-10 08:50:25',1);
-INSERT INTO `changelog` VALUES (360,63,'Variation Effect Predictor 2.1','<p><br /> * option to filter the output based on frequencies in 1000 Genomes populations<br /> * new US East database server available for querying<br /> * ability to use local file cache in place of or alongside connecting to an Ensembl database<br /> * new \"standalone\" mode does not depend on API installation or network connection<br /> * significant improvements to speed of script<br /> * whole-genome mode now default (no disadvantage for smaller datasets)<br /> * improved status output with progress bars<br /> * regulatory region consequences now reinstated and improved<br /> * modification to output file - Transcript column is now Feature, and is followed by a Feature_type column</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-06-23 09:37:44',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (363,64,'Lamprey genome','<p>A full annotated gene set for the lamprey genome</p>','','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',97245,'2011-07-01 13:24:22',97245,'2011-07-01 13:36:45',1);
-INSERT INTO `changelog` VALUES (364,64,'Human cDNA update','<p>New cDNA db for human.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','new',14183,'2011-07-01 13:41:40',14183,'2011-07-20 12:21:37',1);
-INSERT INTO `changelog` VALUES (365,64,'GRCh37.p5','<p>Adding the fifth patch release for the human assembly. This alters the assembly information in all human databases.</p>','','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','patched',14183,'2011-07-01 13:44:01',14183,'2011-07-19 08:20:05',1);
-INSERT INTO `changelog` VALUES (366,64,'GRCh37.p5 annotation','<p>Annotation of the patches in the other features db, including projection of annotation from the primary assembly.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',14183,'2011-07-01 13:45:26',14183,'2011-08-10 08:49:02',1);
-INSERT INTO `changelog` VALUES (367,64,'Cow genebuild','<p>A new genebuild has been done on the cow UMD 3.1 assembly.</p>\r\n<p>A new otherfeatures database has also been prepared.</p>','','handed_over','Genebuild','Y','Y','Y','N','Y','N','Y','new',97238,'2011-07-02 23:07:13',97238,'2011-08-01 22:53:38',1);
-INSERT INTO `changelog` VALUES (368,64,'Mouse gene set update','<p>The merged gene set has been updated to incorporate the latest Vega manual annotation.</p>','','handed_over','Genebuild','N','Y','N','N','Y','N','N','new',97238,'2011-07-02 23:12:45',9335,'2011-07-22 10:11:24',1);
-INSERT INTO `changelog` VALUES (370,64,'Tasmanian Devil Genome','<p>A genebuild on the Tasmanian Devil 7.0 assembly has been created along with an otherfeatures database containing RNASeq models.</p>','','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',29,'2011-07-05 10:59:07',97245,'2011-07-22 10:24:22',1);
-INSERT INTO `changelog` VALUES (371,64,'Ensembl 64 mart databases','<p>Full build of all seven marts for release 64</p>','','declared','Mart','N','N','N','N','N','N','N','N/A',25629,'2011-07-05 12:53:16',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (372,64,'Xref projections','<p>Project GO IDs and gene names to species.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',25629,'2011-07-06 07:38:01',23,'2011-08-19 13:41:19',1);
-INSERT INTO `changelog` VALUES (373,64,'Update to Ensembl-Havana GENCODE gene set (release 9)','<p>Update to Ensembl-Havana GENCODE gene set (release 9) based on Ensembl gene set and latest Havana gene annotation.</p>','Note that this core database will contain the new GRC patches, hence the declaration for assembly change and the required repeat masking. These modifications have been declared by Susan already.','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','new',9335,'2011-07-06 09:30:09',9335,'2011-07-22 10:10:40',1);
-INSERT INTO `changelog` VALUES (374,64,'Xrefs','<p>Update xrefs for human, mouse, <span style=\"font-family: \'Lucida Grande\'; font-size: 12px;\">sea squirt ciona intestinalis and ciona savignyi, madagascar hedgehog, western european hedgehog, mouse lemur, platypus, bushbaby, shrew, squirrel</span></p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-07-06 09:32:25',23,'2011-08-19 13:40:12',1);
-INSERT INTO `changelog` VALUES (375,64,'GENCODE RNA-Seq','','','postponed','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2011-07-06 09:54:57',5132,'2011-08-17 15:28:04',1);
-INSERT INTO `changelog` VALUES (376,64,'Human Vega annotation','<p>Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 44. Annotation by Havana of chromosome 14 has been completed.</p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2011-07-06 10:23:13',97245,'2011-07-26 14:11:11',1);
-INSERT INTO `changelog` VALUES (377,64,'Mouse Vega annotation','<p>Manual annotation of mouse from Havana has been updated, including annotation of the MHC region on chromosome 17. The data represents the annotation presented in Vega release 44.</p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',161,'2011-07-06 10:24:50',97245,'2011-07-26 14:10:39',1);
-INSERT INTO `changelog` VALUES (379,64,'New Regulatory Data','<ul>\r\n<li>New Mouse MEL cell-line regulatory build, including <a href=\"http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase\">Dnase-Seq</a>, and <a href=\"http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhTfbs\">ChIP-Seq</a> for CTCF, p300, cMyb, USF2, Rad21, NELFe and Max. All data is from ENCODE, following their <a href=\"http://genome.ucsc.edu/ENCODE/terms.html\">data policies</a>.</li>\r\n<li>New Human CD4 ChIP-Seq data for CBP, p300, MOF, PCAF, Tip60, HDAC1, HDAC2, HDAC3 and HDAC6 (<a href=\"http://www.ncbi.nlm.nih.gov/pubmed?term=19698979\">Wang et al, 2009</a>). A new regulatory build was made to incorporate this data. </li>\r\n</ul>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-07-06 15:38:07',100304,'2011-08-12 16:18:55',1);
-INSERT INTO `changelog` VALUES (380,64,'schema change','<p>is_ref will be added to the alt_allele table to show which is the reference gene.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',23,'2011-07-06 15:40:58',23,'2011-08-19 13:40:41',1);
-INSERT INTO `changelog` VALUES (381,64,'Embl/ Genbank flat file dumps','','','declared','Core','N','N','N','N','N','N','N','N/A',23,'2011-07-06 15:41:36',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (382,64,'MotifFeatures: PWM Scores Rounded','<p>MotifFeature PWM scores were rounded to 3 decimal places.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-07-06 15:42:45',100304,'2011-08-11 15:59:59',1);
-INSERT INTO `changelog` VALUES (383,64,'Schema version update','<p>patch_63_64_a.sql</p>\r\n<p>update schema version to 64</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',103537,'2011-07-06 15:45:54',23,'2011-08-19 13:42:18',1);
-INSERT INTO `changelog` VALUES (384,64,'Mouse cDNA update','<p>The latest set of cDNAs for mouse (as of 19/JUL/2011) from the <br />European Nucleotide Archive and NCBI RefSeq were aligned to the <br />current genome using <a title=\"Exonerate\" href=\"http://www.ebi.ac.uk/~guy/exonerate/\" target=\"_blank\">Exonerate</a>. There are 1,223 new cDNAs with a total of 15,200 new alignments for Ensembl 64.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',102717,'2011-07-06 15:50:21',102717,'2011-07-20 12:41:59',1);
-INSERT INTO `changelog` VALUES (385,64,'Flagging obsolete Uniprot proteins','<p>Flag the obsolete proteins in Uniprot used as supporting evidence</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',101214,'2011-07-06 15:51:21',101214,'2011-08-01 10:10:34',1);
-INSERT INTO `changelog` VALUES (386,64,'Flagging obsolete Ensembl proteins','<p>Flag obsolete human Ensembl proteins used as supporting evidence</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',101214,'2011-07-06 15:52:15',101214,'2011-08-01 10:10:03',1);
-INSERT INTO `changelog` VALUES (387,64,'dbSNP 133 import','<p>dbSNP Build 133 for cow based on the UMD_3.1 assembly.</p>\r\n<p> </p>','','handed_over','Variation','N','N','N','N','N','N','Y','patched',3,'2011-07-06 16:26:18',102503,'2011-07-14 14:58:59',1);
-INSERT INTO `changelog` VALUES (388,64,'LRG variant import','<p>variants on LRG sequences</p>','','handed_over','Variation','N','N','N','N','N','N','Y','patched',3,'2011-07-06 16:28:08',99616,'2011-08-15 09:30:21',1);
-INSERT INTO `changelog` VALUES (389,64,'Phenotype annotations','<ul>\r\n<li>COSMIC import update. Minor changes in COSMIC sample names</li>\r\n<li>OMIM, NHGRI GWAS catalog, UniProt and EGA updates</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','Y','patched',3,'2011-07-06 16:30:16',102503,'2011-08-10 09:59:04',1);
-INSERT INTO `changelog` VALUES (390,64,'Schema changes','<ul>\r\n<li>Schema changes for structural variations \r\n<ul>\r\n<li>Add a structural_variation_feature table: store the coordinates</li>\r\n<li>Modification of the structural_variation table: remove the coordinates</li>\r\n</ul>\r\n</li>\r\n</ul>\r\n<ul>\r\n<li>Additional enum in variation source table for LSDBs</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-07-06 16:32:31',99616,'2011-08-04 09:19:56',1);
-INSERT INTO `changelog` VALUES (391,64,'Web display updates','<ul>\r\n<li>For the variation displays, we will add more detail to the consequence table, including displays showing the DNA sequence change and amino acid changes.</li>\r\n<li>Add a Phenotype panel (MIM diseases + variation annotations) in the Gene section</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-07-06 16:34:04',102503,'2011-09-05 13:36:40',1);
-INSERT INTO `changelog` VALUES (392,64,'update consequences for transcript alleles','<p>update human and mouse variation transcript alleles due to new gene builds</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,'2011-07-06 16:36:39',3,'2011-08-12 10:23:22',1);
-INSERT INTO `changelog` VALUES (393,64,'LRG import','<p>Import of new LRG sequences </p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',99616,'2011-07-06 16:50:32',99616,'2011-08-15 09:30:52',1);
-INSERT INTO `changelog` VALUES (394,64,'Structural variation','<ul>\r\n<li>Update structural variation data from DGVa for Human, Mouse, Dog and Pig.</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',102503,'2011-07-07 07:31:50',3,'2011-08-12 10:16:24',1);
-INSERT INTO `changelog` VALUES (395,64,'MicroArray Mapping','<p>Micro array mapping has been performed for those species with new assemblies or updated gene builds.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-07-07 09:43:45',1273,'2011-08-19 14:21:26',1);
-INSERT INTO `changelog` VALUES (396,64,'DNA methylation DAS tracks','<p>We have updated the set of DNA methylation DAS tracks using data available from the ENCODE project.</p>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-07-07 09:48:20',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (397,64,'Pairwise alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> \r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs cow lastz alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs tasmanian devil lastz alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human haplotype alignments for high coverage blastz-net alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">pig vs cow lastz alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">opossum vs tasmanian devil lastz alignments</li>\r\n</ul>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs lamprey tblat alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">lamprey vs Ciona intestinalis tblat alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">lamprey vs Danio rerio tblat alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">lamprey vs Gasterosteus aculeatus tblat alignments</li>\r\n</ul>\r\n</span></p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:07:12',49918,'2011-08-11 09:10:42',1);
-INSERT INTO `changelog` VALUES (398,64,'Multiple alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">12way-mammal EPO alignments to incorporate new cow</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">19way-amniota Pecan alignments to incorporate new cow</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">35way-mammal low-coverage-EPO alignments (new cow)</li>\r\n</ul>\r\n</span></p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:08:57',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (399,64,'Syntenies','<ul>\r\n<li><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">human-cow synteny</span></li>\r\n<li><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">human-gorilla synteny<br /></span></li>\r\n<li><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">pig-cow synteny<br /></span></li>\r\n</ul>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:09:52',49918,'2011-08-11 09:11:22',1);
-INSERT INTO `changelog` VALUES (400,64,'ProteinTrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<h4 style=\"line-height: normal; font-weight: bold; font-size: 13pt; margin-top: 25px; margin-right: 0px; margin-bottom: 4px; margin-left: 0px; color: #003366; padding: 0px;\"><span style=\"color: #000000; font-weight: normal; font-size: 13px; line-height: 17px;\">GeneTrees (protein-coding) with new/updated genebuilds and assemblies</span></h4>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering using hcluster_sg</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments using MCoffee without the exon-disaligner module, or Mafft</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference including the recent \'possible_ortholog\',\'putative gene split\' and \'contiguous gene split\' exceptions</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">GeneTree stable ID mapping</li>\r\n</ul>\r\n<p> </p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:31:54',98792,'2011-07-07 14:32:22',1);
-INSERT INTO `changelog` VALUES (401,64,'ncRNAtrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Classification based on Rfam model</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments with infernal</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using RaxML</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using FastTree2 and RaxML-light for very big families</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional multiple sequence alignments with Prank (w/ genomic flanks)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional phylogenetic reconstruction using PhyML and NJ</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic tree merging using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference</li>\r\n</ul>\r\n</span></p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:33:07',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (402,64,'Protein Families','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">\r\n<h4 style=\"line-height: normal; font-weight: bold; font-size: 13pt; margin-top: 25px; margin-right: 0px; margin-bottom: 4px; margin-left: 0px; color: #003366; padding: 0px;\"><span style=\"color: #000000; font-weight: normal; font-size: 13px; line-height: 17px;\">Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.</span></h4>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering by MCL</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple Sequence Alignments with MAFFT</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Family stable ID mapping</li>\r\n</ul>\r\n</span></p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:34:25',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (403,64,'Compara dumps','<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 20 way PECAN multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 20 way GERP constrained elements</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 12 way EPO multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ProteinTrees</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ncRNAtrees</li>\r\n</ul>\r\n<p> </p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:35:51',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (404,64,'API/schema changes','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">changes in the class hierarchy (NestedSet-Member-AlignedMember) to achieve better flexibility and fight code redundancy</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">changes in the API: introduction of GeneTreeNode and GeneTreeMember classes to better represent our trees</li>\r\n</ul>\r\n<p> </p>','','declared','Compara','N','N','N','N','N','N','N','N/A',98792,'2011-07-07 14:36:47',98792,'2011-08-22 09:20:12',1);
-INSERT INTO `changelog` VALUES (405,64,'Gorilla 3.1 projection','<p>A new AGP file was provided for gorilla, using the same contigs but with different gaps sizes. Genes from the e63 release (assembly gorGor3) were projected onto the updated assembly (gorGor3.1). All genes from the e63 gene set were mapped to the new assembly. A small number of features from the \'RNASeq gene\' and \'<span class=\"menu_option\">Human RefSeq/ENA cDNA</span>\' track were not mapped to the new assembly because their exons spanned across a gap that had changed size.</p>','','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','new',5132,'2011-07-07 21:04:22',5132,'2011-08-05 14:24:12',1);
-INSERT INTO `changelog` VALUES (406,64,'Removal of ambiguous bases from Takifugu rubripes','<p>Removed the \'R\' and \'Y\' ambiguous bases from scaffold_20 in takifugu_rubripes_core_64_4.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',5132,'2011-07-13 09:24:20',97245,'2011-07-22 10:23:49',1);
-INSERT INTO `changelog` VALUES (407,64,'patch_63_64_a - Schema version','<p>The schema_cersion entry in the meta table has been patched to version 64.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-07-13 09:26:00',1273,'2011-08-19 14:21:51',1);
-INSERT INTO `changelog` VALUES (408,64,'patch_63_64_b - Cell type experimental factor ontology ID','<p>The cell_type table has had an efo_id field added to represent links to the Experimental Factor Ontology.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-07-13 09:27:51',1273,'2011-08-19 14:22:07',1);
-INSERT INTO `changelog` VALUES (409,64,'patch_63_64_c - Experimental meta data','<p>A patch has been applied to add fields to capture experimental meta data e.g. archive & pubmed IDs</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1273,'2011-07-13 09:28:48',1273,'2011-08-19 14:22:23',1);
-INSERT INTO `changelog` VALUES (410,64,'Updated mouse otherfeatures db: New CCDS import','','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',102717,'2011-08-01 10:18:56',102717,'2011-08-01 15:57:51',1);
-INSERT INTO `changelog` VALUES (411,64,'Update human otherfeatures db: new CCDS import','','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',102717,'2011-08-01 10:19:26',102717,'2011-08-01 15:33:23',1);
-INSERT INTO `changelog` VALUES (412,64,'Updated human RefSeq gene import','<p>The imported RefSeq gene set was updated in human otherfeatures. The RefSeq gene count increased from 23733 in e63 to 24435 in e64.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',5132,'2011-08-05 15:57:39',5132,'2011-08-06 13:10:06',1);
-INSERT INTO `changelog` VALUES (413,64,'Corrected CTCF, Nanog, p300 and Smad1 Mouse ES ChIP-Seq datasets','<p>We identified an issue with our analysis of the CTCF, Nanog, p300 and Smad1 for the ES cell line from Chen et al., 2008. The raw reads were clipped to 26bp, re-aligned, and new peak calls were made. This correction enabled a significant increase in the number of mapped reads, making the new peaks more trustworthy.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-08-10 09:34:33',100304,'2011-08-11 16:00:24',1);
-INSERT INTO `changelog` VALUES (414,64,'New H3K36me3 Peak Calls using CCAT','<p>We have changed the peak calling method for H3K36me3 datasets. The new method uses CCAT (Xu et al, 2010), configured for histone marks and with a sliding window of 1000bp. This method has enabled an increase in the number and length of H3K36me3 calls.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',100304,'2011-08-10 09:39:21',100304,'2011-08-11 16:00:56',1);
-INSERT INTO `changelog` VALUES (415,64,'Linkage_type change in ontology_xref','<p>Change to linkage_type column in table ontology_ref. Values to be tested in healthchecks.</p>\r\n<p>patch_63_64_d.sql</p>','','declared','Core','N','N','N','N','N','N','N','N/A',103537,'2011-08-11 10:53:29',103537,'2011-08-11 10:54:28',1);
-INSERT INTO `changelog` VALUES (416,64,'structural','<p> </p>\r\n<ul>\r\n<li>Add COSMIC structural variation data (Human). CANCELLED</li>\r\n</ul>','','cancelled','Variation','N','N','N','N','N','N','N','N/A',3,'2011-08-12 10:15:40',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (417,64,'User data on Multi-species view','<p>User data is now viewable on Multi-species view</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-08-12 15:01:36',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (418,64,'Configuration panel improvements','<p>A number of changes have been made to the display of the configuration panel (accessed via the \"Configure this page\" button), including a new menu structure with grouping for similar track types</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-08-12 15:04:18',NULL,NULL,1);
-INSERT INTO `changelog` VALUES (419,64,'Configuring supporting evidence for regulatory features','<p>Configuration for regulatory evidence is now accessible via two links in the Regulation section of the menu for the configuration panel - \"Open chromatin & TFBS\" and \"Histones & polymerases\".</p>\r\n<p>From these links you can access a matrix to choose cell line and evidence type options, as well as changing the renderer for the tracks. These tracks are no longer accessible from other sections of regulation configuration.</p>\r\n<p> </p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-08-12 15:21:20',97803,'2011-08-17 15:59:33',1);
-INSERT INTO `changelog` VALUES (420,64,'Auto-resizing images','<p>If you set image width to be \"best fit\", the images will now resize to fit inside the browser window when it is resized</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',97803,'2011-08-17 16:01:47',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (1,59,'Changelog','<p>As of release 59, Ensembl will use a changelog to track detailed updates to the data and code. This will be separate from the release news, which will focus on major updates such as new species and web features.</p>\r\n\r\n<p>The changelog is stored in the new ensembl_production database, rather than ensembl_website.</p>','sauausatuhusahsu','handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2010-05-18 11:04:18',2,'2010-07-16 09:36:02',1);
+INSERT INTO `changelog` VALUES (3,59,'Ensembl marts for release 59','<p>Full build of seven marts:<br />- sequence mart.<br />- ensembl mart: possible orthologs added.<br />- snp mart: somatic data set added.<br />- ontology mart.<br />- vega mart<br />- functional genomics mart.<br />- genomic features mart.</p>','','handed_over','Mart','N','N','N','N','N','N','N','N/A',2,100169,'2010-05-27 16:32:04',36,'2010-07-27 14:38:25',1);
+INSERT INTO `changelog` VALUES (4,59,'external database references','<p>Update External database references for:-</p>\r\n<ul>\r\n<li>Human</li>\r\n<li>Mouse</li>\r\n<li>Cow</li>\r\n<li>Chicken</li>\r\n</ul>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2010-05-28 09:35:36',36,'2010-07-27 14:36:03',1);
+INSERT INTO `changelog` VALUES (5,59,'Update to human RepeatMasking','<ul>\r\n<li>Update to human Repeatmasking: this involves re-running the RepeatMasker analysis on toplevel slices, with the \'-nolow\' flag, so that low complexity regions are not masked. </li>\r\n</ul>','','handed_over','Genebuild','Y','N','Y','N','N','N','N','new',2,5132,'2010-05-28 14:19:01',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (6,59,'Update human otherfeatures db','<p>Update human otherfeatures database:</p>\r\n<ul>\r\n<li>New CCDS models</li>\r\n</ul>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,5132,'2010-05-28 14:20:33',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (8,59,'New species name meta-values with corresponding helper methods','<p>A set of new meta key-value pairs are inserted into all Core databases:</p>\r\n<ul>\r\n<li>species.production_name (a string that may be used to refer to a particular species in e.g. database tables or file names)</li>\r\n<li>species.scientific_name (the full bi- or trinomial scientific name of the species)</li>\r\n<li>species.short_name (a short string, often based on the common name, useful for labels in GUIs etc.)</li>\r\n</ul>\r\n<p>For each of these, the Bio::EnsEMBL::DBSQL::MetaContainer class now also contains a get_* method for retrieval of the corresponding meta value (get_short_name(), etc.). There is also a new get_common_name() method.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,896,'2010-06-21 13:29:37',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (9,59,'ResultFeature Collection Normalisation','<p>All result_feature collections (Human & Mouse) have been normalised using a simple by read count method(RPKM), enabling more meaningful visual comparisons using the multi-wiggle displays. </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-01 10:45:56',1273,'2010-07-21 11:26:05',1);
+INSERT INTO `changelog` VALUES (10,59,'Mouse IKMC xrefs and features','<p>Support mouse IKMC (International Mouse Knockout Consortium) links by creating a set of simple features to show the genomic extent of the knockouts.</p>','','handed_over','Core','N','N','N','N','N','N','N','patched',2,36,'2010-06-01 10:56:32',36,'2010-07-16 09:37:58',1);
+INSERT INTO `changelog` VALUES (11,59,'Update Amazon data sets','<p>Update Amazon data sets for MySQL and FASTA dumps.</p>','','handed_over','Core','N','N','N','N','N','N','N','patched',2,36,'2010-06-01 10:57:48',36,'2010-07-27 14:46:21',1);
+INSERT INTO `changelog` VALUES (12,59,'Gene name and GO term projections','<p>Assign gene names and GO terms to species where they are not well covered by projection from well-annotated species, using Compara homologies.</p>','','handed_over','Core','N','N','N','N','N','N','N','patched',2,36,'2010-06-01 10:58:59',36,'2010-07-16 09:38:24',1);
+INSERT INTO `changelog` VALUES (13,59,'Schema patch: annotated_feature.summit','<p>The annotated_feature table now has a dedicated peak \'summit\' field (patch_58_59_c.sql). API support has been added both to the eFG and the ensembl-analysis APIs.</p>\r\n<p> </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-01 16:18:51',1273,'2010-07-21 11:26:38',1);
+INSERT INTO `changelog` VALUES (14,59,'Update to human ensembl-vega','<p>Update to the human havana annotation shown in the \'Vega Havana\' gene track</p>','','postponed','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2010-06-01 16:33:58',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (15,59,'Schema patch: probe.description','<p>The probe table has been patched (patch_58_59_b) to add a description column. Appropriate API support has also been added to the eFG and ensembl-analysis APIs</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-02 10:50:35',1273,'2010-07-21 11:27:43',1);
+INSERT INTO `changelog` VALUES (16,59,'Schema path: regulatory_feature.binary_string_project','<p>The regulatory_feature table has been redefined (patch_58_59_d) to add a new binary_string and projected columns to store information generated from the Regulatory Build. API has also be added to the RegulatoryFeature class and associated adaptor.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-02 10:54:49',1273,'2010-07-21 11:28:08',1);
+INSERT INTO `changelog` VALUES (17,59,'Mouse Projection Regulatory Build','<p>The Mouse Regulatory Build has been regenerated using a new \'projection\' method. Core(MultiCell) RegulatoryFeatures are only be projected to these sparsely annotated cell lines if more annotation is available i.e. RegulatoryFeatures are not be built if there is no supporting evidence on the given cell line.</p>\r\n<p>This reintroduces some data from different cell lines which do not have associated \'core\' features (e.g. DNAse1) along with some new TFBS data.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-02 11:08:53',2,'2010-07-21 11:49:11',1);
+INSERT INTO `changelog` VALUES (18,59,'New chip-seq datasets','<p><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">Add ENCODE Chip-seq datasets for the following cell types:</span></p>\r\n<ul>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">K562: Update of the Current Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">GM12878: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">H1 ES: New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">HeLa: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">HepG2: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">HUVEC: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">No Regulatory Build for this cell line in this release </span></li>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">NHEK: </span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">New Regulatory Build for this cell line</span></li>\r\n</ul>\r\n<p><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\"><br />Add mouse TF Chip-Seq datasets from Chen et all (2008)</span></p>\r\n<ul>\r\n<li><span style=\"font-family: arial, sans-serif; font-size: small;\"><span style=\"border-collapse: collapse; font-size: 13px;\">Update of the Current Mouse ES Reg</span></span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;\">ulatory Build</span></li>\r\n</ul>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2010-06-02 11:24:50',100304,'2010-07-28 09:38:30',1);
+INSERT INTO `changelog` VALUES (19,59,'Schema change','<p>We will have the following schema patches to the Ensembl Core schema:</p>\r\n<ol>\r\n<li>Update schema version, as usual.</li>\r\n<li>Add new exception types (\'PATCH_NOVEL\' and \'PATCH_FIX\') to the assembly_exception table. This is to allow for patched assemblies.</li>\r\n<li>Modify the splicing_event table so that instead of a \'type\' field there is an \'attrib_type_id\' pointing to the attrib_type table. The short enumerated codes were too terse.</li>\r\n<li>A unique index in the object_xref table (\'object_type_idx\') is being extended to include the \'analysis_id\'. This is to allow two object Xrefs for the same object using two different analyses.</li>\r\n<li>A new meta key \'schema_type\' (with value \'core\' for Ensembl Core databases) will be inserted into all Core databases.</li>\r\n</ol>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2010-06-02 13:21:16',36,'2010-07-27 14:37:17',1);
+INSERT INTO `changelog` VALUES (20,59,'Drosophila melanogaster update','<p>Update of D. melanogaster gene set to release 5.25 (FlyBase 2010_02).</p>','','handed_over','Core','N','Y','N','N','Y','N','N','new',2,98587,'2010-06-02 15:35:39',737,'2010-07-21 11:37:03',1);
+INSERT INTO `changelog` VALUES (21,59,'Drosophila melanogaster update','<ul>\r\n<li>Affy mapping update for D. melanogaster 5.25</li>\r\n<li>Regulatory elements update from REDfly v2.2</li>\r\n</ul>\r\n<p> </p>','','handed_over','Funcgen','N','Y','N','N','Y','N','N','new',2,98587,'2010-06-02 15:53:11',98587,'2010-07-28 13:40:44',1);
+INSERT INTO `changelog` VALUES (22,59,'Variation data','Import of dbSNP 131 for Human\r\n and calculation of variation consequences and tag SNPs<br />\r\nImport of the CNV probes from the Affymetrix Genome 6 array <br />\r\nImport new LRG sequences<br />\r\nCorrect population sizes (currently 1 or 0 only)<br />\r\nCorrect zebrafish display strain defaults <br />\r\nsomatic mutation substitutions from 70 genes involved in cancer (COSMIC) \r\nUpdate UniProt and DGVa data\r\n<p>Update variation consequences (in transcript_variation table ) for new gene sets in: cow, horse, chicken, platypus, mouse, orangutan</p>\r\n','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2010-06-02 17:15:57',3,'2010-07-21 13:25:43',1);
+INSERT INTO `changelog` VALUES (23,59,'Update of mouse gene set','<p>Update of mouse gene set incorporating new Vega genes, implementing new code for HavanaAdder.</p>','','handed_over','Genebuild','N','Y','N','Y','Y','N','N','patched',2,97238,'2010-06-02 21:21:11',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (24,59,'Selenocysteine update','<p>Update 172 transcripts across 25 species to remove 3<span class=\"misspell\"> base pair</span> introns where there should be a selenocysteine.</p>\r\n<p>The following species are affected:</p>\r\n<ul>\r\n<li>bos taurus</li>\r\n<li>choloepus hoffmanni </li>\r\n<li>dasypus novemcinctus </li>\r\n<li>dipodomys ordii </li>\r\n<li>echinops telfairi </li>\r\n<li>equus caballus </li>\r\n<li>erinaceus europaeus </li>\r\n<li>felis catus </li>\r\n<li>gallus gallus </li>\r\n<li>gorilla gorilla </li>\r\n<li>macropus eugenii </li>\r\n<li>microcebus murinus </li>\r\n<li>myotis lucifugus </li>\r\n<li>ochotona princeps </li>\r\n<li>ornithorhynchus anatinus </li>\r\n<li>otolemur garnettii</li>\r\n<li>pongo pygmaeus </li>\r\n<li>procavia capensis </li>\r\n<li>pteropus vampyrus </li>\r\n<li>sorex araneus </li>\r\n<li>spermophilus tridecemlineatus </li>\r\n<li>tarsius syrichta </li>\r\n<li>tupaia belangeri </li>\r\n<li>tursiops truncatus </li>\r\n<li>vicugna pacos </li>\r\n</ul>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,29,'2010-06-03 09:42:53',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (25,59,'New human assembly patches','<p>Update human assembly to include sequence for the new assembly patches provided by the GRC (patch_release_1).</p>\r\n<ul>\r\n<li>Assembly patches are toplevel and non-reference</li>\r\n</ul>','','handed_over','Genebuild','Y','N','Y','N','N','N','N','new',2,5132,'2010-06-03 10:09:15',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (26,59,'Human Regulatory Build - 6 New cell lines & data update','<p>The Human Regulatory Build has been regenerated to incorporate the 5 new ENCODE cell lines: GM12878, H1ES, HeLa, HepG2, and NHEK.</p>\r\n<p>The new data has also been used to update the core MultiCell and existing cell line specific build i.e. K562, IMR90, GM06990, CD4. </p>\r\n<p> </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-03 10:28:02',100304,'2010-07-28 09:55:38',1);
+INSERT INTO `changelog` VALUES (27,59,'Ensembl-Havana merge (GENCODE gene set)','<p>There will be a new Ensembl-Havana merge gene set incorporating new annotation from Vega database.</p>','','postponed','Genebuild','N','Y','Y','Y','N','N','N','new',2,9335,'2010-06-03 10:32:06',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (28,59,'Variation API','<p>Add a new 1000 Genomes set<br />modify call for nearest gene to variation feature<br />HGVS nomenclature on proteins</p>\r\nChanges to API and schema to separate somatic and germline variations','','handed_over','Variation','N','N','N','N','N','N','N','new',2,99616,'2010-06-03 10:59:21',3,'2010-07-21 11:58:01',1);
+INSERT INTO `changelog` VALUES (29,59,'Additional mapping for marmoset','<p>An additional contig to scaffold mapping for unplaced and unlocalized scaffolds</p>\r\n<p>Update of the corresponding gene coordinates</p>','','handed_over','Genebuild','N','N','Y','N','N','N','N','patched',2,97245,'2010-06-03 10:59:58',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (30,59,'Variation schema','<p><br />New enums for 1000 Genomes and also for precious SNPs in the validation status column<br />add schema type key into the meta table</p>','','handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2010-06-03 11:01:15',3,'2010-07-21 11:47:00',1);
+INSERT INTO `changelog` VALUES (31,59,'Mouse cDNA update','<p>Mouse cDNA update</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','new',2,97245,'2010-06-03 11:01:25',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (32,59,'cDNA based gene annotation of human assembly patches','<p>Annotate human assembly patches with cDNA based gene models.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,14183,'2010-06-03 11:07:24',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (33,59,'Array Mapping','<p>Array mapping and Transcript xrefs have been regenerated for species which have updated genome assemblies or genebuilds.</p>','','handed_over','Funcgen','N','N','N','N','Y','N','N','N/A',2,1273,'2010-06-03 11:12:51',100304,'2010-07-28 09:40:07',1);
+INSERT INTO `changelog` VALUES (34,59,'Mouse ChIP-Seq data','<p><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; color: #555555; white-space: pre;\">Transcription Factor Chip-Seq data has been added (Chen </span><span style=\"font-size: 13px; border-collapse: collapse; color: #555555; white-space: pre;\"><em>et al</em></span><span style=\"font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; color: #555555; white-space: pre;\"> 2008)</span></p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-03 11:36:54',100304,'2010-07-28 09:55:05',1);
+INSERT INTO `changelog` VALUES (35,59,'Ontology database','<p>We will provide the ensembl_ontology_59 database with updated data from Gene Ontology (GO) and Sequence Ontology (SO).</p>','','handed_over','Core','N','N','N','N','N','N','N','new',2,896,'2010-06-03 12:07:02',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (36,59,'Saccharomyces cerevisiae core database','<p>Core database from Ensembl Genomes (updated March 2010 from SGD, currently in EG5) in 58 schema, patched to 59 schema when sql available. Also corresponding other_features database containing ESTs.</p>','Contact arnaud@ebi.ac.uk about yeast databases','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,101216,'2010-06-03 14:58:52',737,'2010-07-21 11:36:41',1);
+INSERT INTO `changelog` VALUES (37,59,'Saccharomyces cerevisiae funcgen database','<p>Database containing Affy array mapping data for Saccharomyces cerevisiae. Currently part of Ensembl Genomes Release 5. Currently 58, will be patched to 59.</p>','Contact arnaud@ebi.ac.uk','handed_over','Funcgen','N','N','N','N','Y','N','N','new',2,101216,'2010-06-03 15:00:29',101255,'2010-07-28 13:49:46',1);
+INSERT INTO `changelog` VALUES (38,59,'Saccharomyces cerevisiae variation database','<p>Variation database containing data from Saccharomyces Resequencing Project at the Sanger Institute. Present in Ensembl Genomes release 5 as schema 58. Will be patched to 59.</p>','contact: Arnaud Kerhornou \r\narnaud@ebi.ac.uk','handed_over','Variation','N','N','N','N','N','N','N','new',2,101216,'2010-06-03 15:02:01',101255,'2010-07-28 13:52:24',1);
+INSERT INTO `changelog` VALUES (39,59,'Drosophila melanogaster','<p>Drosophila melanogaster variation database based on DPGP 1.0</p>','','handed_over','Variation','N','Y','N','N','N','N','N','new',2,98587,'2010-06-03 17:15:59',98587,'2010-07-28 13:41:23',1);
+INSERT INTO `changelog` VALUES (40,59,'external db id','<p>Fixing dna align feature tables of otherfeatures databases for various species by adding external db ids</p>\r\n<p> </p>\r\n<p>WARNING, missing external_db_ids from Anolis_carolinensis DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Bos_taurus DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Bos_taurus DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Danio_rerio DATABASE_CORE dna_align_feature<br />WARNING, missing external_db_ids from Danio_rerio DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Drosophila_melanogaster DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Equus_caballus DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Saccharomyces_cerevisiae DATABASE_OTHERFEATURES dna_align_feature<br />WARNING, missing external_db_ids from Taeniopygia_guttata DATABASE_OTHERFEATURES dna_align_feature</p>\r\n<p> </p>','','declared','Genebuild','N','N','N','N','N','N','N','patched',2,1011,'2010-06-04 12:13:42',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (41,59,'Pairwise alignments','<p>Add new haplotype alignments for human vs high coverage blastz-net alignments<br /><br /> * H.sap-P.tro<br /> * H.sap-G.gor<br /> * H.sap-P.pyg<br /> * H.sap-M.mul<br /> * H.sap-M.mus<br /> * H.sap-R.nor<br /> * H.sap-C.fam<br /> * H.sap-B.tau<br /> * H.sap-S.scr<br /> * H.sap-E.cab<br /> * H.sap-O.ana<br /> * H.sap-M.dom<br /> * H.sap-G.gal<br /><br />New blastz-net due to changes in marmoset assembly<br /><br /> * H.sap-C.jac</p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-06-04 12:15:46',49918,'2010-07-16 09:44:17',1);
+INSERT INTO `changelog` VALUES (42,59,'Multiple alignments','<p> * 33 way epo low coverage<br /> * 6 way epo primates<br /> * 11 way epo eutherian mammals<br /> * Add MT alignments for fish, 11 and 33 way EPO alignments<br /> * Map changes to marmoset assembly in 16-way mecator/pecan placental mammals</p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-06-04 12:17:11',49918,'2010-07-16 09:44:49',1);
+INSERT INTO `changelog` VALUES (43,59,'Compara dumps','<p> * EMF dumps for 6 way EPO multiple alignments<br /> * EMF dumps for 11 way EPO multiple alignments<br /> * EMF dumps for 16 way mecator/pecan multiple alignments<br /> * EMF dumps for 33 way EPO multiple aligments<br /> * BED files for 33 way GERP constrained elements<br /> * EMF dumps for GeneTrees</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-06-04 12:18:11',96753,'2010-07-27 14:39:16',1);
+INSERT INTO `changelog` VALUES (44,59,'Families','<p>Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.<br /><br /> * Clustering by MCL<br /> * Multiple Sequence Alignments with MAFFT<br /> * Family stable ID mapping</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-06-04 12:19:02',49918,'2010-07-16 09:45:08',1);
+INSERT INTO `changelog` VALUES (45,59,'Gene Homlogies','<p>GeneTrees with new/updated genebuilds and assemblies<br /><br /> * Updated build of ncRNA trees<br /> * Clustering using hcluster_sg<br /> * Multiple Sequence Alignments using consistency-based MCoffee meta-aligner<br />(mafftgins+muscle+kalign+probcons) and exon-skipping aware \"skipper\" algorithm<br /> * Homology inference including the recent \'possible_ortholog\' type and \'putative gene split\' and<br />\'contiguous gene split\' exceptions<br /> * Pairwise gene-based dN/dS calculations for high coverage species pairs only<br /> * GeneTree stable ID mapping</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-06-04 12:20:02',49918,'2010-07-16 09:45:33',1);
+INSERT INTO `changelog` VALUES (46,59,'Schema changes','<p>* Addition of extra column in dnafrag table to hold information on whether the fragment is reference or non-reference.</p>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-06-04 12:20:45',49918,'2010-07-16 09:45:52',1);
+INSERT INTO `changelog` VALUES (47,59,'assembly fixes','<p>The assembly / seq region tables of otherfeatures databaess for these species will be sync. with their core databases bos_taurus_otherfeatures_58_4g<br />sus_scrofa_otherfeatures_58_9b<br />pan_troglodytes_otherfeatures_58_21m<br />danio_rerio_otherfeatures_58_8d<br />pongo_pygmaeus_otherfeatures_58_1d<br /><br /></p>','','handed_over','Genebuild','Y','N','N','N','N','N','N','patched',2,1011,'2010-06-04 12:25:30',5132,'2010-07-16 13:16:15',1);
+INSERT INTO `changelog` VALUES (48,59,'human cdna update','<p>new human cdna update database with integrated assembly patches</p>','','handed_over','Genebuild','Y','Y','N','N','N','N','N','new',2,1011,'2010-06-04 12:29:08',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (49,59,'Change name of EMBL database to European Nucleotide Archive','<p>Change name of EMBL database to European Nucleotide Archive to reflect the new official name. External reference sources will be the most obvious change.</p>','','declared','Core','N','N','N','N','N','N','N','patched',2,36,'2010-06-04 12:36:07',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (50,59,'Meta schema_type','<p>A meta entry has been added to the eFG DBs to capture the schema type \'funcgen\' (patch_58_59_e).</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-08 14:32:26',100304,'2010-07-28 09:31:06',1);
+INSERT INTO `changelog` VALUES (51,59,'variation displays','The LRG display now has tables listing differences between the LRG and the reference sequence.<br />\r\nThe context panel of the variation page has been updated to show if the variant overlaps a regulatory region, structural variants or conserved region\r\n','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2010-06-09 17:29:51',3,'2010-07-21 13:24:37',1);
+INSERT INTO `changelog` VALUES (52,59,'Schema patch: result_feature partitions','<p>The result_feature table partitions have been modified slightly to reflect the true default zoom levels in the \'Region in Detail\' view (patch_58_59_f). Collection data has been regenerated accordingly.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-10 13:19:52',100304,'2010-07-28 09:40:54',1);
+INSERT INTO `changelog` VALUES (53,59,'Meta table changes','<p>These changes are intended to solidify the requirements for names in Ensembl and will reduce the amount of name conversion which occurs in the codebase.</p>\r\n<table class=\"confluenceTable\">\r\n<tbody>\r\n<tr>\r\n<th class=\"confluenceTh\">meta key</th> <th class=\"confluenceTh\">usage</th> <th class=\"confluenceTh\">required</th> <th class=\"confluenceTh\">stable</th> <th class=\"confluenceTh\">regular expression</th> <th class=\"confluenceTh\">example value</th>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.production_name</td>\r\n<td class=\"confluenceTd\">Used for a computing scenario e.g. writing a file to disk.</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">\r\n$[a-z0-9_]+^</pre>\r\n</div>\r\n</div>\r\n</td>\r\n<td class=\"confluenceTd\">homo_sapiens</td>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.scientific_name</td>\r\n<td class=\"confluenceTd\">The full name of the species, which should replace the call\r\nMetaContainer->get_Species()->binomial()\r\n</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">-</td>\r\n<td class=\"confluenceTd\">Homo sapiens</td>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.common_name</td>\r\n<td class=\"confluenceTd\">The common name of the species, which can equal the value from taxonomy</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">-</td>\r\n<td class=\"confluenceTd\">human</td>\r\n</tr>\r\n<tr>\r\n<td class=\"confluenceTd\">species.short_name</td>\r\n<td class=\"confluenceTd\">A name which is short enough to be used in space-constrained areas (such as tabs on the web site)</td>\r\n<td class=\"confluenceTd\">yes</td>\r\n<td class=\"confluenceTd\">no</td>\r\n<td class=\"confluenceTd\">-</td>\r\n<td class=\"confluenceTd\">human</td>\r\n</tr>\r\n</tbody>\r\n</table>','The link between core to compara and web code to compara is a perfect example of the problem and with the introduction of more specific names (strain types from Ensembl Genomes and trinomial named species) this is something we need to put a stop to now.','handed_over','Core','N','N','N','N','N','N','N','N/A',2,737,'2010-06-11 11:27:13',2,'2010-08-05 10:27:39',1);
+INSERT INTO `changelog` VALUES (54,59,'Update mouse otherfeatures db','<p>Update mouse otherfeatures db</p>\r\n<ul>\r\n<li>New CCDS models</li>\r\n</ul>','','handed_over','Genebuild','N','Y','N','N','N','N','N','patched',2,5132,'2010-06-18 14:46:05',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (55,59,'miRanda miRNA Target update','<p>The human miRanda miRNA Targets set has been updated and a new mouse set has been added. These have been supplied by the Enright lab at the EBI . NOTE: These were generated using a revised conservative methodology and hence are a subset of those available via http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/ </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-06-25 14:50:49',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (56,59,'Public plugins','<p class=\"space-below\">We are overhauling public-plugins/admin, as it is very out of date. This will probably affect very few users, but for those that do use it, there will be quite a few changes in the next couple of releases so we wanted to give plenty of notice!</p>\r\n\r\n<p class=\"space-below\">Firstly, we are creating a new public plugin, \'orm\', which will reduce and ultimately remove our reliance on Class::DBI::Sweet by replacing it with Rose::DB::Object. Access to non-essential web functionality, including user accounts, will be ported to this plugin over the coming releases. This plugin will also be a requirement for the admin plugin, since the new CRUD interface uses Rose for its ORM (object relational mapping) component.</p>\r\n\r\n<p class=\"space-below\">Note that the core web code (in /modules) is in the process of being changed to use DBI directly for access to the ensembl_website database, for example for help and news. This is so that simple mirror sites do not need to install the Rose ORM suite and all its dependencies.<p>\r\n\r\n<p>If you have any questions, please email us at dev@ensembl.org.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2010-07-21 10:40:21',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (57,59,'Removal of Object::Help','<p>The module EnsEMBL::Web::Object::Help and its associated Factory, as well as the EnsEMBL::Web::Data classes for help records, have been removed from the web code, as they were no longer needed. If you have any custom modules in the Help namespace (e.g. Components), please change them to use Hub. See for example EnsEMBL::Web::Component::Help::View for examples of how to substitute \'hub\' for \'object\' and how to get data from the ensembl_website database using DBSQL::WebsiteAdaptor (you may need to extend the adaptor in your plugin).</p>\r\n',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2010-07-27 16:26:36',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (58,59,'Key and Zmenu for Xref','The xref display and description is now fixed on the vertical drawing (whole genome), now showing the exact xref and associated gene. Also a key has been added to describe which pointer is which. And finally the Zmenu is now working properly describing the gene and xref accordingly.',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2010-07-29 11:38:09',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (59,60,'data','<p>update of UniProt identifier links including phenotype information <br /> import of new information from NHGRI <br /> import of new data sets for structural variants from DGVa<br /> import of an expanded data set for all short somatic sequence variants from COSMIC <br /> GVF (Genome Variation Format) dumps for all variants<br /> update of variant consequences for new human gene set</p>\r\n<p>update of variant consequences for new zebrafish assembly and gene setimport new set of 150,000 Zebrafish variants</p>\r\n<p>import of variants submitted on LRG_7 from Uniprot</p>\r\n<p> </p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2010-08-13 10:36:14',3,'2010-10-06 12:13:22',1);
+INSERT INTO `changelog` VALUES (60,60,'Array Mapping','<p>The array mapping pipeline will be run for those species which have new assemblies, gene build or new array designs. This includes an update to the latest version of the Phalanx OneArray for human.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-08-13 11:10:09',1273,'2010-11-05 14:30:02',1);
+INSERT INTO `changelog` VALUES (61,60,'BindingMatrix','<p>A new BindingMatrix class will represent position weight matrices (PWMs) loaded from Jaspar or inferred directly from Chip-Seq data. This will ultimately be able to identify the consequence of a sequence change at a given location, with respect to the PWM score. patch_59_60_c.sql contains the relevant changes to update the schema to support this data.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,1273,'2010-08-13 11:19:34',100304,'2010-11-05 10:49:29',1);
+INSERT INTO `changelog` VALUES (62,60,'MotifFeature','<p>A new MotifFeature class has been added to represent the genomic mapping of a position weight matrix (BindingMatrix). patch_59_60_c.sql contains the relevant schema updates.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,1273,'2010-08-13 11:22:44',100304,'2010-11-05 10:49:09',1);
+INSERT INTO `changelog` VALUES (63,60,'Schema patch: Schema version','<p>patch_59_60_a.sql updates the meta table, changing the schema_version meta_value to 60.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,1273,'2010-08-13 11:24:05',100304,'2010-11-05 10:49:59',1);
+INSERT INTO `changelog` VALUES (64,60,'Schema patch: associated_feature_type','<p>patch_59_60_b.sql updates the associated_feature_type table to support feature_type to feature_type associations. The relevant adaptors have also been updated to reflect the new table fields and values.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,1273,'2010-08-13 11:26:09',100304,'2010-11-05 10:50:19',1);
+INSERT INTO `changelog` VALUES (65,60,'RegulatoryBuild update','<p>The human RegulatoryBuild has been updated and re-annotated based on the new ChIP-Seq data sets.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-08-13 11:30:20',100304,'2010-11-05 10:47:39',1);
+INSERT INTO `changelog` VALUES (66,60,'Position Weight Matrix (PWM) mapping and visualisation','<p>PWM mappings which used to be associated with the RegulatoryFeatures, are now associated with the AnnotatedFeatures representing the specific Transcription Factor Binding Site predictions. This utilises the new MotifFeature and BindingMatrix classes. These new data are available as new tracks in the Regulation panel as well as Region in Detail.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-08-13 11:33:19',100304,'2010-11-05 10:46:50',1);
+INSERT INTO `changelog` VALUES (67,60,'New chip-seq datasets from ENCODE','<p>93 new ENCODE Chip-Seq datasets for existing cell lines will be added.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,NULL,NULL,100304,'2010-11-05 10:46:00',1);
+INSERT INTO `changelog` VALUES (68,60,'Update to human vega annotation','<p>An update to Vega human annotation</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2010-08-13 15:12:56',161,'2010-09-23 14:28:41',1);
+INSERT INTO `changelog` VALUES (69,60,'Ensembl marts for release 60','<p>Release 60 Ensembl marts (all species)<br />Ensembl Genes 60<br /> • Addition of new species Ailuropoda melanoleuca (Panda)</p>\r\n<p> • GNF data has been updated via Gene Expression Atlas (http://www.ebi.ac.uk/gxa/)</p>\r\n<p> • Germ line and Somatic mutations are separated in both filter and attributes.</p>\r\n<p>Ensembl variation 60<br /> • Ensembl Variation mart and Ensembl Gene mart are connected via ensembl gene stable-ids for Human</p>',NULL,'handed_over','Mart','N','N','N','N','N','N','N','N/A',2,NULL,NULL,25629,'2010-11-03 10:21:15',1);
+INSERT INTO `changelog` VALUES (70,60,'Ontology database','A new ontology database (\"ensembl_ontology_60\") will be built using the latest data from GO and SO.',NULL,'handed_over','Core','N','N','N','N','N','N','N','new',2,896,'2010-08-19 09:55:26',896,'2010-08-24 12:01:02',1);
+INSERT INTO `changelog` VALUES (71,60,'Gencode gene set update','Update to the Ensembl/Havana Gencode gene set using the latest Vega gene set.',NULL,'handed_over','Genebuild','N','Y','Y','N','N','N','N','new',2,9335,'2010-08-19 09:58:12',9335,'2010-08-25 14:44:42',1);
+INSERT INTO `changelog` VALUES (72,60,'Human cDNA update','<p>Updated set of cDNA alignments to the human genome.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,14183,'2010-08-19 10:00:06',14183,'2010-09-24 09:38:40',1);
+INSERT INTO `changelog` VALUES (73,60,'Rabbit chromosomes','Chromosome mapping added for the rabbit genome\r\nCoordinates updated accordingly',NULL,'handed_over','Genebuild','Y','Y','Y','N','N','N','N','patched',2,97245,'2010-08-19 10:07:26',97245,'2010-08-19 12:00:37',1);
+INSERT INTO `changelog` VALUES (74,60,'Human (GRCh37) assembly patch release 2','<p>Addition of the GRCh37 patch release 2 patches. These are toplevel, non-reference regions of the assembly.</p>',NULL,'handed_over','Genebuild','Y','N','Y','N','N','N','N','new',2,14183,'2010-08-19 10:11:38',14183,'2010-09-24 09:40:02',1);
+INSERT INTO `changelog` VALUES (75,60,'Updated human otherfeatures db: EST alignments','Human ESTs were realigned.\r\nNew EST-based genes were produced from these EST alignments.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,5132,'2010-08-19 10:11:45',5132,'2010-08-24 11:55:59',1);
+INSERT INTO `changelog` VALUES (76,60,'Panda genebuild','<p>The first genebuild for the panda genome</p>',NULL,'handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,97245,'2010-08-19 10:13:59',97245,'2010-09-06 09:12:32',1);
+INSERT INTO `changelog` VALUES (77,60,'Update human otherfeatures db: new CCDS import','Update to CCDS set for human',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,5132,'2010-08-19 10:15:17',5132,'2010-08-24 11:56:25',1);
+INSERT INTO `changelog` VALUES (78,60,'Updated mouse otherfeatures db: New CCDS import','<p>Update to CCDS set for mouse</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2010-08-19 10:16:02',5132,'2010-09-23 21:46:32',1);
+INSERT INTO `changelog` VALUES (79,60,'cDNA based gene annotation of human assembly patches','<p>Annotate the human assembly patches using Exonerate\'s cDNA2genome model, which aligns cDNAs to the genome using annotation identifying the coding regions of the cDNAs.</p>','This annotation will be stored in the other features database.','handed_over','Genebuild','N','N','N','N','N','N','N','new',2,14183,'2010-08-19 10:17:33',14183,'2010-09-28 09:33:18',1);
+INSERT INTO `changelog` VALUES (80,60,'Families','<p>Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa</p>\r\n<p>Clustering by MCL</p>\r\n<p>Multiple Sequence Alignments with MAFFT</p>\r\n<p>Family stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,NULL,NULL,49918,'2010-11-05 10:53:26',1);
+INSERT INTO `changelog` VALUES (81,60,'Gene Homologies','<p>GeneTrees with new/updated genebuilds and assemblies</p>\r\n<p>Updated build of ncRNA trees</p>\r\n<p>Clustering using hcluster_sg</p>\r\n<p>Multiple Sequence Alignments using consistency-based MCoffee meta-aligner (mafftgins+muscle+kalign+probcons) and exon-skipping aware \"skipper\" algorithm</p>\r\n<p>Homology inference including the recent \'possible_ortholog\' type and \'putative gene split\' and \'contiguous gene split\' exceptions</p>\r\n<p>Pairwise gene-based dN/dS calculations for high coverage species pairs only</p>\r\n<p>GeneTree stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-08-19 11:06:43',49918,'2010-11-05 10:53:54',1);
+INSERT INTO `changelog` VALUES (82,60,'Zebrafish genebuild','<p>Full genebuild on the new Zv9 assembly</p>','This genebuild will include RNA-Seq gene models','handed_over','Genebuild','Y','Y','Y','Y','Y','N','N','new',2,29,'2010-08-23 09:37:17',29,'2010-11-05 10:49:48',1);
+INSERT INTO `changelog` VALUES (83,60,'Gene name and GO term projections','<p>Gene names and GO xrefs will be projected from species where there is high coverage to species where there is lower coverage. Panda will be included as a target for these projections.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','patched',2,36,'2010-08-24 09:40:04',23,'2010-11-05 10:46:30',1);
+INSERT INTO `changelog` VALUES (84,60,'external database references','<p>Update external database references for human, mouse and Xenopus</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2010-08-24 11:10:08',23,'2010-11-05 10:50:14',1);
+INSERT INTO `changelog` VALUES (85,60,'GO Xrefs are now Ontology Xrefs','<p>The go_xref table is renamed to ontology_xref. The Bio::EnsEMBL::GoXref Perl module is renamed to Bio::EnsEMBL::OntologyXref.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,NULL,NULL,23,'2010-11-05 10:50:50',1);
+INSERT INTO `changelog` VALUES (86,60,'Pairwise Alignments','<p>Lastz-net alignments</p>\r\n<ul>\r\n<li>H.sap-A.mel</li>\r\n<li>H.sap-O.cun</li>\r\n<li>C.fam-A.mel</li>\r\n</ul>\r\n<p>Blat-alignments</p>\r\n<ul>\r\n<li>H.sap-D.rer </li>\r\n<li>M.mus-D.rer</li>\r\n<li>R.nor-D.rer</li>\r\n<li>G.gal-D.rer</li>\r\n<li>T.rub-D.rer</li>\r\n<li>D.rer-X.tro</li>\r\n<li>C.int-D.rer</li>\r\n<li>C.sav-D.rer</li>\r\n<li>G.acu-D.rer</li>\r\n<li>O.lat-D.rer</li>\r\n<li>D.rer-T.nig</li>\r\n</ul>\r\n<p>Non-reference alignments for human vs high coverage blastz-net alignments</p>\r\n<ul>\r\n<li>H.sap-P.tro </li>\r\n<li>H.sap-G.gor</li>\r\n<li>H.sap-P.pyg</li>\r\n<li>H.sap-M.mul</li>\r\n<li>H.sap-M.mus</li>\r\n<li>H.sap-R.nor</li>\r\n<li>H.sap-C.fam</li>\r\n<li>H.sap-B.tau</li>\r\n<li>H.sap-S.scr</li>\r\n<li>H.sap-E.cab</li>\r\n<li>H.sap-O.ana</li>\r\n<li>H.sap-M.dom</li>\r\n<li>H.sap-G.gal</li>\r\n</ul>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-08-24 16:41:35',49918,'2010-11-05 10:54:21',1);
+INSERT INTO `changelog` VALUES (87,60,'Multiple alignments','<p>34 way epo low coverage</p>\r\n<p>12 way epo eutherian mammals</p>\r\n<p>5 way epo fish</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-08-24 16:43:34',49918,'2010-11-05 10:55:00',1);
+INSERT INTO `changelog` VALUES (88,60,'Mouse cDNA update','<p>Updated set of cDNA alignments to the mouse genome.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,101214,'2010-08-24 16:47:56',101214,'2010-09-27 14:19:42',1);
+INSERT INTO `changelog` VALUES (89,60,'Flagging Translation attribute where the evidence was removed','<p>Add a flag to the translation where a human Ensembl translation used as evidence was removed from the current human database. These are indicated on the web display by colouring them in grey on transcript supporting evidence view.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,101214,'2010-08-24 16:57:29',161,'2010-11-04 14:51:23',1);
+INSERT INTO `changelog` VALUES (90,60,'Flagging Translation attribute where the Uniprot evidence was removed','<p>Add a flag to the translation where a supporting evidence from Uniprot was removed from Uniprot database. These are indicated on the web display by colouring them in grey on transcript supporting evidence view.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,101214,'2010-08-24 17:02:12',161,'2010-11-04 14:52:16',1);
+INSERT INTO `changelog` VALUES (91,60,'Updating the ENCODE excluded regions','Update of the ENCODE excluded regions',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,9335,'2010-08-25 14:44:25',9335,'2010-08-26 17:03:46',1);
+INSERT INTO `changelog` VALUES (92,60,'API and schema change','<p>schema change for ensembl genomes to store the population size for each frequency calculation</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2010-08-25 16:16:39',3,'2010-10-06 12:06:41',1);
+INSERT INTO `changelog` VALUES (93,60,'Fix duplicate transcript attributes','<p>Duplicate transcript attributes removed</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2010-08-31 09:48:23',5132,'2010-09-01 17:09:03',1);
+INSERT INTO `changelog` VALUES (94,60,'Translations removed for retrotransposed transcripts',NULL,NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,97245,'2010-09-01 13:30:12',97245,'2010-09-01 13:40:43',1);
+INSERT INTO `changelog` VALUES (95,60,'homo_sapiens rnaseq data','<p>Rnaseq data from transcriptome sequencing done by illumina on human tissues will be provided in a stand-alone database, ie no mart / compara relationships.</p>\r\n<p> </p>\r\n<p>Core, web and releaes coordinatoer has been informed.</p>','Rnaseq data from transcriptome sequencing done by illumina on human tissues will be provided in a stand-alone database, ie no mart / compara relationships.\r\n\r\n\r\nCore, web and releaes coordinatoer has been informed. ','declared','Genebuild','N','N','N','N','N','N','N','N/A',2,1011,'2010-09-06 15:12:14',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (96,60,'Synteny','<p>H.sap-C.jac</p>\r\n<p>H.sap-O.cun</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,49918,'2010-09-07 11:34:08',49918,'2010-11-05 10:55:16',1);
+INSERT INTO `changelog` VALUES (97,60,'Schema patch: probe_feature.cigar_line','<p>patch_59_60_d.sql The probe_feature table has been patched to change the cigar_line field to a varchar from a free text field.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,1273,'2010-09-08 17:12:02',1273,'2010-11-05 14:30:42',1);
+INSERT INTO `changelog` VALUES (98,60,'Schema patch: regulatory_attribute.attribute_table_name','<p>patch_59_60_e.sql The regulatory_attribute table has been modified to allow \'motif\' as an attribute_feature_table.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,1273,'2010-09-09 11:24:36',1273,'2010-11-05 14:31:16',1);
+INSERT INTO `changelog` VALUES (99,60,'Large scale changes to webcode','<p>There are a number of changes to how web pages are configured and rendered which will affect plugin developers, most notably to EnsEMBL::Web::Configuration and EnsEMBL::Web::Document::HTML modules, and $SiteDefs::OBJECT_TO_SCRIPT</p><p>See <a href=\"/info/docs/webcode/changes_60.html\">here</a> for full details.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2010-10-01 16:01:45',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (100,60,'Autocomplete Gene searching on Location pages','<p>The navigation bar on location pages has been changed. Locations can now be typed in one input box, rather than three, and there is a new input to search for genes.</p>\r\n<p>This new box features an autocomplete dropdown for all genes with xref display labels, and will take you to the <strong>location</strong> of the gene you searched for.</p>','Fixed some of Simon\'s typos :)','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2010-10-22 15:48:08',2,'2010-11-05 12:15:27',1);
+INSERT INTO `changelog` VALUES (101,60,'History and Bookmarks in tabs','<p>When you are logged in, recent browsing history is stored on dropdowns accessible from the tabs in the header of the website (up to 5 links per tab). Up to 5 bookmarks are also available from these dropdowns, ordered by most frequently used.</p>\r\n<p> </p>\r\n<p>There is also a dropdown from the species tab, providing quick access to all species home pages. This is available even if you are not logged in.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2010-10-22 15:53:30',2,'2010-11-05 12:16:41',1);
+INSERT INTO `changelog` VALUES (102,60,'Gene Ontology view','<p>The Gene Ontology page on the Transcript page has changed. Instead there is now a <strong>Gene Ontology</strong> sub-menu with an <strong>Ontology Image</strong> and an <strong>Ontology Table</strong>.</p>\r\n<p>The image visualises the term graph of Go terms and the terms closest in the goslim and goa subset for cellular_component, biological_process and molecular_function.</p>\r\n<p>The table lists the go terms for forcellular_component, biological_process and molecular_function and thier closes term(s) in the goslim and goa subset.</p>\r\n<p> </p>\r\n<p>Both new pages make use of the Ontology API, and the Ontology image uses EnsEMBL::Web::Tools::OntologyVisualisation. <strong>In principle this could be used with any OBO ontology</strong>.</p>\r\n<p> </p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,101273,'2010-10-26 14:49:52',2,'2010-11-05 12:18:15',1);
+INSERT INTO `changelog` VALUES (103,60,'Transcript xrefs (external references) on gene page','<p>For genes, on the external references page, we now list an additional table with the all xrefs (external references) of all transcripts of the gene. As this can be a large number, a subset is show by default. this defaults can be changed using the Configure this page link.</p>',NULL,'declared','Web','N','N','N','N','N','N','N','N/A',2,101273,'2010-10-26 14:54:25',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (104,60,'Download as CSV','<p>Pages with tabulated data now have a \"Download view as CSV\" button at the bottom of the left hand menu. These files can be opened in Excel or other spreadsheet programs.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2010-10-27 12:53:44',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (105,60,'Upgrade to Gene - Variation Table page','<p>The Variation Table page has been redesigned to cope with the large amounts of data it can display.</p>\r\n<p>Initially you will see a summary table of available consequence types, and clicking on the \"Show\" links here will display additional tables with information about the relevant variations.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2010-11-02 16:04:26',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (106,60,'RNA-Seq data on location views','<p>RNA-seq data supporting the introns for RNA Seq genes can be rendered with the height of the features scaled according to the read coverage (upto a maximum of 50).</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,161,'2010-11-04 15:38:04',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (112,60,'New web page - Multi/GeneTree','<p>In order that external sites can link directly to Ensembl on a gene tree stable ID, we have created a new view that does just that. It uses the same image code as the genetree for a specific gene, but with all nodes expanded.</p>\r\n<p>Sample link: http://www.ensembl.org/Multi/GeneTree/Image?gt=ENSGT00590000083062</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2010-11-05 12:35:40',2,'2010-11-05 12:38:09',1);
+INSERT INTO `changelog` VALUES (113,60,'Assembly and genebuild information on archive links','<p>On species-specific pages, the \"View in archive site\" panel (accessible from the footer of every page) now shows assembly and genebuild information for each archive, to make it easier to choose the right archive.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2010-11-05 12:41:04',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (114,60,'Structural Variation tab','<p>Structural variations are now displayed in their own <a href=\"http://www.ensembl.org/Homo_sapiens/StructuralVariation/Summary?sv=nsv455827\">tab.</a>Currently this dispays a context iamge and tables of overlapping features. The number of available view for this feature type will be extended in release 61</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,121,'2010-11-05 13:03:27',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (115,61,'C.elegans WS220','<p>The data on this site is a direct import of the WormBase WS220 frozen dataset. Included are annotated operons, genes, transcripts and CDSs as well as RNAi and BLAST/BLAT homology data. Information about the location of available fosmid clones is also included. In addition Affymetrix and Agilent cross references for C.elegans expression arrays have been added.<br />The WS220 dataset is the anniversary frozen release of WormBase C.elegans data. All data used in the frozen releases is available from the WormBase FTP site and links to permanent websites can be found on the WormBase home page.<br />We have included C.elegans in the Ensembl system to allow people to access the data through the Ensembl user interface (both for visualisation and data mining) and to provide cross-species integration through our comparative genomics resources (such as homologous gene links and protein family pages).</p>','Need to sort out the affy_mapping with Nathan/Dan.','declared','Wormbase','Y','Y','Y','N','Y','Y','N','new',2,NULL,NULL,14179,'2010-11-25 14:36:51',1);
+INSERT INTO `changelog` VALUES (116,61,'Ensembl Marts for release 61','<p>Full build of all 7 marts for all species.</p>',NULL,'handed_over','Mart','N','N','N','N','N','N','N','N/A',2,25629,'2010-11-09 16:01:53',25629,'2011-01-27 10:47:42',1);
+INSERT INTO `changelog` VALUES (117,61,'77 Human ChIP-Seq datasets added','<p>New datasets from ENCODE and the Epigenomics Roadmap were added, which complement existing cell types. A new cell type, K562b was created. 2 sets already in the database, previously associated to K562, were corrected, being now associated to K562b. There is no regulatory build for K562b due the scarcity of data specific for this cell line, which is a variant of K562.</p>','Import post-poned due to concentration on speed of displays and other urgent development','postponed','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2010-11-09 16:35:51',1273,'2010-11-10 14:03:01',1);
+INSERT INTO `changelog` VALUES (119,61,'Human cDNA update','<p>Updated set of cDNA alignments to the human genome.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,14183,'2010-11-10 13:51:16',14183,'2010-11-30 17:12:59',1);
+INSERT INTO `changelog` VALUES (120,61,'seq region synonyms','<p>New table seq_region_synonym added to allow multiple names for sequence regions.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2010-11-10 13:55:31',23,'2011-01-19 14:41:41',1);
+INSERT INTO `changelog` VALUES (121,61,'external database references','<p>Human, mouse, rat and tree shrew will be updated.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2010-11-10 13:57:26',23,'2011-01-19 14:43:31',1);
+INSERT INTO `changelog` VALUES (122,61,'Array Mapping','<p>Array mapping was updated on all species which have had an update to their genome assemblies or gene builds. The probe/set to transcript xrefs were recalculated across all species.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-11-10 14:05:40',1273,'2011-01-28 16:59:00',1);
+INSERT INTO `changelog` VALUES (123,61,'Mouse Regulatory Build','<p>The mouse RegulatoryBuild was re-run to re-introduce some data which had been omitted in the previous build.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2010-11-10 14:08:24',100304,'2011-01-19 14:39:42',1);
+INSERT INTO `changelog` VALUES (124,61,'Haplotype correction','<p>Correction of an error that added one extra N to the end of the alternative versions of the chromosomes for five of the haplotypes. The altered alternative chromosomes are: HSCHR6_MHC_MANN, HSCHR6_MHC_MCF, HSCHR6_MHC_SSTO, HSCHR4_1 and HSCHR17_1.</p>','This will be updated in all databases containing the human assembly (core, otherfeatures, cdna and rnaseq).','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,14183,'2010-11-10 14:20:26',14183,'2010-12-06 13:25:35',1);
+INSERT INTO `changelog` VALUES (125,61,'Zebrafish Havana merge','<p>A merge of the zebrafish core gene set with Havana manual annotation. The core gene set has been altered to include missing genes that were lost in e60 due to a problem in gene clustering.</p>',NULL,'handed_over','Genebuild','N','Y','N','Y','Y','N','N','new',2,29,'2010-11-11 09:39:37',29,'2011-01-07 13:58:11',1);
+INSERT INTO `changelog` VALUES (126,61,'GENCODE gene set update','<pre>GENCODE gene set update (release 6)<br /><br />Update to the Ensembl/Havana GENCODE gene set using the latest Vega gene<br />set</pre>\r\n<p> </p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,9335,'2010-11-11 09:43:42',9335,'2011-01-19 15:23:52',1);
+INSERT INTO `changelog` VALUES (127,61,'GO term and gene name projections','<p>Gene display names and GO terms will be projected from high-coverage species to those with lower coverage.</p>','All species EXCEPT: \r\n\r\nC. elegans\r\nC. intestinalis\r\nC. savignyi\r\nFly\r\nYeast','handed_over','Core','N','N','N','N','N','N','N','patched',2,36,'2010-11-11 13:21:59',25629,'2010-12-10 16:56:50',1);
+INSERT INTO `changelog` VALUES (130,61,'Ontology database','<p>The Ensembl Ontology database will as usual be populated with the latest available versions of the</p>\r\n<ul>\r\n<li>Gene Ontology (GO)</li>\r\n<li>Sequence Ontology (SO)</li>\r\n<li>Experimental Factor Ontology (EFO)</li>\r\n</ul>','The EFO ontology will be included if we\'re able to get an OBO file from them in time (we didn\'t).','handed_over','Core','N','N','N','N','N','N','N','new',2,896,'2010-11-11 14:08:28',896,'2010-12-02 15:05:28',1);
+INSERT INTO `changelog` VALUES (131,61,'Data','<p>- import dbSNP 132 (human), zebrafinch, Tetraodon and new variation databases for cat, opossum</p>\r\n<p>- import dbSNP for further species if available in time (mouse, rat, zebrafish)</p>\r\n<p>- import new release of HGMD database</p>\r\n<p>- corrections to Affymetrix CNV probe data</p>\r\n<p>- import PorcineSNP60 BeadChip</p>\r\n<p>- update of zebrafish variation consequences for new gene build</p>\r\n<p>- variations will now be flagged and retained instead of failed and deleted for species with a new import of dbSNP</p>\r\n<p>- produce GVF file dumps of all variants by species</p>\r\n<p><br />- for Tetraodon, the Ensembl-assigned variation names (\'ENSTNISNP...\') used prior to release 61 have been replaced with the dbSNP-assigned rsIds. If the<br />mapping between the Ensembl and rsIDs is required, there is a tab-separated file available for download on the ftp-site:<br /> ftp://ftp.ebi.ac.uk/pub/software/ensembl/snp/tetraodon/Tetraodon_Ensembl_SNP_id_to_dbSNP_rsid.txt.gz.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,96712,'2010-11-11 14:59:04',3,'2011-01-14 14:59:34',1);
+INSERT INTO `changelog` VALUES (132,61,'Updates to mouse and human Vega annotation','<p>The Vega annotation for both human and mouse has been updated. This matches the annotation presented in Vega release 41.</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2010-11-11 18:07:21',161,'2011-01-28 16:54:52',1);
+INSERT INTO `changelog` VALUES (133,61,'new rnaseq database','<p>I will provide a new databases which consists of the core tables ; the data will data from the human bodymap project ( rnasesq data ). This is a new database which has not been released before. This was originally planned for e60.</p>','I will provide a new databases which consists of the core tables ; the data will data from the human bodymap project ( rnasesq data ). This is a new database which has not been released before. This was originally planned for e60.','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,1011,'2010-11-12 13:37:35',5132,'2011-01-07 14:02:14',1);
+INSERT INTO `changelog` VALUES (134,61,'mouse cDNA update','<p>mouse cDNA update</p>','mouse cDNA update - performed by Thibaut','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,1011,'2010-11-12 13:42:18',101214,'2010-12-06 13:15:49',1);
+INSERT INTO `changelog` VALUES (135,61,'Families','<p>Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.<br />   * Clustering by MCL <br />   * Multiple Sequence Alignments with MAFFT<br />   * Family stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-12 15:37:40',22288,'2011-01-07 12:35:51',1);
+INSERT INTO `changelog` VALUES (136,61,'Gene Homologies','<p>GeneTrees with new/updated genebuilds and assemblies<br />   * Updated build of ncRNA trees<br />   * Clustering using hcluster_sg   <br />   * Multiple Sequence Alignments using consistency-based MCoffee meta-aligner<br />   * Homology inference including the recent \'possible_ortholog\' type and \'putative gene split\' and <br />     \'contiguous gene split\' exceptions<br />   * Pairwise gene-based dN/dS calculations for high coverage species pairs only<br />   * GeneTree stable ID mapping</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,NULL,NULL,22288,'2011-01-07 12:37:09',1);
+INSERT INTO `changelog` VALUES (137,61,'Zebrafish Vega annotation','<p>Manual annotation of zebrafish from Havana is now present in Ensembl. This represetns the annotation presented in Vega release 40</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2010-11-12 17:20:12',161,'2010-11-23 11:15:18',1);
+INSERT INTO `changelog` VALUES (138,61,'Mouse gene set update','<p>A merge of Ensembl core gene set and Vega manual annotation.</p>\r\n<p>The core gene set has been improved by incorporating new data resources which had become available since the last NCBIM37 genebuild (April 2007), resulting in the correction of existing gene models and the recovery of new mouse genes with human orthologues.</p>\r\n<p>A new otherfeatures database is also available.</p>\r\n<p>RepeatMask data have been updated by re-running RepeatMasker with options \"-nolow -s -species mouse\".</p>',NULL,'handed_over','Genebuild','N','Y','Y','Y','Y','N','N','new',2,97238,'2010-11-13 16:21:57',97238,'2010-11-25 13:25:34',1);
+INSERT INTO `changelog` VALUES (139,61,'New assembly for lizard','<p>A new assembly for lizard</p>',NULL,'handed_over','Genebuild','Y','Y','Y','N','Y','N','N','new',2,97245,'2010-11-15 09:07:00',97245,'2010-11-18 15:31:31',1);
+INSERT INTO `changelog` VALUES (140,61,'Turkey','<p>The first genebuild for turkey</p>',NULL,'handed_over','Genebuild','Y','Y','Y','N','Y','N','N','new',2,97245,'2010-11-15 09:43:22',97245,'2010-11-25 14:29:34',1);
+INSERT INTO `changelog` VALUES (141,61,'New Canonical Transcript definition','<p>For previous releases, the canonical transcript of a gene has been set to the transcript with the longest translation (for coding genes) or to the transcript with the longest mRNA (for noncoding genes). From release 61, the canonical transcript for human and mouse will now be set to the longest CCDS transcript. Where no CCDS transcript exists for the gene, the longest Ensembl-HAVANA merge transcript will be used.</p>',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','N/A',2,5132,'2010-11-15 09:58:12',5132,'2011-01-07 14:03:10',1);
+INSERT INTO `changelog` VALUES (142,61,'Pairwise Alignments','<p>Human - Lizard tBlat - net</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,NULL,NULL,22288,'2011-01-07 12:38:19',1);
+INSERT INTO `changelog` VALUES (143,61,'Pairwise Alignments','<p>Human - Turkey tBlat net</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-15 11:51:11',22288,'2011-01-07 12:43:33',1);
+INSERT INTO `changelog` VALUES (144,61,'Pairwise Alignments','<p>Turkey - Chicken Lastz</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-15 11:52:04',22288,'2011-01-10 09:47:15',1);
+INSERT INTO `changelog` VALUES (145,61,'Pairwise Alignments','<p>Lizard - Chicken Lastz</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-15 11:53:04',22288,'2011-01-10 09:45:52',1);
+INSERT INTO `changelog` VALUES (146,61,'Pairwise Alignments','<p>Dog - Horse Lastz</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-15 11:53:47',22288,'2011-01-10 09:46:16',1);
+INSERT INTO `changelog` VALUES (147,61,'Pairwise Alignments','<p>**Removing chicken - zebrafinch tBlat</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-15 11:55:43',22288,'2011-01-10 09:52:28',1);
+INSERT INTO `changelog` VALUES (148,61,'Multiple alignments','<p>Chicken - Turkey -Zebrafinch EPO multiple alignment</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2010-11-15 12:30:36',22288,'2011-01-10 09:53:01',1);
+INSERT INTO `changelog` VALUES (150,61,'Removal of ambiguous bases from human DNA sequence','<p>Ambiguous bases have been replaced with \'N\' for the following two human contigs:</p>\r\n<ul>\r\n<li>contig::AF152363.1:1:185763:1. This contig held 28 ambiguous bases: S(4), W(6), M(5), K(4), R(5), Y(4).</li>\r\n<li>contig::AF152364.1:1:170452:1. This contig held 4 ambiguous bases: S(1), W(1), Y(1), K(1).</li>\r\n</ul>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2010-11-15 13:39:50',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (156,61,'Updated CCDS','<p>Updated CCDS databases for Human and Mouse. Populates other_features with new gene models and serves data for CCDS Public Note DAS track.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,102717,'2010-11-19 11:11:15',97238,'2011-01-19 14:40:13',1);
+INSERT INTO `changelog` VALUES (157,61,'embl and genbank dumps','<p>Onlt the reference sequence will be dumped in the main directory for embl and genbank. Unique non-reference regions(haplotype/par regions) will now be dumped in a subdirectory and only contain the unique regions.</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,NULL,NULL,23,'2011-01-19 14:45:13',1);
+INSERT INTO `changelog` VALUES (159,61,'Chromosome and haplotype synonyms','<p>Addition of synonyms for the human chromosomes and haplotypes in the seq_region_synonym tables of the human databases.</p>',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,14183,'2010-12-06 13:29:14',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (162,61,'Schema and API changes','<p>- import dbSNP 132 (human including 1000 genomes data, zebrafinch) and also new variation species (cat, opossum, Tetraodon)<br />- import new release of HGMD database<br />- import of new Cosmic (somatic mutation) data<br />- import Illumina PorcineSNP60 BeadChip for pig<br />- import OMIM, NHGRI and UniProt phenotype data for variants<br />- import new DGVa data sets for structural variants<br />- import new variants submitted using LRG sequences that have been accessioned by dbSNP<br />- move CNV probe data to structural variation table<br />- update of zebrafish and mouse variation consequences for new gene build<br />- produce GVF file dumps of all variants and their consequence by species<br />- variants from 1kG unique to Jan09 submission to be flagged as \"withdrawn by 1000 genomes\"<br />- new set for OMIM data, failed variants<br />- split InDel variation class into insertions and deletions</p><p>- For speed purposes, store the variation set membership of each variation feature in the variation_feature table</p>\r\n<p><br />API fix: <br />to correct TranscriptAlleles.pm translated transcript sequence to include the * stop codon at the end of the string so that STOP_LOSTs are not missed.<br /><br /></p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2010-12-13 09:44:05',3,'2011-01-07 12:07:17',1);
+INSERT INTO `changelog` VALUES (164,61,'19-way pecan multiple alignment','<p>Added turkey + Rabbit + Lizard genomes</p>',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-01-10 10:46:43',22288,'2011-01-19 14:56:07',1);
+INSERT INTO `changelog` VALUES (165,61,'Favourite tracks','<p>You can now use the star icon in the configuration panel (accessed via the Configure this page button below the left navigation menu) to mark tracks as favourites.</p>\r\n<p>These can then be displayed together by clicking the \'Favourite tracks\' link in the panel\'s navigation menu.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-01-19 14:50:33',97803,'2011-01-19 14:52:01',1);
+INSERT INTO `changelog` VALUES (166,61,'***IMPORTANT FOR DEVELOPERS*** Schema change to session_record table','<p>There has been a schema change to the session_record table in the ensembl_web_user_db database.</p>\r\n<p> </p>\r\n<p>As we do not provide dumps of this database, you MUST run the script /utils/update_session_record.pl when updating to the new code for this release, otherwise track configuration will no longer be stored correctly. This script both alters the table and updates all existing configurations to work with the new code.</p>\r\n<p> </p>\r\n<p>Further changes to this table will probably be coming over the next few releases. You will be notified here in cases where an action is required.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-01-19 15:00:41',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (167,61,'New popups on images','<p>Configurable tracks now generate a popup when hovering over the track name. This popup provides an easy way to change the track\'s renderer or remove it from the image without having to go to the configuration panel. The popup also provides information about the track.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-01-19 15:04:55',97803,'2011-02-02 10:17:57',1);
+INSERT INTO `changelog` VALUES (169,61,'\'Did you know...\' box is back','<p>The \'Did you know\' box on the home page is back. It displays tweets of ensembl. This has been implemented with the New Twitter API. New cpan module installed Net::Twitter.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-01-31 10:07:34',99923,'2011-01-31 10:08:08',1);
+INSERT INTO `changelog` VALUES (179,61,'Static server','<p>Ensembl can now serve static files - images, css and javascript - from a different URL, specified in SiteDefs as $ENSEMBL_STATIC_SERVER.</p>\r\n<p>This change reduces server load as cookies will not be registered for the static domain.</p>\r\n<p>If no ENSEMBL_STATIC_SERVER variable is set, the site will behave as it did previously.</p>\r\n<p> </p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-02-02 10:17:13',102019,'2011-02-02 10:31:50',1);
+INSERT INTO `changelog` VALUES (181,61,'Changes to ZMenu plugins','<p>ZMenu plugins now work in the same way as the rest of the code.</p>\r\n<p>Previously all modules matching the required namespace would be called, starting from the most important plugin and ending with the core code.</p>\r\n<p>Now only the first matching namespace will be used, and as a result plugin code should be changed to call $self->SUPER::content in the content function where required.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-02-02 10:20:13',102019,'2011-02-02 10:25:15',1);
+INSERT INTO `changelog` VALUES (185,62,'Patch for panda','Transcript supporting features added for pseudogenes',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,97245,'2011-02-04 10:52:56',97245,'2011-02-14 16:09:17',1);
+INSERT INTO `changelog` VALUES (186,62,'Patch for rabbit','Geneset re-clustered\r\nTranscript supporting features added for pseudogenes\r\nAssembly updated to match the official ncbi one','The underlying contig sequences have not changed and the sequence of the toplevel sequences has not changed either\r\nBut, the rank of some sequences has changed','handed_over','Genebuild','Y','Y','N','N','N','N','N','new',2,97245,'2011-02-04 11:02:50',97245,'2011-02-14 16:10:02',1);
+INSERT INTO `changelog` VALUES (187,62,'Patch for marmoset','Deprecated contig sequences removed\r\nRaw-computes re-run\r\nGeneset re-clustered\r\nMapping added\r\nTranscript supporting features for pseudogenes added\r\nNew seq region synonyms',NULL,'handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,97245,'2011-02-04 11:07:47',97245,'2011-02-14 16:09:40',1);
+INSERT INTO `changelog` VALUES (188,62,'Rerun Xrefs pipeline for Yeast','Update the external_db table, and rerun the xrefs pipeline.','Arnaud Kerhornou, arnaud@ebi.ac.uk is the person to contact.','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',2,101255,'2011-02-04 11:32:44',101255,'2011-03-09 17:10:33',1);
+INSERT INTO `changelog` VALUES (189,62,'Human Vega annotation','Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 42','Vega 42 has yet to be released (but will be released before Ensembl)','handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,101273,'2011-02-04 11:52:12',101273,'2011-02-21 15:30:32',1);
+INSERT INTO `changelog` VALUES (190,62,'Rebuild otherfeatures database for Yeast.','Rebuild otherfeatures database, cleaning up long EST alignments.','Contact: arnaud@ebi.ac.uk\r\n\r\nRemoved too long EST alignments.','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',2,101255,'2011-02-07 11:08:35',101255,'2011-03-09 17:09:50',1);
+INSERT INTO `changelog` VALUES (191,62,'Patch for mouse','Patched the mouse Ensembl-Havana merged gene set to maintain its consistency with the latest CCDS gene set (as of 9 February 2011).',NULL,'handed_over','Genebuild','N','Y','N','Y','Y','N','N','patched',2,97238,'2011-02-07 12:00:54',97238,'2011-02-18 15:58:32',1);
+INSERT INTO `changelog` VALUES (192,62,'patch_61_62_a Update meta schema version','meta schema_version has be updated to 62',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:04:07',1273,'2011-03-09 10:09:02',1);
+INSERT INTO `changelog` VALUES (193,62,'patch_61_62_b interdb_stable_id','A interdb_stable_id field has been added to the motif_feature and external_feature tables. NOTE: This is not an \'Ensembl stable ID\', and will only be used internally to enable inter-DB linking between the variation and funcgen schemas. These are not guaranteed to be stable between Ensembl releases.',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:07:54',1273,'2011-03-09 11:00:34',1);
+INSERT INTO `changelog` VALUES (194,62,'patch_61_62_c feature_type Sequence Ontology fields','so_name and so_accession will be added to the feature_type table to enable display of Sequence Ontology information and linking to the ensembl_ontology DB',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:09:58',1273,'2011-03-09 11:00:52',1);
+INSERT INTO `changelog` VALUES (195,62,'ResultFeature DBFile Collections','Where possible data from the result_feature table has been moved outside of the database to indexed binary \'.col\' files. The ResultFeatureAdaptor now uses the new core DBFile::CollectionAdaptor and DBFile::FileAdaptor to access these data directly.',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:17:32',1273,'2011-03-09 11:05:39',1);
+INSERT INTO `changelog` VALUES (196,62,'Bio::EnsEMBL::DBFile::FileAdaptor','A new base class for accessing data from flat files',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:26:05',1273,'2011-02-25 15:52:42',1);
+INSERT INTO `changelog` VALUES (197,62,'Bio::EnsEMBL::DBFile::CollectionAdaptor','A new class to access Collection Feature data stored in flat files.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:30:14',1273,'2011-02-25 15:53:15',1);
+INSERT INTO `changelog` VALUES (198,62,'Array Mapping','<p>Genomic and transcript alignments and transcript xref annotation has been re-run for all species with new genome assemblies or genebuilds.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 11:33:29',1273,'2011-04-04 14:26:14',1);
+INSERT INTO `changelog` VALUES (199,62,'patch_61_62_a: Schema version patch','Patch file patch_61_62_a.sql, updates the schema version of a core database to 62.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,896,'2011-02-08 11:37:45',896,'2011-02-16 10:50:55',1);
+INSERT INTO `changelog` VALUES (200,62,'Ontology database','Database ensembl_ontology_62 with latest available GO, SO, and EFO ontologies.\r\n\r\nSynonyms will now be included in a new \'synonym\' table.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,896,'2011-02-08 11:39:04',103537,'2011-02-15 16:44:21',1);
+INSERT INTO `changelog` VALUES (201,62,'New Array Imports','<p>New Illumina Infinium arrays: HumanMethylation27K HumanMethylation450K New Rat array: Phalanx OneArray</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-08 13:24:22',1273,'2011-04-04 14:26:47',1);
+INSERT INTO `changelog` VALUES (202,62,'Schema diagrams for online documentation','Schema diagrams for online for core database documentation.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-02-08 13:35:56',103537,'2011-03-07 15:12:43',1);
+INSERT INTO `changelog` VALUES (203,62,'patch_61_62_b: synonym field extension','Patch file patch_61_62_b.sql, extends field synonym in external_synonym table to 100 chars.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-02-08 13:41:11',896,'2011-02-16 10:51:18',1);
+INSERT INTO `changelog` VALUES (204,62,'patch_61_62_c: index for db_name, db_release','Patch file patch_61_62_c.sql adds unique index to db_name, db_release fields in external_db table.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-02-08 13:45:02',103537,'2011-02-28 16:20:08',1);
+INSERT INTO `changelog` VALUES (205,62,'Human otherfeatures','Removed EST alignments with hcoverage <90 and perc_ident <94.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2011-02-08 21:05:36',5132,'2011-02-16 13:04:28',1);
+INSERT INTO `changelog` VALUES (206,62,'GENCODE gene set update (release 7)','Update to the Ensembl/Havana GENCODE gene set based on a complete re-annotation of the Ensembl gene set and combined with the latest Vega gene set',NULL,'handed_over','Genebuild','N','Y','N','Y','N','N','N','new',2,9335,'2011-02-09 10:09:18',9335,'2011-02-23 09:39:02',1);
+INSERT INTO `changelog` VALUES (207,62,'Human cDNA update','New cDNA db for human.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,14183,'2011-02-09 10:33:01',14183,'2011-02-23 09:20:36',1);
+INSERT INTO `changelog` VALUES (208,62,'GRCh37.p3','Adding the third patch release for the human assembly. This alters the assembly information in all human databases.',NULL,'handed_over','Genebuild','N','N','Y','N','N','N','N','patched',2,14183,'2011-02-09 10:34:57',14183,'2011-02-18 17:55:08',1);
+INSERT INTO `changelog` VALUES (209,62,'GRCh37.p3 annotation','Annotation of the patches in the other features db.',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,14183,'2011-02-09 10:36:15',14183,'2011-03-07 09:21:23',1);
+INSERT INTO `changelog` VALUES (210,62,'Patch_61_62_d: Experimental Group Description','<p>This change serves to support a better annotation of data sources.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','patched',2,100304,'2011-02-09 10:37:10',100304,'2011-04-04 14:14:24',1);
+INSERT INTO `changelog` VALUES (211,62,'Mart databases','<p>News for release 62:<br />________________<br /><br />Ensembl Genes 62:<br /><br />Addition of new species Nomascus leucogenys (Gibbon)<br />Xenopus tropicalis new assembly (JGI 4.2)<br />Human updated to GRCh37.p3<br />Pongo pygmaeus has been renamed to Pongo abelii<br />Gene Ontology Filter and Attribute section has been modified and all three domains have now been merged into one. <br />Error reported by users regarding broken homolog attributes between C. elegans and C. intestinalis has been fixed.<br />Exon ID filter in transcript event attributes has been removed as this was causing confusion for users.<br />Germline and Somatic variation information attribute sections now contain \"Consequence specific allele\" attribute.<br /><br />Ensembl Variation 62:<br /><br />Pongo pygmaeus has been renamed to Pongo abelii<br />SIFT and PolyPhen filters and attributes added<br />Variation->Gene Associated Information->Consequence specific allele attribute added <br />Variation Set filters now multi select<br />General variation filters->Filter by variation ID (Users can now filter variants from multiple sources e.g. rs123, CM000001)<br /><br /></p>',NULL,'handed_over','Mart','N','N','N','N','N','N','N','N/A',2,25629,'2011-02-09 10:49:20',25629,'2011-04-01 14:30:04',1);
+INSERT INTO `changelog` VALUES (212,62,'Update of Human functional genomics data','<p>New datasets from ENCODE and the Epigenomics Roadmap, covering existing cell lines. The Regulatory Build was rerun for cell lines with new data.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-02-09 10:51:58',100304,'2011-04-04 14:06:45',1);
+INSERT INTO `changelog` VALUES (213,62,'Xrefs','Update external database references.','Ian is away on holiday at the moment and as he does the xref mapping, I am not sure what species he is mapping for 62 or what changes will be made. Ian to modify this declaration when he returns.','handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-02-09 11:03:34',23,'2011-03-07 10:35:12',1);
+INSERT INTO `changelog` VALUES (214,61,'Test','Test',NULL,'declared','Web','N','N','N','N','N','N','N','N/A',2,102019,'2011-02-09 11:04:36',102019,'2011-02-09 12:43:43',1);
+INSERT INTO `changelog` VALUES (215,62,'xref projection','Project GO ids and gene names to species. Make alterations to zebrafish projections.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-02-09 11:08:39',25629,'2011-03-10 08:31:38',1);
+INSERT INTO `changelog` VALUES (216,62,'EMBL/Genbank dumps','<p>EMBL & Genbank dumps for all species</p>',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-02-09 11:25:48',25629,'2011-04-01 14:00:10',1);
+INSERT INTO `changelog` VALUES (217,62,'patch_61_62_d: remove field display_label_linkable','Patch file patch_61_62_d.sql removes field display_label_linkable from table external_db.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-02-09 12:30:26',896,'2011-02-16 10:52:31',1);
+INSERT INTO `changelog` VALUES (218,62,'new variation saccharomyces_cerevisiae database','<p>Provide the variation saccharomyces_cerevisiae database</p>','contact: arnaud@ebi.ac.uk','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',2,101255,'2011-02-09 12:47:20',101255,'2011-03-18 15:45:14',1);
+INSERT INTO `changelog` VALUES (219,62,'New funcgen saccharomyces_cerevisiae database','funcgen saccharomyces_cerevisiae database built by EG Team on 61 schema, and patched to 62 subsequently.','contact: arnaud@ebi.ac.uk','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','new',2,101255,'2011-02-09 12:47:55',101255,'2011-03-09 17:05:00',1);
+INSERT INTO `changelog` VALUES (220,62,'Import of LRG sequences','Newly published LRG sequences will be imported',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-09 13:16:45',99616,'2011-03-08 13:32:07',1);
+INSERT INTO `changelog` VALUES (221,62,'Gibbon build','First release of gene build for Gibbon, Nomascus leucogenys (Northern white-cheeked gibbon). Assembly: Nleu1.0.','New species.','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,102717,'2011-02-09 14:39:49',102717,'2011-02-23 15:08:34',1);
+INSERT INTO `changelog` VALUES (222,62,'Ontology API','Addition of fetch_all_by_name() method to the OntologyTermAdaptor to fetch ontology terms by their names or synonyms.\r\n\r\nAdditional synonym() method for OntologyTerm objects to get their synonyms.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,896,'2011-02-09 14:53:25',896,'2011-02-16 10:53:31',1);
+INSERT INTO `changelog` VALUES (223,62,'Zebrafish WGS/clone assembly track','Added a WGS/clone assembly track.','This only affects the misc features tables','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,29,'2011-02-09 14:58:17',29,'2011-03-07 17:33:59',1);
+INSERT INTO `changelog` VALUES (224,62,'Flagging obsolete Uniprot proteins','Flagging Transcript attribute where the Uniprot evidence was removed',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-02-09 17:17:26',101214,'2011-03-04 15:50:26',1);
+INSERT INTO `changelog` VALUES (225,62,'Flagging obsolete Ensembl proteins','Flagging Transcript attribute where the evidence was removed from 2x genomes','Finally we ran it against all species because almost all of them have Ensembl human proteins as evidence','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-02-09 17:27:08',101214,'2011-03-10 12:02:10',1);
+INSERT INTO `changelog` VALUES (226,62,'Mouse RefSeq import','RefSeq annotations imported into the mouse otherfeatures database',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2011-02-10 09:28:00',5132,'2011-02-18 09:09:07',1);
+INSERT INTO `changelog` VALUES (227,62,'Xenopus tropicalis new assembly 4.2','New assembly of Xenopus tropicalis version 4.2','Should be on time','handed_over','Genebuild','Y','Y','N','Y','N','N','N','new',2,101214,'2011-02-10 10:17:18',101214,'2011-02-22 14:25:59',1);
+INSERT INTO `changelog` VALUES (228,62,'Human Body Map missing liver','Add the liver models',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-02-10 10:18:58',101214,'2011-03-04 15:51:32',1);
+INSERT INTO `changelog` VALUES (229,62,'Mouse cDNA update','New cDNA db for mouse. ens-staging2: mus_musculus_cdna_62_37o',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','new',2,102717,'2011-02-10 11:15:39',102717,'2011-03-08 09:12:00',1);
+INSERT INTO `changelog` VALUES (230,62,'Updated human otherfeatures db: new CCDS import','Update to CCDS set for human',NULL,'handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,102717,'2011-02-10 11:20:19',102717,'2011-03-08 13:51:01',1);
+INSERT INTO `changelog` VALUES (231,62,'Updated mouse otherfeatures db: New CCDS import','Update to CCDS set for mouse',NULL,'handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,102717,'2011-02-10 11:21:35',5132,'2011-03-11 16:22:52',1);
+INSERT INTO `changelog` VALUES (232,62,'nada','ceci n\'est pas une declaration',NULL,'cancelled','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-02-10 14:27:32',3,'2011-03-10 16:36:05',1);
+INSERT INTO `changelog` VALUES (233,62,'New variation consequences','New variation consequences due to a schema change linking consequences to allele and transcript rather than just to a variation and transcript',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 14:50:05',99616,'2011-03-10 13:59:47',1);
+INSERT INTO `changelog` VALUES (234,62,'HGVS coordinates stored in database','HGVS coordinates for variant alleles will be pre-calculated and stored in the database. These were previously calculated on the fly.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 14:52:38',99616,'2011-03-10 14:00:57',1);
+INSERT INTO `changelog` VALUES (235,62,'New variation database','<p>The human variation database will be built fresh from dbSNP release 132 due to data updates by dbSNP.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','new',2,99616,'2011-02-10 14:56:43',99616,'2011-03-21 10:22:04',1);
+INSERT INTO `changelog` VALUES (236,62,'Data import/update from external sources','<p>Allele frequencies from 1000 Genomes Project. Variation submissions on LRGs from UniProt. Structural variation data from DGVa. Somatic mutation data from Cosmic. Variation phenotype data from OMIM, NHGRI, UniProt and EGA. Variation synonyms from UniProt.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 15:03:00',99616,'2011-03-21 10:23:31',1);
+INSERT INTO `changelog` VALUES (237,62,'New variation database','Fresh build from dbSNP 132.',NULL,'cancelled','Variation','N','N','N','N','N','N','N','new',2,99616,'2011-02-10 15:05:05',99616,'2011-03-10 14:01:23',1);
+INSERT INTO `changelog` VALUES (238,62,'Data import/update from external sources','Structural variation data from DGVa.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 15:07:44',99616,'2011-03-10 14:15:47',1);
+INSERT INTO `changelog` VALUES (239,62,'patch_61_62_a: Meta schema version','Meta schema version update',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:10:52',99616,'2011-03-10 14:02:09',1);
+INSERT INTO `changelog` VALUES (240,62,'patch_61_62_b: Alter failed_variation','Drop the subsnp_id column from failed_variation',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 15:23:25',99616,'2011-03-10 14:16:12',1);
+INSERT INTO `changelog` VALUES (241,62,'patch_61_62_c: Introduce failed_allele table','Add a table to store failed alleles',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 15:25:12',99616,'2011-03-10 14:22:05',1);
+INSERT INTO `changelog` VALUES (242,62,'patch_61_62_d: Add type column to source table','Introduce a type column (enum) to indicate the type of a source',NULL,'handed_over','Variation','N','N','N','N','N','N','N','patched',2,99616,'2011-02-10 15:26:46',99616,'2011-03-10 14:20:55',1);
+INSERT INTO `changelog` VALUES (243,62,'patch: Table to store study data','A new table to store description of studies will be introduced and foreign keys to this table will be introduced in variation_annotation and structural_variation tables.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:30:04',99616,'2011-03-10 14:03:33',1);
+INSERT INTO `changelog` VALUES (244,62,'patch: Rationalize data type for allele columns','The data type of allele columns in e.g. allele, variation and variation_feature will be harmonized to use varchar.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:41:40',99616,'2011-03-10 14:22:35',1);
+INSERT INTO `changelog` VALUES (245,62,'patch: Table to store supporting structural variations','A new table to store supporting structural variations will be introduced',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:50:04',99616,'2011-03-10 14:17:03',1);
+INSERT INTO `changelog` VALUES (246,62,'BLAT patch','<p>for aesthetic reasons, we will flip the strand of paired 3\'-ESTs</p>','the DNA-align-features were patched for display reasons','handed_over','EnsemblGenomes','N','N','N','N','N','N','N','patched',2,14179,'2011-02-10 15:50:54',14179,'2011-04-04 14:14:05',1);
+INSERT INTO `changelog` VALUES (247,62,'patch: Table to store variation consequences on regulatory regions','A table to support storing variation consequences on regulatory regions will be introduced',NULL,'cancelled','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:51:50',99616,'2011-03-10 14:23:57',1);
+INSERT INTO `changelog` VALUES (248,62,'patch: Re-design of the transcript_variation table','Variation consequences will be stored by allele instead of by variation. The transcript_variation table will be modified to accommodate this. In addition, HGVS coordinates will be stored as well.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:54:50',99616,'2011-03-10 14:19:03',1);
+INSERT INTO `changelog` VALUES (249,62,'patch: Drop somatic column from source table','The somatic column will be dropped from source and instead introduced in the variation table.',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:56:25',99616,'2011-03-10 14:06:11',1);
+INSERT INTO `changelog` VALUES (250,62,'API changes','<p>The API will be updated to accommodate schema patches.</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 15:58:35',99616,'2011-04-12 09:39:42',1);
+INSERT INTO `changelog` VALUES (251,62,'Families','Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.\r\n * Clustering by MCL\r\n * Multiple Sequence Alignments with MAFFT\r\n * Family stable ID mapping',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-02-10 16:01:21',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (252,62,'SIFT and PolyPhen consequences','<p>Non-synonymous coding consequences evaluated by SIFT and PolyPhen will be calculated</p>',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-10 16:01:24',99616,'2011-03-21 10:22:55',1);
+INSERT INTO `changelog` VALUES (253,62,'Gene Homologies','GeneTrees (protein-coding) with new/updated genebuilds and assemblies\r\n * Clustering using hcluster_sg\r\n * Multiple sequence alignments using MCoffee\r\n * Phylogenetic reconstruction using TreeBeST\r\n * Homology inference including the recent \'possible_ortholog\',\r\n\'putative gene split\' and \'contiguous gene split\' exceptions\r\n * Pairwise gene-based dN/dS scores for high coverage species\r\npairs only\r\n * GeneTree stable ID mapping',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-02-10 16:04:30',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (254,62,'GeneTrees (ncRNA) with new/updated genebuilds and assemblies','* Classification based on RFAM model\r\n * Multiple sequence alignments with infernal\r\n * Phylogenetic reconstruction using RaxML\r\n * Additional multiple sequence alignments with Prank (w/ genomic flanks)\r\n * Additional phylogenetic reconstruction using PhyML and NJ\r\n * Phylogenetic tree merging using TreeBeST\r\n * Homology inference',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-02-10 16:05:38',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (255,62,'Pairwise Alignments','* Non-reference alignments for human vs high coverage blastz-net\r\n * human vs gibbon lastz.\r\n * human vs marmoset lastz\r\n * human vs rabbit lastz\r\n * xenopus vs mouse tblat-net\r\n * xenopus vs chicken tblat-net\r\n * xenopus vs tetraodon tblat-net\r\n * xenopus vs human tblat-net\r\n * xenopus vs danio tblat-net',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-02-10 16:06:54',22288,'2011-03-16 10:05:44',1);
+INSERT INTO `changelog` VALUES (256,62,'Multiple alignments','* update 6way-primate-epo alignments to incorporate new marmoset seq_region names\r\n * update 12way-mammal-epo alignments to incorporate new marmoset seq_region names\r\n * update 19way-amniota-pecan alignments to incorporate new marmoset seq_region names\r\n * 35way-mammal low-coverage-epo alignments (addition of gibbon and new marmoset seq_region names)',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-02-10 16:08:58',22288,'2011-03-16 10:06:12',1);
+INSERT INTO `changelog` VALUES (257,62,'patch_61_62_e Addition of dbfile_registry table','<p>A dbfile_registry table has been added to store the filepaths of result feature collection (.col) files</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-11 11:53:22',100304,'2011-04-04 14:15:28',1);
+INSERT INTO `changelog` VALUES (258,62,'Binding Matrix: simpler representation of matrix frequencies','<p>This change intends to make the representation simpler, towards something that can applied to different formats.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-02-11 13:04:43',100304,'2011-04-04 14:05:35',1);
+INSERT INTO `changelog` VALUES (259,62,'xrefs','Update human external database references.',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2011-02-14 16:14:35',23,'2011-03-07 10:35:38',1);
+INSERT INTO `changelog` VALUES (260,62,'xrefs','Update external database references',NULL,'handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2011-02-14 16:16:39',23,'2011-03-07 10:36:23',1);
+INSERT INTO `changelog` VALUES (261,62,'schema changes','* meta.meta_value has been extended to TEXT (previously it was VARCHAR) and the corresponding indexes have been fixed.\r\n\r\n* analysis.module has been extended to VARCHAR(255) - previously it was VARCHAR(80)\r\n\r\n* mapping_session.prefix column has been added to allow EnsEmblGenomes to track their different types of stable_ids',NULL,'handed_over','Compara','N','N','N','N','N','N','N','N/A',2,22288,'2011-02-17 10:34:34',22288,'2011-03-16 10:06:35',1);
+INSERT INTO `changelog` VALUES (262,62,'PolIII Transcription Associated Regulatory Features','<p>The Regulatory Build now also annotates Regulatory Features associated to PolIII Transcription.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-02-22 09:15:47',100304,'2011-04-04 14:07:16',1);
+INSERT INTO `changelog` VALUES (263,62,'Support for BigWig format','<p>In addition to BAM format, the Ensembl website now supports attachment of BigWig data via URL. Click on \"Manage Your Data\" then select \"Attach Remote File\" from the lefthand menu.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2011-02-22 15:54:52',2,'2011-04-13 16:36:04',1);
+INSERT INTO `changelog` VALUES (264,62,'Export data on structural variation','<p>Enabling data to be exported for the variation page. (same functionalities as on location, gene and transcript)</p>',NULL,'postponed','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-02-22 16:06:58',99923,'2011-04-12 13:57:42',1);
+INSERT INTO `changelog` VALUES (265,62,'Export on Karyotype','<p>Will try to get the karyotype exported to PDF and other formats. Export button just below the karyotype image</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-02-22 16:07:45',99923,'2011-04-12 13:59:35',1);
+INSERT INTO `changelog` VALUES (266,62,'BED Format export','<p>Adding BED format to the export functionality on location, genes, transcript and variation.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-02-22 16:10:01',99923,'2011-04-12 13:59:49',1);
+INSERT INTO `changelog` VALUES (267,62,'Highlighting row in feature table for variation','<p>When clicking on a SNP on the karyotype for phenotype, the corresponding row (variation) is highlighted in the feature table</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-02-22 16:11:01',99923,'2011-04-12 14:00:07',1);
+INSERT INTO `changelog` VALUES (268,62,'Add a variation set for variations flagged as failed','Variations that have been flagged as failed will be grouped in a variation set named \'Failed variations\'',NULL,'handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-02-23 12:38:27',99616,'2011-03-10 14:06:36',1);
+INSERT INTO `changelog` VALUES (269,62,'Mouse RegBuild update','<p>The Mouse RegulatoryBuild has been rerun to include some MotifFeatures which we re previously being excluded. Input data sets remained the same, hence structures are unaffected.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-25 15:45:34',100304,'2011-04-04 14:08:37',1);
+INSERT INTO `changelog` VALUES (270,62,'patch_61_62_f regulatory_feature.fset_seq_region_idx','<p>A new regulatory_feature unique index has replaced two older indexes.</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-25 15:51:49',100304,'2011-04-04 14:12:26',1);
+INSERT INTO `changelog` VALUES (271,62,'Core schema patches','<p>Core schema patches have been propagated to the funcgen schema where appropriate i.e. patch_61_62_g - synonym_field_extension patch_61_62_h - external_db.db_name_idx patch_61_62_i - drop_external_db.display_label_linkable</p>',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-02-25 16:57:49',100304,'2011-04-04 14:13:13',1);
+INSERT INTO `changelog` VALUES (272,62,'Line numbers on exon view','Line numbering can now be added to exon sequence when configuring the exon view page',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-03-04 09:15:44',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (273,62,'Resizable control panel','The control panel which appears for page configurations, exports, etc. can now be resized and moved around the page',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-03-04 09:17:35',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (274,62,'patch_61_62_j - extend meta.meta_key','Extended the length of the meta_key field to handle longer values',NULL,'handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-03-04 10:06:53',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (275,62,'Searchable content','<p>The ensembl search now includes content from the Help database and from static content pages, for example species homepages.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,161,'2011-03-10 16:10:18',161,'2011-04-12 14:00:38',1);
+INSERT INTO `changelog` VALUES (283,62,'Supporting Evidence','<p>Supporting Evidence View, ie the view that shows the alignments of transcripts/exons and evidence, is now configurable.</p>',NULL,'handed_over','Web','N','N','N','N','N','N','N','N/A',2,161,'2011-04-12 14:07:23',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (284,63,'BioMart 63 databases','<p>Ensembl Genes 63:</p>\r\n<p>Updated to new Microbat assembly Myoluc2.0</p>\r\n<p>Updated to new Yeast assembly EF3</p>\r\n<p>Added a new Exon ID filter to the GENE->Limit to genes filter. <br />Reinstated the protein allele attribute in the Variation->GERMLINE VARIATION INFORMATION attribute section.<br />The PRIDE team have collaborated with us to reinstate the linking between the Ensembl Gene mart and the PRIDE mart.<br />The Exon ID was removed from the Transcript Event attribute section as this was misleading.<br />The text (bp) was removed from the GO attributes.<br />Gene and transcript biotype attributes have been added to the Sequence attribute section.<br />The HGNC symbol link has been updated.<br />The following external references are now stored on gene IDs: EntrezGene, WikiGene, RFAM, MIM, MIM_GENE, MIM_MORBID, miRBase, UniGene, Uniprot_genename, DBASS3, DBASS5</p>\r\n<p><br /> Ensembl Variation 63:</p>\r\n<p>Updated mouse to dbSNP 132<br />Phenotypes in the GENERAL VARIATION FILTERS->Phenotype filter drop down have had all commas removed as this caused problems for the biomart code which resulted in incorrect filtering.<br />Peptide shift attribute has been reinstated in the Variation->GENE ASSOCIATED INFORMATION attribute section.<br />The Variation->SEQUENCE VARIATION->Variation annotation attribute section has been renamed Phenotype annotation<br />Variation ID attribute has been renamed Variation Name<br /><br /><br />Ensembl Regulation 63:<br /><br />\"Is projected\" attribute added to the Regulatory features.<br />Annotated features have now been renamed to Regulatory Evidence<br />Useful text information on how to use the filters and attributes for this mart has been added to the top of the filter panel and the top of the attribute panel on the interface. <br /><br />Vega 43:<br /><br />Human and Danio manual annotation has been updated to represent the annotation presented in Vega release 43.</p>','','handed_over','Mart','N','N','N','N','N','N','N','N/A',2,25629,'2011-04-21 09:21:42',25629,'2011-06-24 09:16:35',1);
+INSERT INTO `changelog` VALUES (285,63,'xref projection','<p>Project GO ids and gene names to species. Make alterations to zebrafish projections.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-04-21 09:49:10',25629,'2011-06-03 10:43:20',1);
+INSERT INTO `changelog` VALUES (286,63,'EMBL & Genbank dumps','<p>EMBL & Genbank dumps for all species</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-04-21 09:49:33',25629,'2011-06-20 12:13:16',1);
+INSERT INTO `changelog` VALUES (287,63,'New core database for Yeast','<p>New core database for Saccharomyces cerevisiae to reflect the new assembly and genebuild from SGD</p>','contact: hpedro@ebi.ac.uk\r\nAlready built and live in EnsemblGenomes website, so it will just need patching to 63.','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',2,103312,'2011-04-21 10:45:53',103312,'2011-05-05 11:13:19',1);
+INSERT INTO `changelog` VALUES (288,63,'New otherfeatures database for Yeast','<p>Rebuilt otherfeatures database with new EST alignments reflecting the new assembly from SGD.</p>','Contact: Helder Pedro hpedro@ebi.ac.uk\r\nAlready built as a 62 schema, just needs patching to 63.','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',2,103312,'2011-04-21 10:51:49',103312,'2011-05-05 11:13:51',1);
+INSERT INTO `changelog` VALUES (289,63,'New funcgen database for Yeast','<p>New functional genomics database for Yeast with new probe mapping to reflect the assembly update from SGD.</p>','Contact: Helder Pedro hpedro@ebi.ac.uk\r\nAlready built, needs patching to 63','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',2,103312,'2011-04-21 10:57:04',101255,'2011-05-26 18:33:21',1);
+INSERT INTO `changelog` VALUES (290,63,'New variation database for Yeast','<p>New variation database for Yeast with mapped variation features to reflect the latest assembly from SGD.</p>','Contact: Helder Pedro hpedro@ebi.ac.uk\r\nAlready done as a 62 schema, needs patching to 63','handed_over','EnsemblGenomes','Y','Y','Y','N','N','N','N','new',2,103312,'2011-04-21 11:02:45',101255,'2011-05-31 09:23:59',1);
+INSERT INTO `changelog` VALUES (291,63,'New microbat assembly','<p>A full gene annotation on the new high coverage microbat assembly, Myoluc2.0</p>','','handed_over','Genebuild','Y','Y','Y','N','Y','N','N','new',2,97245,'2011-04-21 13:21:25',97245,'2011-05-09 13:05:40',1);
+INSERT INTO `changelog` VALUES (292,63,'Removed duplicated dna in panda','<p>Scaffold dna sequences removed from the dna table</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,97245,'2011-04-21 13:22:20',97245,'2011-05-09 10:20:55',1);
+INSERT INTO `changelog` VALUES (293,63,'Rabbit xrefs','<p>Missing xrefs added for ncRNAs</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,97245,'2011-04-21 16:19:21',97245,'2011-05-09 10:20:30',1);
+INSERT INTO `changelog` VALUES (294,63,'Human Vega annotation','<p>Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 43. Annotation by Havana of chromosome 12 has been completed and that of chromosome 14 is nearly finished.</p>\r\n<p> </p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2011-04-26 12:21:29',100304,'2011-05-26 15:37:58',1);
+INSERT INTO `changelog` VALUES (295,63,'Zebrafish Vega annotation','<p>Manual annotation of zebrafish from Havana has been updated. This represents the annotation presented in Vega release 43. There is an increase of about 50Mb of annotated sequence, with an extra 1300 annotated loci.</p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2011-04-26 12:22:49',100304,'2011-05-26 15:38:48',1);
+INSERT INTO `changelog` VALUES (296,63,'GRCh37.p4','<p>GRCh37.p4 added to the human databases.</p>','This adds the sequence and assembly data associated with GRCh37.p4 to the human databases.','postponed','Genebuild','Y','N','Y','N','N','N','N','N/A',2,14183,'2011-04-26 13:20:38',14183,'2011-05-10 10:54:54',1);
+INSERT INTO `changelog` VALUES (297,63,'GRCh37.p4 annotation','<p>Gene annotation of the patches in the otherfeatures db.</p>','Addition of assembly patch gene annotation using a \'light-weight\' annotation strategy, instead of the full genebuild process.','postponed','Genebuild','N','N','N','Y','N','N','N','patched',2,14183,'2011-04-26 13:25:03',14183,'2011-05-10 10:55:46',1);
+INSERT INTO `changelog` VALUES (298,63,'Human cDNA update','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 13px;\">The latest set of cDNAs for human (as of 05/May/2011) from the <br />European Nucleotide Archive and NCBI RefSeq were aligned to the <br />current genome using <a style=\"color: #3366bb;\" title=\"Exonerate\" href=\"http://www.ebi.ac.uk/~guy/exonerate/\" target=\"_blank\">Exonerate</a>. There are 1104 new cDNA alignments for Ensembl 63</span></p>\r\n<p> </p>','','handed_over','Genebuild','N','N','N','N','N','N','N','new',2,14183,'2011-04-26 13:27:02',100304,'2011-05-26 10:30:35',1);
+INSERT INTO `changelog` VALUES (299,63,'Update schema version','<p> </p>\r\n<p># Description:</p>\r\n<p># Update schema_version in meta table to 63.</p>\r\n<p> </p>\r\n<p>UPDATE meta SET meta_value=\'63\' WHERE meta_key=\'schema_version\';</p>\r\n<p> </p>\r\n<p># Patch identifier</p>\r\n<p>INSERT INTO meta (species_id, meta_key, meta_value)</p>\r\n<p> VALUES (NULL, \'patch\', \'patch_62_63_a.sql|schema_version\');</p>\r\n<p> </p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-04-28 10:05:44',103537,'2011-05-19 12:47:30',1);
+INSERT INTO `changelog` VALUES (300,63,'Indexing changes for core database.','<p> </p>\r\n<p>Change stable Id version to not null, default 1 in exon_stable_id, gene_stable_id, transcript_stable_id, translation_stable_id, gene_archive.</p>\r\n<p>Create unique index on stable_id and verision for gene_archive.</p>\r\n<p>Create a unique index for table umapped_object. </p>\r\n<p> </p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-04-28 10:11:21',103537,'2011-05-19 12:48:49',1);
+INSERT INTO `changelog` VALUES (301,63,'Remove field dbprimary_acc_linkable from external_db table.','<p>Remove field dbprimary_acc_linkable from external_db table.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-04-28 10:12:13',103537,'2011-05-19 12:49:19',1);
+INSERT INTO `changelog` VALUES (302,63,'Mouse cDNA update','<p>The latest set of cDNAs for mouse (as of 05/May/2011) from the <br />European Nucleotide Archive and NCBI RefSeq were aligned to the <br />current genome using <a title=\"Exonerate\" href=\"http://www.ebi.ac.uk/~guy/exonerate/\" target=\"_blank\">Exonerate</a>. There are 1009 new cDNA alignments for Ensembl 63.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,102717,'2011-04-28 13:32:23',102717,'2011-05-18 12:48:48',1);
+INSERT INTO `changelog` VALUES (303,63,'New rhesus macaque variation database','<p>Based on dbSNP 131</p>','Postponed until a dbSNP build with more complete clustering is available.','postponed','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-03 09:51:03',99616,'2011-05-16 10:18:49',1);
+INSERT INTO `changelog` VALUES (304,63,'New Cow Assembly','<p>The first genebuild on cow assembly UMD3.1.</p>','Cow will now be available for the next release (64).','postponed','Genebuild','Y','Y','Y','Y','Y','N','N','new',2,97238,'2011-05-03 10:02:32',97238,'2011-05-09 09:59:22',1);
+INSERT INTO `changelog` VALUES (305,63,'Update to Ensembl-Havana GENCODE gene set (release 8)','<p>Update to Ensembl-Havana GENCODE gene set (release 8) - this is based on updated Ensembl gene set and latest Havana gene annotation.</p>','The database will contains the latest GRC patches (p4) declared by Susan.','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','new',2,9335,'2011-05-03 10:04:27',9335,'2011-05-23 16:13:51',1);
+INSERT INTO `changelog` VALUES (306,63,'Updates to human phenotype associations','<p>OMIM, UniProt, NHGRI GWAS catalog, HGMD mutations, COSMIC</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-03 10:07:23',99616,'2011-06-03 14:22:06',1);
+INSERT INTO `changelog` VALUES (307,63,'New mouse variation database','<p>Based on dbSNP 132</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-03 10:11:08',99616,'2011-06-03 14:22:34',1);
+INSERT INTO `changelog` VALUES (308,63,'Import of new LRGs','','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-03 10:11:55',99616,'2011-06-03 14:27:02',1);
+INSERT INTO `changelog` VALUES (309,63,'Updated Regulation API Tutorial','','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 11:32:53',100304,'2011-05-31 10:51:00',1);
+INSERT INTO `changelog` VALUES (310,63,'Add attrib_id column to variation_set','<p>An attrib_id column is added to variation_set in order to be able to provide general and human-friendly names to variation sets without breaking the web display.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-03 13:25:55',99616,'2011-06-03 14:22:59',1);
+INSERT INTO `changelog` VALUES (311,63,'Update structural variation data from DGVa','<p>Update done only for Human, Mouse, Pig and Dog.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-03 13:27:14',102503,'2011-06-08 13:14:38',1);
+INSERT INTO `changelog` VALUES (312,63,'Flagging obsolete Uniprot proteins','<p>Flag the obsolete proteins in Uniprot used as supporting evidence. 122 proteins used as evidence were flagged as obsolete for this release.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-05-03 13:30:10',100304,'2011-06-14 10:11:30',1);
+INSERT INTO `changelog` VALUES (313,63,'Flagging obsolete Ensembl proteins','<p>Flag obsolete human Ensembl proteins used as supporting evidence for other species. 364 proteins used as evidence were flagged as obsolete.</p>','Except the human...','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-05-03 13:32:42',100304,'2011-06-14 10:13:27',1);
+INSERT INTO `changelog` VALUES (314,63,'patch_62_63_a - Schema Version','<p>This patch updates the schema version</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-05-03 13:41:20',1273,'2011-05-24 10:08:55',1);
+INSERT INTO `changelog` VALUES (315,63,'patch_62_63_b - binding_matrix.analysis_id','<p>This patch updates the the analysis_id field of the binding_matrix tables to a smallint</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-05-03 13:43:35',1273,'2011-05-24 10:09:13',1);
+INSERT INTO `changelog` VALUES (316,63,'Removal of lowercase letter at the end of all database names','<p>For release 63 it has been decided to remove the lowercase letter at the end of all database names as it is confusing for users and provides little meaning about actual data changes.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-05-03 13:45:25',25629,'2011-06-03 10:44:05',1);
+INSERT INTO `changelog` VALUES (317,63,'MicroArray Mapping','<p>Mapping of expression arrays to Ensembl Transcripts has been updated for Human, Mouse, Rat and Zebrafish. We also included an updated version of the Phalanx OneArray for Rat.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-05-03 13:49:55',100304,'2011-06-22 12:53:04',1);
+INSERT INTO `changelog` VALUES (318,63,'RegulatoryFeatureAdaptor::fetch_all','<p>The base fetch_all method has been over-ridden for the RegulatoryFeatureAdaptor, this now defaults to returning only the MultiCell RegulatoryFeatures, as the other generic methods do.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-05-03 13:58:56',1273,'2011-05-25 12:31:55',1);
+INSERT INTO `changelog` VALUES (319,63,'Update xrefs for core databases','<p>Update xrefs for Human, Mouse, Rat, Pig, Macaque, Chimp, Orangutan, Fugu and Stickleback.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-05-03 14:00:03',23,'2011-05-26 11:56:39',1);
+INSERT INTO `changelog` VALUES (320,63,'Logic name update','<p>Whenever possible, logic names updated to be consistent across all databases</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,97245,'2011-05-03 14:19:14',97245,'2011-06-03 11:02:34',1);
+INSERT INTO `changelog` VALUES (321,63,'ResultFeatureAdaptor method over-rides','<p>Where appropriate some of the base feature adaptor methods have been over-riden, this prevents some API errors due to the nature of the ResultFeature storage </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-05-03 14:06:41',1273,'2011-06-03 16:01:13',1);
+INSERT INTO `changelog` VALUES (322,63,'Added Motif Features for Missing Jaspar Matrices','<p>Motif Features were added for the following Jaspar Matrices: </p>\r\n<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">E2F1: MA0024.1 (2315 sites)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">NFKB: MA0105.1 (2040)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BHLHE40: PB0111.1 (46); PB0007.1 (276)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Nrsf: MA0138.1 (4321)</li>\r\n</ul>\r\n<p> </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 15:16:41',100304,'2011-05-31 10:45:44',1);
+INSERT INTO `changelog` VALUES (323,63,'API web documentation overhaul','<p>Replace PDoc system with Doxygen + Perl Filter to produce API reference web pages.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103988,'2011-05-03 15:26:45',103988,'2011-06-28 15:30:37',1);
+INSERT INTO `changelog` VALUES (324,63,'Changed Motif Features score to [0-1] relative affinity scale','<p>Instead of showing the absolute score from the MOODs software, we now display a [0-1] linear relative value between the maximum (1) and minimum (0) score. This is to make it coherent with the API BindingMatrix::relative_affinity function and to make it easier for the user to interpret the score. </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 15:27:26',100304,'2011-05-31 10:50:08',1);
+INSERT INTO `changelog` VALUES (325,63,'patch_62_64_c : Added binding_matrix.threshold','<p>A new threshold float field was added to the Binding Matrix to store the minimum score for Motif Features from each matrix (patch_62_63_c).</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 15:32:00',1273,'2011-05-25 12:11:33',1);
+INSERT INTO `changelog` VALUES (326,63,'Added species-specific thresholds to Binding Matrices','<p>Added to each Binding Matrix the lowest score for Motif Features belonging to that matrix and that species. This will make it easier for people using the API to know if the potential binding affinity for a given sequence goes above the currently used threshold (ie would be classified as a binding site). </p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 15:41:13',100304,'2011-05-31 10:53:57',1);
+INSERT INTO `changelog` VALUES (327,63,'Schema changes','<p># structural variation schema changes:</p>\r\n<p>- Change the columns name from bound_start to inner_start and bound_end to inner_end</p>\r\n<p>- Add a column for validation status</p>\r\n<p>- Change the column class to class_attrib_id, using more detailled SO terms.</p>\r\n<p><br /># moved failed descriptions into attribute table <-- Postponed</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-05-03 15:58:42',99616,'2011-06-03 14:24:03',1);
+INSERT INTO `changelog` VALUES (328,63,'Cleaned Regulatory Regions in chromosomal boundaries','<p>In some rare cases, regulatory regions can pass the boundaries of sequence regions (chromosomes or scaffolds). These cases will be removed as they are likely to be artifactual. For release 63, 18 mouse regulatory features were removed.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 15:59:00',100304,'2011-05-31 10:54:38',1);
+INSERT INTO `changelog` VALUES (329,63,'LRG data','<p>import LRG variant data</p>\r\n<p>add LRG consequences to the database</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-05-03 16:01:34',99616,'2011-06-03 14:24:25',1);
+INSERT INTO `changelog` VALUES (330,63,'Update of Regulation Metadata','<p>CTCF is now classified generically as a \"Transcription Factor\" instead of \"Insulator\"</p>\r\n<ul>\r\n</ul>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-05-03 16:01:50',100304,'2011-05-31 10:49:27',1);
+INSERT INTO `changelog` VALUES (331,63,'New individual genotypes','<p>Individual genotypes from Penn State University:</p>\r\n<ul>\r\n<li>Han Chinese Individual (YanHuang Project)</li>\r\n<li>Seong-Jin Kim (SJK, GUMS/KOBIC)</li>\r\n<li>Anonymous Irish Male</li>\r\n<li>Individual from the Extinct Palaeo-Eskimo Saqqaq (Saqqaq Genome Project)</li>\r\n<li>Individual from the Extinct Palaeo-Eskimo Saqqaq, high confidence SNPs (Saqqaq Genome Project)</li>\r\n<li>Anonymous Korean individual, AK1 (Genomic Medicine Institute) : Individual genotype</li>\r\n<li>Misha Angrist (Personal Genome Project)</li>\r\n<li>Henry Louis Gates Jr (Personal Genome Project) </li>\r\n<li>Henry Louis Gates Sr (Personal Genome Project) </li>\r\n<li>Rosalynn Gill (Personal Genome Project)</li>\r\n<li>Marjolein Kriek (Leiden University Medical Centre)</li>\r\n<li>Stephen Quake (Stanford)</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,102503,'2011-05-03 16:03:37',99616,'2011-06-03 14:24:58',1);
+INSERT INTO `changelog` VALUES (332,63,'xref sources to be moved to gene level','<p>The following External database sources have been moved up to the Gene level :-</p>\r\n<p>DBASS3, DBASS5, EntrezGene, miRBase, RFAM, UniGene, Uniprot_genename, WikiGene, MIM_GENE and MIM_MORBID.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2011-05-04 13:20:54',23,'2011-05-26 11:57:49',1);
+INSERT INTO `changelog` VALUES (333,63,'pairwise alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<div><span style=\"font-size: small;\"><span style=\"font-size: 13px; line-height: 17px;\"><br /></span></span></div>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs marmoset lastz</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs microbat lastz</li>\r\n</ul>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:13:42',98792,'2011-06-08 13:35:42',1);
+INSERT INTO `changelog` VALUES (334,63,'multiple alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">6way-primate-epo alignments to incorporate new marmoset</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">12way-mammal-epo alignments to incorporate new marmoset</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">19way-amniota-pecan alignments to incorporate new marmoset</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">35way-mammal low-coverage-epo alignments ( new marmoset and microbat )</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">5way-fish (new mappings with HMM derived anchors)</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:14:43',98792,'2011-06-08 13:34:46',1);
+INSERT INTO `changelog` VALUES (335,63,'syntenies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human marmoset synteny</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:15:23',98792,'2011-06-08 13:36:21',1);
+INSERT INTO `changelog` VALUES (336,63,'ProteinTrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<p style=\"font-size: 10pt; line-height: 13pt; color: #000000; font-weight: normal; margin-top: 10px; margin-right: 0px; margin-bottom: 10px; margin-left: 0px; padding: 0px;\">GeneTrees (protein-coding) with new/updated genebuilds and assemblies</p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering using hcluster_sg</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments using MCoffee, without the exon-disaligner module (AKA decaf)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference including the recent \'possible_ortholog\',\'putative gene split\' and \'contiguous gene split\' exceptions</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Pairwise gene-based dN/dS scores for high coverage species pairs only</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">GeneTree stable ID mapping</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:16:31',98792,'2011-06-08 13:38:07',1);
+INSERT INTO `changelog` VALUES (337,63,'ncRNAtrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Classification based on RFAM model</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments with infernal</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using RaxML</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional multiple sequence alignments with Prank (w/ genomic flanks)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional phylogenetic reconstruction using PhyML and NJ</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic tree merging using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:17:17',98792,'2011-06-08 13:40:49',1);
+INSERT INTO `changelog` VALUES (338,63,'families','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering by MCL</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple Sequence Alignments with MAFFT</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Family stable ID mapping</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:17:51',98792,'2011-06-08 13:41:49',1);
+INSERT INTO `changelog` VALUES (339,63,'data dumps','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 19 way PECAN multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 19 way GERP constrained elements</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 12 way EPO multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 6 way EPO primate multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 5 way fish EPO alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 5 way fish EPO alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ProteinTrees</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ncRNAtrees</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:18:51',98792,'2011-06-20 12:44:32',1);
+INSERT INTO `changelog` VALUES (340,63,'schema changes','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ol style=\"font-size: 10pt; line-height: 13pt; list-style-type: decimal;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">The linking table \'species_set\' is renamed into \'species_set_genome_db\'</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">There will be a new, \"header\" table called \'species_set\' for which \'species_set_id\' will be [obviously, unique] primary key.</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">species_set.species_set_id will become a foreign key for species_set_genome_db.species_set_id</li>\r\n</ol>\r\n<p> </p>','','postponed','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-05-04 15:20:06',98792,'2011-06-08 13:37:22',1);
+INSERT INTO `changelog` VALUES (341,63,'Zebrafish Vega merge','<p>A new Vega gene set has been merged with the Ensembl geneset from release 61.</p>','','handed_over','Genebuild','N','Y','N','Y','N','N','N','new',2,29,'2011-05-05 08:57:49',29,'2011-05-19 13:06:48',1);
+INSERT INTO `changelog` VALUES (342,63,'update variation consequences','<p>update variation consequences on human, zebrafish and cow due to new gene sets</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-05-05 16:08:12',99616,'2011-06-03 14:25:24',1);
+INSERT INTO `changelog` VALUES (343,63,'Uploading zipped files','<p>Upload of custom data (BED, GFF, etc) now supports both .zip and .gz formats seamlessly. Files are unzipped during uploading and stored on our servers in uncompressed format.</p>','Needs testing with a few different formats!','handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2011-05-09 13:26:47',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (344,62,'Test','<p>Link test</p>\r\n<p><a title=\"Ensembl\" href=\"http://www.ensembl.org\">Ensembl</a></p>','Test','declared','Web','N','N','N','N','N','N','N','N/A',2,102019,'2011-05-18 12:25:17',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (345,63,'Lucene plugin','<p>Our plugin for the Lucene search engine has been made public. Please note that this is only the web interface - it requires a Lucene web service to connect to. We intend to provide instructions on how to set up your own Lucene server in a future release.</p>\r\n<p>The main web code for simple text-based searching (UniSearch) has also been refactored, and old code removed. This should make it much easier to develop additional plugins for other search engines - see the lucene plugin for the modules you will need to create.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,2,'2011-05-19 09:17:20',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (346,63,'Update ancestral alleles','<p>Update of the ancestral allele annotation for variations to primarily use data from the Ensembl Compara Ortheus calls. The ancestral allele data source priority is::</p>\r\n<p>1. Compara high confidence</p>\r\n<p>2. Compara low confidence</p>\r\n<p>3. Ancestral allele calls reported by Dr Jim Mullikin (http://www.ncbi.nlm.nih.gov/books/NBK44409/)</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,99616,'2011-05-24 15:31:54',99616,'2011-06-03 14:25:42',1);
+INSERT INTO `changelog` VALUES (347,63,'ResultFeatureAdaptor ExperimentalChip support removed','<p>Support for ResultFeatures originating from ExperimentalChips (i.e. array experiments) has been removed.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-05-25 12:34:43',1273,'2011-06-03 16:01:35',1);
+INSERT INTO `changelog` VALUES (348,63,'Update to CCDS and RefSeq models in human otherfeatures database','<p>Imported CCDS models into human otherfeatures databases. (CCDS Data freeze 9 February 2011).</p>\r\n<p>Imported RefSeq models into human otherfeatures database.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2011-05-25 13:34:51',5132,'2011-06-02 13:39:46',1);
+INSERT INTO `changelog` VALUES (349,63,'Sortable tracks on images','<p>Tracks on <strong>Region in detail</strong> and <strong>Region overview</strong> pages can now be reordered by dragging them to a new position on the image.</p>\r\n<p>There is also an interface for this in the control panel, which is available on the following additional views:</p>\r\n<ul>\r\n<li>Location: Alignments (image), Multi-species view</li>\r\n<li>Gene: Summary, Regulation</li>\r\n<li>Regulation: Feature context</li>\r\n<li>Variation: Genomic context</li>\r\n</ul>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-05-31 08:27:34',97803,'2011-05-31 08:28:12',1);
+INSERT INTO `changelog` VALUES (350,63,'Favourite tracks saved across all configurations','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 12px;\">If you make a track your favourite on one page, it will be marked as a favourite on all pages where it appears.</span></p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-05-31 08:28:59',97803,'2011-05-31 08:33:45',1);
+INSERT INTO `changelog` VALUES (351,63,'Download genotype information as CSV','<p>The download view as csv has been enabled for the individual genotype information. The tables can now be downloaded as CSV format.</p>\r\n<p>http://www.ensembl.org/Homo_sapiens/Variation/Individual?r=9:22125003-22126003;v=rs1333049;vdb=variation;vf=19660490</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-05-31 08:32:51',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (352,63,'Tracks on location based Multi-species and Alignments (image) views are now configurable on a species by species basis','<p>There is now a dropdown with a species list in the configuration panel for these pages. Only tracks for the selected species will be displayed, to make configuration easier.</p>\r\n<p> </p>\r\n<p>On Multi-species view, there is an <strong>All species</strong> option, which contains options for which alignments to show.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-05-31 08:32:58',97803,'2011-05-31 08:33:23',1);
+INSERT INTO `changelog` VALUES (353,63,'Species selection on Multi-species view is saved','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 12px;\">Your choice of secondary species is saved for each primary species so that when you come back to the site you don\'t have to make the selection again.</span></p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-05-31 08:34:20',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (354,63,'New style popup menus on images','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 12px;\">The menus which appear when you click on tracks on images (e.g. Region in detail) have been redesigned.</span></p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-05-31 08:34:53',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (355,63,'New style regulation configuration matrix','<p>The <strong>Evidence types</strong> matrix has been redesigned so that it fits more easily in the configuration panel.</p>\r\n<p> </p>\r\n<p>The checkboxes have been replaced with a grid, with colours indicating the status of the options - light blue for off, dark blue for on, grey for unavailable.</p>\r\n<p> </p>\r\n<p>Options can be changed by clicking on the grid, and there is also the ability to select or deselect all options in a column or row from a menu which appears when hovering over the labels for that column or row.</p>\r\n<p> </p>\r\n<p>Additionally, selection can be performed by holding down the left mouse button and dragging over the grid, but note that this performs a toggle operation, so any options in your selection which were on will be turned off, and vice versa. (This functionality is not available in IE 8 and older.)</p>\r\n<p> </p>\r\n<p>Finally, there is a filter input, allowing for quick identification of required options.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-05-31 08:43:46',97803,'2011-05-31 14:31:57',1);
+INSERT INTO `changelog` VALUES (356,63,'Download as CSV button on tables','<p>Most tables on the site now have a button to download the data as a CSV file in the table header (to the right of the filter).</p>\r\n<p> </p>\r\n<p>If you hover over the button you will get a popup with options to download the entire table, or just the data visible at the time. Clicking on the button without waiting for this popup will download the visible data.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-06-02 10:03:53',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (357,63,'Pie graphs to display alleles frequencies by population','<p>Web display: Add pie graphs in the Variation -> Population genetics pages, for the 1000 genomes populations</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,102503,'2011-06-02 14:32:01',99616,'2011-06-03 14:26:11',1);
+INSERT INTO `changelog` VALUES (358,63,'Probe features in gff export','<p>Probe features are now included in the export for GFF Format.</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,99923,'2011-06-06 16:14:06',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (359,63,'CAGE-defined TSS (K562)','<p>CAGE-defined transcription start sites for K562 cell line imported into the human otherfeatures database. Data provided by Riken as part of the ENCODE collaboration. Data from additional cell lines expected in due course.</p>','','cancelled','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2011-06-09 10:49:20',5132,'2011-06-10 08:50:25',1);
+INSERT INTO `changelog` VALUES (360,63,'Variation Effect Predictor 2.1','<p><br /> * option to filter the output based on frequencies in 1000 Genomes populations<br /> * new US East database server available for querying<br /> * ability to use local file cache in place of or alongside connecting to an Ensembl database<br /> * new \"standalone\" mode does not depend on API installation or network connection<br /> * significant improvements to speed of script<br /> * whole-genome mode now default (no disadvantage for smaller datasets)<br /> * improved status output with progress bars<br /> * regulatory region consequences now reinstated and improved<br /> * modification to output file - Transcript column is now Feature, and is followed by a Feature_type column</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-06-23 09:37:44',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (363,64,'New species: Lamprey','<p>Petromyzon_marinus_7.0 is a new assembly of the sea lamprey (<em>Petromyzon marinus</em>) provided by the lamprey consortium. The gene set for lamprey was built using the Ensembl pipeline. Gene models are based on genewise alignments of lamprey proteins and other proteins from Uniprot. The protein based gene models were then extended using lamprey cDNA. To improve the accuracy of models generated from distant species, transcriptome data was used to filter out the different gene models. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated. The final gene set consists of 6,993 projected protein coding genes containing 14,104 transcripts, 47 pseudogenes and 2,628 ncRNAs. More detailed information on the genebuild can be found <a title=\"Lamprey home page\" href=\"http://www.ensembl.org/Petromyzon_marinus/Info/Index\" target=\"_blank\">here</a>.</p>','','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,97245,'2011-07-01 13:24:22',5132,'2011-09-09 13:17:26',1);
+INSERT INTO `changelog` VALUES (364,64,'Human: updated cDNA alignments','<p>A new cdna database was created for e64: The latest set of cDNAs for human (as of 14/July/2011) from the European Nucleotide Archive and NCBI RefSeq were aligned to the current genome using Exonerate. A total of 245,557 cDNAs were aligned to the genome, showing an increase of 2,770 compared to release 63.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','new',4,14183,'2011-07-01 13:41:40',5132,'2011-09-09 13:22:02',1);
+INSERT INTO `changelog` VALUES (365,64,'Human: assembly updated to GRCh37.p5','<p>The human genome assembly was updated to GRCh37.p5 and the assembly infomation in all human databases has been altered accordingly. This minor assembly update contains 105 assembly patches. The DNA sequence for the primary assembly (chromosomes 1-22, X, Y, unlocalized scaffolds and unplaced scaffolds) remains unchanged.</p>','','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','patched',4,14183,'2011-07-01 13:44:01',5132,'2011-09-09 13:22:28',1);
+INSERT INTO `changelog` VALUES (366,64,'Human: GRCh37.p5 gene annotation','<p>The patches for GRCh37.p5 were annotated using a combination of manual annotation, annotation projected from the primary assembly and annotation derived from cDNA and protein alignment evidence. Annotation of the patches is stored in the otherfeatures database.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',4,14183,'2011-07-01 13:45:26',5132,'2011-09-09 13:23:41',1);
+INSERT INTO `changelog` VALUES (367,64,'New assembly and genebuild: Cow UMD3.1','<p>The cow gene annotation in e64 is an entirely new genebuild based on the UMD 3.1 assembly produced by Center for Bioinformatics and Computational Biology (CBCB) at <a href=\"http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml\">University of Maryland</a>.</p>\r\n<p>The assembly was downloaded from here:</p>\r\n<p><a href=\"ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Bos_taurus/Bos_taurus_UMD_3.1/\">ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Bos_taurus/Bos_taurus_UMD_3.1/</a></p>\r\n<p>The gene annotation was generated using three different sources, namely <em>Bos taurus</em> proteins from UniProtKB and NCBI, UniProt mammalian and vertebrate proteins and finally translations of Ensembl human genes. The alignment of above evidence to the genome followed procedures in the standard Ensembl <a href=\"http://www.ensembl.org/info/docs/genebuild/genome_annotation.html\">genebuild pipeline</a>. The gene-building procedure on the UMD3.1 assembly identified 19994 protein-coding genes and 797 pseudogenes.cDNA and EST sequences were aligned to the genome using Exonerate.</p>\r\n<p>More detailed information about the cow genebuild can be found at <a href=\"http://www.ensembl.org/Bos_taurus/Info/Index\">http://www.ensembl.org/Bos_taurus/Info/Index</a></p>\r\n<p> </p>','','handed_over','Genebuild','Y','Y','Y','N','Y','N','Y','new',2,97238,'2011-07-02 23:07:13',5132,'2011-09-09 13:19:34',1);
+INSERT INTO `changelog` VALUES (368,64,'Mouse: gene set updated','<p>The Ensembl/HAVANA merged gene set was updated to incorporate the latest manual annotation from the HAVANA team. This annotation from HAVANA is also displayed in the <a title=\"Mouse Vega website\" href=\"http://vega.sanger.ac.uk/Mus_musculus/Info/Index\" target=\"_self\">VEGA release 44</a>. This includes annotation of the MHC region on chromosome 17.</p>','','handed_over','Genebuild','N','Y','N','N','Y','N','N','new',3,97238,'2011-07-02 23:12:45',5132,'2011-09-09 13:23:12',1);
+INSERT INTO `changelog` VALUES (370,64,'New species: Tasmanian devil','<p>The Tasmanian devil (<em>Sarcophilus harrisii</em>) 7.0 assembly, provided by Illumina and the Wellcome Trust Sanger Institute, has been added as a new species to Ensembl for release 64. The Ensembl genome annotation pipeline was used to identify genes. Models built from Tasmanian devil proteins and cDNAs were given priority over predictions from other vertebrate species. 5,663 transcript models made from paired end Illumina RNASeq were added into the gene build where they added a novel model or splice variant. In total 22,391 protein-coding gene models were constructed. The final gene set consists of 18,775 protein coding genes containing 24,035 transcripts, 178 pseudogenes and 1,466 ncRNAs. More detailed information on the genebuild can be found <a title=\"Tasmanian devil home page\" href=\"http://www.ensembl.org/Sarcophilus_harrisii/Info/Index/\" target=\"_blank\">here</a>. An otherfeatures database containing RNASeq models is also provided.</p>','','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,29,'2011-07-05 10:59:07',5132,'2011-09-09 13:20:31',1);
+INSERT INTO `changelog` VALUES (371,64,'Ensembl 64 mart databases','<p style=\"text-align: justify;\">Ensembl Genes 64:</p>\r\n<p style=\"text-align: justify;\"> </p>\r\n<p style=\"text-align: justify;\">Added new species Lamprey (Petromyzon marinus) and Tasmanian devil (Sarcophilus harrisii)</p>\r\n<p style=\"text-align: justify;\">Updated to new human patch GRCh37.p5</p>\r\n<p style=\"text-align: justify;\">Updated to new cow assembly UMD 3.1</p>\r\n<p style=\"text-align: justify;\">Updated gorilla assembly to gorGor3.1</p>\r\n<p style=\"text-align: justify;\">Added SIFT and PolyPhen scores to the variation attributes.<br />RefSeq DNA now replaced by RefSeq mRNA and RefSeq ncRNA filters and attributes.<br /><br /><br /> Ensembl Variation 64:</p>\r\n<p style=\"text-align: justify;\"> </p>\r\n<p style=\"text-align: justify;\">Updated cow to dbSNP 133<br />Added SIFT and PolyPhen score filters and attributes to the human germline and somatic variation datasets.<br />Updated Human somatic variation dataset to include data from COSMIC 54</p>\r\n<p style=\"text-align: justify;\">Structural variation:</p>\r\n<p style=\"text-align: justify;\"> Source and DGVa study accession filters have been set up to allow users to </p>\r\n<p style=\"text-align: justify;\"> select the source and study they are interested in. <br /> The attribute sections have been re-organised to make them more user friendly. <br /> Variant type and Allele type attributes have been included for this release.<br /> New structural variation datasets have been added for mouse, dog and pig.<br /><br />Ensembl Regulation 64:<br /><br />EXTERNAL FEATURES sections have been renamed to OTHER REGULATORY REGIONS<br />Hyperlinks have been added to link to the regulatory build information<br />Sequence Read Archive (SRA) experiment accession has been added to the REGULATORY EVIDENCE sections in filters and attributes along with hyperlinks more information.<br /><br /><br />Vega 44:<br /><br />Human and Mouse manual annotation has been updated to represent the annotation presented in Vega release 44.</p>','','handed_over','Mart','N','N','N','N','N','N','N','N/A',2,25629,'2011-07-05 12:53:16',25629,'2011-09-08 09:45:18',1);
+INSERT INTO `changelog` VALUES (372,64,'Xref projections','<p>Gene ontology (GO) identifiers and gene names have been projected for all species including the new lamprey and Tasmanian devil species.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-07-06 07:38:01',25629,'2011-09-09 10:03:46',1);
+INSERT INTO `changelog` VALUES (373,64,'Human: gene set updated','<p>The human gene set for e64 was updated and is equivalent to GENCODE (http://www.gencodegenes.org/) version 9. Annotation from HAVANA was retrieved from the Vega database release 44 (http://vega.sanger.ac.uk/Homo_sapiens/Info/Index). This includes the ABO gene on a GRC patch that has been annotated by HAVANA as well as the completed manual annotation of chromosome 14. This release of GENCODE contains 20900 protein-coding genes. The human set also includes an updated set (May 2011) of the CCDS (http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) set of 25521 transcripts models.</p>','Note that this core database will contain the new GRC patches, hence the declaration for assembly change and the required repeat masking. These modifications have been declared by Susan already.','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','new',4,9335,'2011-07-06 09:30:09',5132,'2011-09-09 13:25:14',1);
+INSERT INTO `changelog` VALUES (374,64,'Xrefs updated','<p>Cross-references (xrefs) to external databases were updated for human, mouse, sea squirts <em>Ciona intestinalis</em> and<em> Ciona savignyi</em>, Madagascan hedgehog tenrec, Western European hedgehog, mouse lemur, platypus, bushbaby, shrew, and squirrel.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-07-06 09:32:25',5132,'2011-09-09 10:07:07',1);
+INSERT INTO `changelog` VALUES (375,64,'GENCODE RNA-Seq','','','postponed','Genebuild','N','N','N','N','N','N','N','N/A',2,5132,'2011-07-06 09:54:57',5132,'2011-08-17 15:28:04',1);
+INSERT INTO `changelog` VALUES (376,64,'Human: Vega annotation updated','<p>Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 44. Annotation by Havana of chromosome 14 has been completed.</p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2011-07-06 10:23:13',5132,'2011-09-09 13:26:29',1);
+INSERT INTO `changelog` VALUES (377,64,'Mouse: Vega annotation updated','<p>Manual annotation of mouse from Havana has been updated, including annotation of the MHC region on chromosome 17. The data represents the annotation presented in Vega release 44.</p>','','handed_over','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2011-07-06 10:24:50',5132,'2011-09-09 13:26:56',1);
+INSERT INTO `changelog` VALUES (379,64,'New Regulatory Data','<ul>\r\n<li>New Mouse MEL cell-line regulatory build, including <a href=\"http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase\">Dnase-Seq</a>, and <a href=\"http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhTfbs\">ChIP-Seq</a> for CTCF, p300, cMyb, USF2, Rad21, NELFe and Max. All data is from ENCODE, following their <a href=\"http://genome.ucsc.edu/ENCODE/terms.html\">data policies</a>.</li>\r\n<li>New Human CD4 ChIP-Seq data for CBP, p300, MOF, PCAF, Tip60, HDAC1, HDAC2, HDAC3 and HDAC6 (<a href=\"http://www.ncbi.nlm.nih.gov/pubmed?term=19698979\">Wang et al, 2009</a>). A new regulatory build was made to incorporate this data. </li>\r\n</ul>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',3,100304,'2011-07-06 15:38:07',1273,'2011-09-09 12:52:02',1);
+INSERT INTO `changelog` VALUES (380,64,'schema change','<p>is_ref will be added to the alt_allele table to show which is the reference gene.</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,23,'2011-07-06 15:40:58',23,'2011-08-19 13:40:41',1);
+INSERT INTO `changelog` VALUES (381,64,'Embl/ Genbank flat file dumps','','','declared','Core','N','N','N','N','N','N','N','N/A',2,23,'2011-07-06 15:41:36',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (382,64,'MotifFeatures: PWM Scores Rounded','<p>MotifFeature PWM scores were rounded to 3 decimal places.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1,100304,'2011-07-06 15:42:45',1273,'2011-09-09 12:54:40',1);
+INSERT INTO `changelog` VALUES (383,64,'Schema version update','<p>patch_63_64_a.sql</p>\r\n<p>update schema version to 64</p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-07-06 15:45:54',23,'2011-08-19 13:42:18',1);
+INSERT INTO `changelog` VALUES (384,64,'Mouse: cDNA alignments updated','<p>A new mouse cdna database was created for e64: The latest set of cDNAs for mouse (as of 19/Jul/2011) from the European Nucleotide Archive and NCBI RefSeq were aligned to the <br />current genome using <a title=\"Exonerate\" href=\"http://www.ebi.ac.uk/~guy/exonerate/\" target=\"_blank\">Exonerate</a>. There are 1,223 new cDNAs with a total of 15,200 new alignments for Ensembl 64.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',3,102717,'2011-07-06 15:50:21',5132,'2011-09-09 13:27:31',1);
+INSERT INTO `changelog` VALUES (385,64,'Flagging withdrawn UniProt proteins','<p>Across all species, 175 human Ensembl translations were flagged on 1193 transcripts and exons, using human e64 as reference. In addition, 193 UniProt proteins were flagged on 555 transcripts and exons, using the August release of UniProt as reference. Please see our <a title=\"Withdrawn evidence blog\" href=\"http://www.ensembl.info/blog/2011/09/06/flagging-the-removed-evidences-of-our-databases/\" target=\"_blank\">blog</a> for more details.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',1,101214,'2011-07-06 15:51:21',5132,'2011-09-09 10:00:44',1);
+INSERT INTO `changelog` VALUES (386,64,'Flagging withdrawn Ensembl proteins','<p>Flagged withdrawn human Ensembl proteins used as supporting evidence. Please see our <a title=\"Withdrawn evidence blog\" href=\"http://www.ensembl.info/blog/2011/09/06/flagging-the-removed-evidences-of-our-databases/\" target=\"_blank\">blog</a> for more details.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',1,101214,'2011-07-06 15:52:15',5132,'2011-09-09 10:24:31',1);
+INSERT INTO `changelog` VALUES (387,64,'Cow dbSNP 133 import','<p>We imported dbSNP Build 133 for cow based on the UMD_3.1 assembly.</p>\r\n<p> </p>','','handed_over','Variation','N','N','N','N','N','N','Y','patched',4,3,'2011-07-06 16:26:18',102503,'2011-09-13 15:58:38',1);
+INSERT INTO `changelog` VALUES (388,64,'LRG variant import','<p>There was an import of variation data from LRGs for CRTAP, FKBP10, LEPRE1 and PPIB. These come from an LSDB for Osteogenesis Imperfecta.</p>','','handed_over','Variation','N','N','N','N','N','N','Y','patched',2,3,'2011-07-06 16:28:08',102503,'2011-09-14 14:17:00',1);
+INSERT INTO `changelog` VALUES (389,64,'Phenotype annotations','<p>All (non-structural) somatic mutations were imported from the latest release 54 of COSMIC, increasing the number of mutations imported from 46080 in release 63 to 49692 for release 64. There have been some minor changes in COSMIC sample names. Variation data was updated with new human phenotype annotations from COSMIC, OMIM, NHGRI GWAS catalog, UniProt and EGA.</p>','','handed_over','Variation','N','N','N','N','N','N','Y','patched',2,3,'2011-07-06 16:30:16',25629,'2011-09-09 10:17:44',1);
+INSERT INTO `changelog` VALUES (390,64,'Schema changes','<ul>\r\n<li>Schema changes for structural variations \r\n<ul>\r\n<li>Add a structural_variation_feature table: store the coordinates</li>\r\n<li>Modification of the structural_variation table: remove the coordinates</li>\r\n</ul>\r\n</li>\r\n</ul>\r\n<ul>\r\n<li>Additional enum in variation source table for LSDBs</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,3,'2011-07-06 16:32:31',102503,'2011-09-13 15:56:52',1);
+INSERT INTO `changelog` VALUES (391,64,'Web display updates','<ul>\r\n<li>For the structural variation we have changed to using the same colours as NCBI.</li>\r\n<li>We added a Phenotype panel (MIM diseases + variation annotations) in the Gene section</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,3,'2011-07-06 16:34:04',3,'2011-09-14 09:16:35',1);
+INSERT INTO `changelog` VALUES (392,64,'Updated consequences for transcript alleles','<p>The variation consequences were recalculated for human and mouse as a result of changes to the gene sets.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,3,'2011-07-06 16:36:39',102503,'2011-09-13 16:00:07',1);
+INSERT INTO `changelog` VALUES (393,64,'LRG import','<p>Import of new LRG sequences </p>','','handed_over','Core','N','N','N','N','N','N','N','N/A',2,99616,'2011-07-06 16:50:32',99616,'2011-08-15 09:30:52',1);
+INSERT INTO `changelog` VALUES (394,64,'Structural variation','<ul>\r\n<li>Update structural variation data from DGVa for Human, Mouse, Dog and Pig.</li>\r\n</ul>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,102503,'2011-07-07 07:31:50',3,'2011-08-12 10:16:24',1);
+INSERT INTO `changelog` VALUES (395,64,'MicroArray Mapping','<p>Micro array mapping has been performed for those species with new assemblies or updated gene builds.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-07-07 09:43:45',1273,'2011-08-19 14:21:26',1);
+INSERT INTO `changelog` VALUES (396,64,'DNA methylation DAS tracks','<p>We have updated the set of DNA methylation DAS tracks using data for over 40 cell lines available from the ENCODE project.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',3,1273,'2011-07-07 09:48:20',1273,'2011-09-15 14:28:40',1);
+INSERT INTO `changelog` VALUES (397,64,'Pairwise alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> \r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs cow lastz alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs tasmanian devil lastz alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human haplotype alignments for high coverage blastz-net alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">pig vs cow lastz alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">opossum vs tasmanian devil lastz alignments</li>\r\n</ul>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">human vs lamprey tblat alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">lamprey vs Ciona intestinalis tblat alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">lamprey vs Danio rerio tblat alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">lamprey vs Gasterosteus aculeatus tblat alignments</li>\r\n</ul>\r\n</span></p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:07:12',96753,'2011-09-09 16:16:43',1);
+INSERT INTO `changelog` VALUES (398,64,'Multiple alignments','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">12way-mammal EPO alignments to incorporate new cow</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">19way-amniota Pecan alignments to incorporate new cow</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">35way-mammal low-coverage-EPO alignments (new cow)</li>\r\n</ul>\r\n</span></p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:08:57',96753,'2011-09-09 16:16:48',1);
+INSERT INTO `changelog` VALUES (399,64,'Syntenies','<ul>\r\n<li><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">human-cow synteny</span></li>\r\n<li><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">human-gorilla synteny<br /></span></li>\r\n<li><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">pig-cow synteny<br /></span></li>\r\n</ul>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:09:52',96753,'2011-09-09 16:16:53',1);
+INSERT INTO `changelog` VALUES (400,64,'ProteinTrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<h4 style=\"line-height: normal; font-weight: bold; font-size: 13pt; margin-top: 25px; margin-right: 0px; margin-bottom: 4px; margin-left: 0px; color: #003366; padding: 0px;\"><span style=\"color: #000000; font-weight: normal; font-size: 13px; line-height: 17px;\">GeneTrees (protein-coding) with new/updated genebuilds and assemblies</span></h4>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering using hcluster_sg</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments using MCoffee without the exon-disaligner module, or Mafft</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference including the recent \'possible_ortholog\',\'putative gene split\' and \'contiguous gene split\' exceptions</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">GeneTree stable ID mapping</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:31:54',96753,'2011-09-09 16:16:58',1);
+INSERT INTO `changelog` VALUES (401,64,'ncRNAtrees and homologies','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Classification based on Rfam model</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple sequence alignments with infernal</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using RaxML</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic reconstruction using FastTree2 and RaxML-light for very big families</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional multiple sequence alignments with Prank (w/ genomic flanks)</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Additional phylogenetic reconstruction using PhyML and NJ</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Phylogenetic tree merging using TreeBeST</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Homology inference</li>\r\n</ul>\r\n</span></p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:33:07',96753,'2011-09-09 16:17:02',1);
+INSERT INTO `changelog` VALUES (402,64,'Protein Families','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\">\r\n<h4 style=\"line-height: normal; font-weight: bold; font-size: 13pt; margin-top: 25px; margin-right: 0px; margin-bottom: 4px; margin-left: 0px; color: #003366; padding: 0px;\"><span style=\"color: #000000; font-weight: normal; font-size: 13px; line-height: 17px;\">Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa.</span></h4>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Clustering by MCL</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Multiple Sequence Alignments with MAFFT</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Family stable ID mapping</li>\r\n</ul>\r\n</span></p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:34:25',96753,'2011-09-09 16:17:08',1);
+INSERT INTO `changelog` VALUES (403,64,'Compara dumps','<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 20 way PECAN multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 20 way GERP constrained elements</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 12 way EPO multiple aligments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">EMF dumps for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">BED files for 35 way low-coverage alignments</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ProteinTrees</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">Data dumps for ncRNAtrees</li>\r\n</ul>\r\n<p> </p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:35:51',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (404,64,'API/schema changes','<p><span style=\"font-family: Helvetica, Arial, sans-serif; font-size: 13px; line-height: 17px;\"> </span></p>\r\n<ul style=\"font-size: 10pt; line-height: 13pt; list-style-type: disc;\">\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">changes in the class hierarchy (NestedSet-Member-AlignedMember) to achieve better flexibility and fight code redundancy</li>\r\n<li style=\"font-size: 10pt; line-height: 13pt; padding: 0px; margin: 0px;\">changes in the API: introduction of GeneTreeNode and GeneTreeMember classes to better represent our trees</li>\r\n</ul>\r\n<p> </p>','','handed_over','Compara','N','N','N','N','N','N','N','N/A',2,98792,'2011-07-07 14:36:47',96753,'2011-09-09 16:17:48',1);
+INSERT INTO `changelog` VALUES (405,64,'Updated assembly: Gorilla 3.1','<p>The gorilla assembly was updated from gorGor3 to gorGor3.1. This new assembly uses the the same underlying contigs, but the gaps sizes were reduced from 1000 bases to 100 bases. Genes from the e63 release (assembly gorGor3) were projected onto the updated assembly (gorGor3.1). All genes from the e63 gene set were mapped to the new assembly. A small number of features from the \'RNASeq gene\' and \'<span class=\"menu_option\">Human RefSeq/ENA cDNA</span>\' track were not mapped to the new assembly because their exons spanned across a gap that had changed size.</p>','','handed_over','Genebuild','Y','Y','Y','Y','N','N','N','new',2,5132,'2011-07-07 21:04:22',5132,'2011-09-09 13:20:06',1);
+INSERT INTO `changelog` VALUES (406,64,'Removal of ambiguous bases from Takifugu rubripes','<p>It is Ensembl policy to only allow AGCTN bases in the DNA table; ambiguous bases are not allowed and are changed to N. Therefore, the \'R\' and \'Y\' ambiguous bases on scaffold_20 were changed to \'N\' for takifugu_rubripes_core_64_4.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',1,5132,'2011-07-13 09:24:20',25629,'2011-09-09 09:53:29',1);
+INSERT INTO `changelog` VALUES (407,64,'patch_63_64_a - Schema version','<p>The schema_cersion entry in the meta table has been patched to version 64.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1,1273,'2011-07-13 09:26:00',1273,'2011-09-09 12:54:02',1);
+INSERT INTO `changelog` VALUES (408,64,'patch_63_64_b - Cell type experimental factor ontology ID','<p>The cell_type table has had an efo_id field added to represent links to the Experimental Factor Ontology.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1,1273,'2011-07-13 09:27:51',1273,'2011-09-09 12:54:19',1);
+INSERT INTO `changelog` VALUES (409,64,'patch_63_64_c - Experimental meta data','<p>A patch has been applied to add fields to capture experimental meta data e.g. archive & pubmed IDs</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',1,1273,'2011-07-13 09:28:48',1273,'2011-09-09 12:53:40',1);
+INSERT INTO `changelog` VALUES (410,64,'Updated mouse otherfeatures db: New CCDS import','<p>This release of the mouse gene set also includes 22147 transcript models as part of an updated version (May 2011) of <a href=\"http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi\">CCDS</a></p>','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',3,102717,'2011-08-01 10:18:56',25629,'2011-09-09 09:28:00',1);
+INSERT INTO `changelog` VALUES (411,64,'Update human otherfeatures db: new CCDS import','','','handed_over','Genebuild','N','N','N','N','N','N','N','patched',2,102717,'2011-08-01 10:19:26',102717,'2011-08-01 15:33:23',1);
+INSERT INTO `changelog` VALUES (412,64,'Human: updated RefSeq gene import','<p>The imported RefSeq gene set was updated in the human otherfeatures database. The RefSeq gene count increased from 23733 in e63 to 24435 in e64. Please note that RefSeq annotates gene models on cDNA sequence and not on the reference genome, meaning that when users choose to translate the RefSeq transcripts off the reference genome that the translations may contain stop codons.</p>','','handed_over','Genebuild','N','N','N','N','N','N','N','N/A',4,5132,'2011-08-05 15:57:39',5132,'2011-09-09 13:29:16',1);
+INSERT INTO `changelog` VALUES (413,64,'Corrected CTCF, Nanog, p300 and Smad1 Mouse ES ChIP-Seq datasets','<p>We identified an issue with our analysis of the CTCF, Nanog, p300 and Smad1 for the ES cell line from Chen et al., 2008. The raw reads were clipped to 26bp, re-aligned, and new peak calls were made. This correction enabled a significant increase in the number of mapped reads, making the new peaks more trustworthy.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-08-10 09:34:33',100304,'2011-08-11 16:00:24',1);
+INSERT INTO `changelog` VALUES (414,64,'New H3K36me3 Peak Calls using CCAT','<p>We have changed the peak calling method for H3K36me3 datasets. The new method uses CCAT (Xu et al, 2010), configured for histone marks and with a sliding window of 1000bp. This method has enabled an increase in the number and length of H3K36me3 calls.</p>','','handed_over','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-08-10 09:39:21',100304,'2011-08-11 16:00:56',1);
+INSERT INTO `changelog` VALUES (415,64,'Linkage_type change in ontology_xref','<p>Change to linkage_type column in table ontology_ref. Values to be tested in healthchecks.</p>\r\n<p>patch_63_64_d.sql</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,103537,'2011-08-11 10:53:29',103537,'2011-08-11 10:54:28',1);
+INSERT INTO `changelog` VALUES (416,64,'structural','<p> </p>\r\n<ul>\r\n<li>Add COSMIC structural variation data (Human). CANCELLED</li>\r\n</ul>','','cancelled','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-08-12 10:15:40',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (417,64,'User data on Multi-species view','<p>User data is now viewable on Multi-species view</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-08-12 15:01:36',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (418,64,'Configuration panel improvements','<p>A number of changes have been made to the display of the configuration panel (accessed via the \"Configure this page\" button), including a new menu structure with grouping for similar track types</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-08-12 15:04:18',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (419,64,'Configuring supporting evidence for regulatory features','<p>Configuration for regulatory evidence is now accessible via two links in the Regulation section of the menu for the configuration panel - \"Open chromatin & TFBS\" and \"Histones & polymerases\".</p>\r\n<p>From these links you can access a matrix to choose cell line and evidence type options, as well as changing the renderer for the tracks. These tracks are no longer accessible from other sections of regulation configuration.</p>\r\n<p> </p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-08-12 15:21:20',97803,'2011-08-17 15:59:33',1);
+INSERT INTO `changelog` VALUES (420,64,'Auto-resizing images','<p>If you set image width to be \"best fit\", the images will now resize to fit inside the browser window when it is resized</p>','','handed_over','Web','N','N','N','N','N','N','N','N/A',2,97803,'2011-08-17 16:01:47',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (422,64,'New phenotype page','<p>New phenotype page added - see <a title=\"Human phenotype page\" href=\"http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000182533;r=3:8775161-8776161\" target=\"_self\">here</a> for human CAV3. Let us know what you think at helpdesk@ensembl.org.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',3,5132,'2011-09-09 10:43:18',102503,'2011-09-13 15:58:07',1);
+INSERT INTO `changelog` VALUES (423,64,'New LRG alignments','<p>New LRG alignments added - see <a title=\"LRG alignment\" href=\"http://www.ensembl.org/Homo_sapiens/LRG/Differences?lrg=LRG_53\" target=\"_self\">here</a> for an example on LRG_53.</p>','','handed_over','Variation','N','N','N','N','N','N','N','N/A',2,5132,'2011-09-09 10:46:46',102503,'2011-09-13 15:58:21',1);
+INSERT INTO `changelog` VALUES (424,65,'Ensembl 65 mart databases','<p>Full build of all 7 marts for all species</p>','','declared','Mart','N','N','N','N','N','N','N','N/A',2,25629,'2011-09-27 09:51:07',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (425,65,'Xref projections','<p>Gene ontology (GO) identifiers and gene names will be projected for all species. Modify Modify projection code to replace UniProt IDs with display labels where applicable.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-09-27 09:52:39',25629,'2011-09-30 10:33:21',1);
+INSERT INTO `changelog` VALUES (426,65,'Mouse cDNA update','<p>New cDNA db for mouse.</p>','','declared','Genebuild','N','N','N','N','N','N','N','new',2,102717,'2011-09-27 09:58:22',102717,'2011-10-10 12:25:54',1);
+INSERT INTO `changelog` VALUES (427,65,'New Chimpanzee assembly','<p>The first genebuild on new Chimpanzee assembly CHIMP2.1.4.</p>','','declared','Genebuild','Y','Y','Y','N','N','N','Y','new',2,102717,'2011-09-27 10:58:09',102717,'2011-09-27 10:58:36',1);
+INSERT INTO `changelog` VALUES (428,65,'LRG Import','<p>Import of new LRG sequences</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,97804,'2011-09-27 10:58:44',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (429,65,'Retrieval of a Transcript\'s Gene','<p>Support has been added to retrieve the <tt>Bio::EnsEMBL::Gene</tt> from an instance of <tt>Bio::EnsEMBL::Transcript</tt>.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',1,97804,'2011-09-27 12:43:28',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (430,65,'Support for Slice Retrieval by a Location String','<p><tt>Bio::EnsEMBL::DBSQL::SliceAdaptor</tt> can retrieve a Slice for a toplevel location string</p>','','declared','Core','N','N','N','N','N','N','N','N/A',1,97804,'2011-09-27 12:45:02',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (431,65,'Memory leak fixes','<p>A number of leaks have been found & fixed in the Ensembl API caused by circular references and unintentional object usage.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,97804,'2011-09-27 12:48:37',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (432,65,'Schema change; new enum for xref.info_type','<p>The enum field <tt>`xref`.`info_type`</tt> has been given a new value called <tt>CHECKSUM</tt> to support xrefs assigned on the basis of a checksum mapping.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,97804,'2011-09-27 13:11:21',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (433,65,'New bushbaby assembly','<p>The bushbaby gene annotation in e65 is based on the high coverage assembly OtoGar3 provided by the Broad Institute.</p>\r\n<p>The gene set for bushbaby was generated using bushbaby and primate proteins as well as human ensembl translations.</p>\r\n<p>The final gene set consists of 19506 protein_coding genes, 1151 pseudogenes and 7276 ncRNAs.</p>\r\n<p>More detailled information can be found <a title=\"Bushbaby home page\" href=\"http://www.ensembl.org/Otolemur_garnettii/Info/Index\" target=\"_blank\">here</a>.</p>','','handed_over','Genebuild','Y','Y','Y','N','Y','N','Y','new',2,97245,'2011-09-27 13:47:13',97245,'2011-09-27 14:08:04',1);
+INSERT INTO `changelog` VALUES (434,65,'Human cdna update','<p>Cdna alignments for human using the most up-to-date set of cDNAs from the European Nucleotide Archive and NCBI RefSeq</p>','','declared','Genebuild','N','Y','N','N','N','N','N','new',2,97245,'2011-09-27 13:53:06',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (435,65,'MT annotation for anole, elephant, panda, rabbit and turkey','<p>MT sequences have been added to the main assembly.</p>\r\n<p>Annotation for those sequences has also been provided</p>','The main gene set has not changed but 13 genes located on the MT chromosome have been added','handed_over','Genebuild','Y','Y','N','N','N','N','N','patched',2,97245,'2011-09-27 13:55:16',97245,'2011-10-03 10:39:48',1);
+INSERT INTO `changelog` VALUES (436,65,'Flagging obsolete Uniprot proteins','<p>Flagging obsolete Uniprot proteins used as supporting evidence for the transcripts and the exons</p>','','declared','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-09-27 14:09:24',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (437,65,'Flagging obsolete Ensembl proteins','<p>Flagging obsolete Human Ensembl proteins used as supporting evidence for the transcripts and the exons</p>','','declared','Genebuild','N','N','N','N','N','N','N','N/A',2,101214,'2011-09-27 14:10:18',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (438,65,'New species: Atlantic cod','<p>The Atlantic cod (Gadus morhua) has been added to Ensembl. The genebuild involved a combination of annotation approaches: the standard genebuild procedure and whole-genome alignment and projection from stickleback.</p>','Delete from Pre site on e65 release day','handed_over','Genebuild','Y','Y','Y','N','N','N','N','new',2,5132,'2011-09-28 09:45:03',5132,'2011-10-08 19:51:26',1);
+INSERT INTO `changelog` VALUES (439,65,'Merge of stable_id tables with their object tables','<p>patch_64_65_b.sql</p>\r\n<p>Schema patch to merge stable_id tables with exon, gene, operon, operon_transcript, translation and transcript tables</p>\r\n<p>Changes to the core API, stable_id mapping scripts, xref_mapping, test modules.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',4,103537,'2011-09-28 10:00:01',97804,'2011-09-29 10:15:43',1);
+INSERT INTO `changelog` VALUES (440,65,'Region Report tool','<p>A new tool plus supporting libraries for creating summaries of requested chromosomal regions.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,103988,'2011-09-28 10:51:26',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (441,65,'Analyses updates','<p>Update in logic_names and descriptions for a more consistent system across species</p>','The production database is being updated to standardize some logic names and update some analyses\' descriptions\r\nThe changes will be propagated by the populate_analysis_description script\r\nIt should only affect logic names and descriptions','declared','Genebuild','N','N','N','N','N','N','N','patched',1,97245,'2011-09-28 13:09:07',97245,'2011-09-28 13:11:52',1);
+INSERT INTO `changelog` VALUES (442,65,'Pfam version numbers removed','<p>Pfam hit names have versions which will be removed</p>','only hit names in the protein feature table will be updated to remove the version number','handed_over','Genebuild','N','N','N','N','N','N','N','patched',1,97245,'2011-09-28 13:11:27',97245,'2011-10-10 11:49:00',1);
+INSERT INTO `changelog` VALUES (443,65,'Assembly name update','<p>Assembly name for lamprey changed from Petromyzon_marinus_7.0 to Pmarinus_7.0</p>','current assembly name is being truncated by web, going for a shorter version','handed_over','Genebuild','N','N','N','N','N','N','N','patched',1,97245,'2011-09-28 13:13:54',97245,'2011-10-10 11:49:29',1);
+INSERT INTO `changelog` VALUES (444,65,'Remove 2-micron plasmid from S.cerevisiae assembly','','contact: arnaud@ebi.ac.uk','handed_over','EnsemblGenomes','Y','Y','N','N','Y','N','N','new',2,101255,'2011-09-28 15:10:11',101255,'2011-10-10 11:10:10',1);
+INSERT INTO `changelog` VALUES (445,65,'Updated otherfeatures db to reflect assembly change','','contact: arnaud@ebi.ac.uk','handed_over','EnsemblGenomes','Y','N','N','N','N','N','N','N/A',2,101255,'2011-09-28 15:11:24',101255,'2011-10-10 11:10:32',1);
+INSERT INTO `changelog` VALUES (446,65,'Updated funcgen db to reflect assembly change','','contact: arnaud@ebi.ac.uk','declared','EnsemblGenomes','Y','Y','N','N','N','N','N','N/A',2,101255,'2011-09-28 15:12:24',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (447,65,'Updated variation db to reflect assembly change','','contact: arnaud@ebi.ac.uk','declared','EnsemblGenomes','Y','Y','N','N','N','N','N','N/A',2,101255,'2011-09-28 15:13:21',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (448,65,'Update human otherfeatures db: new CCDS import','<pre>Update to CCDS set for human</pre>','','declared','Genebuild','N','Y','N','N','N','N','N','patched',2,102717,'2011-09-28 15:19:47',102717,'2011-09-29 09:45:20',1);
+INSERT INTO `changelog` VALUES (449,65,'Updated mouse otherfeatures db: New CCDS import','<pre>Update to CCDS set for mouse</pre>','There is no update to the mouse core database this release therefore we will no update the CCDS models. This is a GENCODE requirement.','postponed','Genebuild','N','Y','N','N','N','N','N','patched',2,102717,'2011-09-28 15:20:32',102717,'2011-10-10 12:26:18',1);
+INSERT INTO `changelog` VALUES (450,65,'Data file support in scheme','<p>A new API and database structure for the storage of large datafile locations and the retrieval of said datafiles.</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,97804,'2011-09-28 16:12:15',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (451,65,'Projection of annotation to GRC assembly patches','<p>Annotation from the primary assembly is projected to the assembly patches. The projected annotation is then supplemented with annotation based on evidence alignment. This annotation is stored in the human otherfeatures database.</p>','','declared','Genebuild','N','N','N','Y','N','N','N','patched',2,14183,'2011-09-29 09:38:22',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (452,65,'Zebrafish VEGA Merge','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 13px;\">Manual annotation of zebrafish from Vega has been updated. </span><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 13px;\"> This represents the annotation presented in Vega release 45. </span></p>','','declared','Genebuild','N','Y','N','N','N','N','N','new',2,29,'2011-09-29 09:56:41',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (453,65,'Zebrafish Markers','<p>Zebrafish SATMAP markers have been given a separate track so they can be easily distinguished from the other markers.</p>','','declared','Genebuild','N','N','N','N','N','N','N','N/A',2,29,'2011-09-29 09:59:12',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (454,65,'MT annotation for Tasmanian Devil','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 13px;\">\r\n<p style=\"font-size: 1em; padding: 0px; margin: 0px;\">MT sequences have been added to the main assembly.</p>\r\n<p style=\"font-size: 1em; padding: 0px; margin: 0px;\">Annotation for those sequences has also been provided</p>\r\n</span></p>','','declared','Genebuild','N','Y','N','N','N','N','N','patched',2,29,'2011-09-29 10:01:50',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (455,65,'Structural variations','<p>Updates data and adds new studies</p>','','declared','Variation','N','N','N','N','N','N','N','N/A',3,102503,'2011-09-29 10:10:54',102503,'2011-09-29 10:20:03',1);
+INSERT INTO `changelog` VALUES (456,65,'Human dbSNP 134 import','<p>Imports of the dbSNP Build 134 for human.</p>\r\n<p> </p>\r\n<p>Import new data types:</p>\r\n<ul>\r\n<li>Global minor allele frequencies</li>\r\n<li>Clinical significance</li>\r\n<li>Suspect variants (will be failed with a new reason code)</li>\r\n</ul>\r\n<div style=\"color: #000000; font-family: Verdana, Arial, Helvetica, sans-serif; font-size: 10px; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: #ffffff; background-position: initial initial; background-repeat: initial initial; margin: 8px;\">\r\n<p> </p>\r\n</div>\r\n<p> </p>','','declared','Variation','N','N','N','N','N','N','Y','N/A',4,102503,'2011-09-29 10:12:28',102503,'2011-09-30 15:29:25',1);
+INSERT INTO `changelog` VALUES (457,65,'Phenotype annotations','<p>Updates from the following sources:</p>\r\n<ul>\r\n<li>NHGRI GWAS catalog</li>\r\n<li>EGA</li>\r\n<li>OMIM</li>\r\n<li>UniProt</li>\r\n</ul>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,102503,'2011-09-29 10:15:07',102503,'2011-09-29 10:15:59',0);
+INSERT INTO `changelog` VALUES (458,65,'Phenotype annotations','<p>Updates from the following sources:</p>\r\n<ul>\r\n<li>NHGRI GWAS catalog</li>\r\n<li>EGA</li>\r\n<li>OMIM</li>\r\n<li>UniProt</li>\r\n</ul>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,102503,'2011-09-29 10:17:11',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (459,65,'Remapping Chimpanzee variations','<p>Remaps the chimp variations to the new assembly (CHIMP2.1.4).</p>','','declared','Variation','N','N','N','N','N','N','Y','N/A',3,102503,'2011-09-29 10:19:30',102503,'2011-09-30 15:29:41',1);
+INSERT INTO `changelog` VALUES (460,65,'New Human Regulation Build','<ul>\r\n<li>150 New ChIP-Seq and Dnase-Seq datasets from ENCODE \r\n<ul>\r\n<li>Including 3 new cell lines: HMEC, HSMM, NH-A</li>\r\n<li>Including 4 new Transcription Factors with available Jaspar PWMs: \r\n<ul>\r\n<li>FoxA1: MA0148.1</li>\r\n<li>FoxA2: MA0047.1; MA0047.2; PB0015.1;</li>\r\n<li>HNF4A: MA0114.1; PB0030.1; PB0134.1</li>\r\n<li>MEF2C: MA0005.1</li>\r\n</ul>\r\n</li>\r\n</ul>\r\n</li>\r\n<li>K562b sets are now part of the K562 regulatory build</li>\r\n<li>H3K27me3 sets are now built using CCAT, like H3K36me3 </li>\r\n<li>Some sets were deprecated: \r\n<ul>\r\n<li>K562 Nfya and Nfyb were deprecated in ENCODE</li>\r\n<li>HepG2 PolII, Srebp1, Srebp2 were removed from the HepG2 regulatory build as these experiments are annotated with treatments. </li>\r\n</ul>\r\n</li>\r\n</ul>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',3,100304,'2011-09-29 10:24:18',100304,'2011-10-10 08:20:00',1);
+INSERT INTO `changelog` VALUES (461,65,'New Mouse Regulatory Build','<ul>\r\n<li>H3K4me3, Oct4, Rbbp5, Wdr5 ChIP-Seq for ES cell-line from Ang et al. (2011)</li>\r\n<li>H3K4me4 ChIP-Seq for MEL cell-line, from ENCODE</li>\r\n</ul>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-09-29 10:31:57',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (462,65,'Schema changes','<p>Changes in the structural variation tables:</p>\r\n<ul>\r\n<li>Added features for the supporting evidences</li>\r\n<li>Merged the structural_variation and supporting_structural_variation tables</li>\r\n<li>Added phenotype and sample information</li>\r\n<li>Added a failed_structural_variation table</li>\r\n<li>Created a table to link the structural variants to their supporting evidences</li>\r\n</ul>\r\n<p>Changes in the genotype tables: rebuilt most of the genotype tables</p>\r\n<p> </p>\r\n<p>Changes to support the new data from dbSNP (currently under design).</p>\r\n<p> </p>','','declared','Variation','N','N','N','N','N','N','N','patched',4,102503,'2011-09-29 10:43:41',102503,'2011-09-30 15:28:52',1);
+INSERT INTO `changelog` VALUES (463,65,'Database schema patches','<ul>\r\n<li>patch_64_65_a: schema version update</li>\r\n<li>patch_64_65_b: Add analysis_id to feature_type to support SegmentationFeature states</li>\r\n<li>patch_64_65_c: add hermaphrodite as a gender</li>\r\n<li>patch_64_65_d: add SegmentationFeature table for the new Segmentation tracks</li>\r\n<li>patch_64_65_e: force regulatory_attribute type to be either \'motif\' or \'annotated\'</li>\r\n<li>patch_64_65_f: Add segmentation as an input_set type</li>\r\n</ul>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',1,100304,'2011-09-29 10:46:42',100304,'2011-09-29 13:34:17',1);
+INSERT INTO `changelog` VALUES (464,65,'Updated Microarray Probe Mappings','<p>Microarray Probe mappings will be updated for species with new assembly or gene build.</p>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-09-29 13:22:51',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (465,65,'Reorganized and Updated documentation','<p>Documentation regarding Regulation data, sources and methodology was reorganized and updated.</p>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',2,100304,'2011-09-29 13:38:50',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (466,65,'external database references','<p><!--StartFragment-->\r\n<p class=\"MsoNormal\"><span style=\"font-size: 10.0pt; font-family: Verdana; mso-bidi-font-family: Verdana;\" lang=\"EN-US\">Human, Mouse, Pig, Ciona Intestinalis, Cow, Pig, Platypus, Chick, Dog, Horse, Tetraodon external database references have been updated.</span><span lang=\"EN-US\"></span></p>\r\n<!--EndFragment--></p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,23,'2011-09-29 14:53:12',103537,'2011-10-03 10:31:58',1);
+INSERT INTO `changelog` VALUES (467,65,'Ancestral alleles','<p>Added ancestral alleles using Compara alignments</p>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,102503,'2011-09-29 15:09:54',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (468,65,'Import COSMIC release 55','<p>Import COSMIC\'s latest release</p>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,101213,'2011-09-29 15:22:11',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (469,65,'New data from dbSNP','<p>Import new data from dbSNP 134:</p>\r\n<p>- Global minor allele frequencies</p>\r\n<p>- Clinical significance</p>\r\n<p>- Suspect variants (will be failed with a new reason code)</p>\r\n<p> </p>\r\n<p>Schema changes to support this data (currently under design)</p>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,101213,'2011-09-29 15:25:07',101213,'2011-09-29 15:39:19',0);
+INSERT INTO `changelog` VALUES (470,65,'Update to Ensembl-Havana GENCODE gene set (release 10)','<p>Updated Ensembl-Havana gene set (GENCODE release 10) based on updated Ensembl gene set and latest Havana gene annotation.</p>\r\n<p> </p>','','declared','Genebuild','N','Y','N','Y','N','N','N','new',4,9335,'2011-09-29 15:25:17',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (471,65,'Protein function predictions for new human genes','<p>We will do an \'update\' run of the protein function prediction pipeline to compute predictions for new and updated human transcripts.</p>\r\n<p> </p>\r\n<p>We will also attempt a complete new run using Compara alignments in place of SIFT and PolyPhen\'s own alignment pipelines, depending on how this goes we may release this set or the update set described above.</p>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,101213,'2011-09-29 15:28:27',101213,'2011-09-29 15:33:41',1);
+INSERT INTO `changelog` VALUES (472,65,'Vega human annotation updated','<p>Manual annotation of human from Havana has been updated. The data represent the annotation presented in Vega release 45.</p>','','declared','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2011-09-29 16:05:16',161,'2011-09-29 16:07:47',1);
+INSERT INTO `changelog` VALUES (473,65,'Vega zebrafish annotation updated','<p>Manual annotation of zebrafish from Havana has been updated. The data represent the annotation presented in Vega release 45.</p>','','declared','Genebuild','N','Y','N','N','N','N','N','new',2,161,'2011-09-29 16:06:54',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (474,65,'Karyotype bands for patches','<p>Store karyoptype bands on the patches so they can be displayed in the browser.</p>','','declared','Genebuild','N','N','N','N','N','N','N','patched',2,14183,'2011-09-29 16:58:55',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (475,65,'Splicing events','<p>Install code to run the alternative splicing events prediction pipeline and update the splicing event data for the species listed below. This is a legacy from the former ASD/ATD and ASTD EC projects hosted at the EBI.<br />ASTD computationally predicted genes in a similar way as Ensembl do every release with a focus on alternative mRNA<br />structures (splicing events, poly(A) sites, TSS) and features (ppt, exon-exon junction types)<br /><br />Since 2010, the storage and display of the alternative information is now an entire part of Ensembl for the following species:<br /> - Homo sapiens,<br /> - Mus musculus,<br /> - Rattus norvegicus,<br /> - Danio rerio,<br /> - Caenorhabditis elegans,<br /> - Drosophila melanogaster</p>','','declared','Core','N','N','N','N','N','N','N','N/A',2,25629,'2011-09-30 10:40:18',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (476,65,'Updated Drosophila melanogaster gene models','<p><span style=\"color: #555555; font-family: \'Luxi Sans\', Helvetica, Arial, Geneva, sans-serif; font-size: 13px;\">FlyBase gene models based on release 5.39 (FB2011_07)</span></p>','','declared','EnsemblGenomes','N','Y','Y','N','Y','N','Y','new',2,98587,'2011-09-30 16:03:18',98587,'2011-10-04 14:24:33',0);
+INSERT INTO `changelog` VALUES (477,65,'Pairwise alignments','<p> </p>\r\n<ul>\r\n<li>[ ] human vs chimpanzee LastZ alignments</li>\r\n<li>[ ] human vs bushbaby LastZ alignments</li>\r\n<li>[ ] cod vs Danio rerio LastZ alignments</li>\r\n<li>[ ] cod vs stickleback LastZ alignments</li>\r\n</ul>\r\n<ul>\r\n<li>[ ] human vs cod Translated Blat alignments</li>\r\n</ul>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:16:03',98792,'2011-09-30 17:30:10',1);
+INSERT INTO `changelog` VALUES (478,65,'Multiple alignments','<ul>\r\n<li>[ ] 6way-primate epo alignments to incorporate new chimpanzee </li>\r\n<li>[ ] 12way-mammal-epo alignments to incorporate new chimpanzee</li>\r\n<li>[ ] 19way-amniota-pecan alignments to incorporate new chimpanzee</li>\r\n<li>[ ] 35way-mammal low-coverage-epo alignments (new chimpanzee and bushbaby)</li>\r\n<li>[ ] 6way-fish-epo alignments (addition of cod)</li>\r\n</ul>\r\n<h4><a name=\"Intentionsforrelease65-Syntenies\"></a></h4>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:16:56',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (479,65,'update variation predictions','','','declared','Variation','N','N','N','N','N','N','N','N/A',2,3,'2011-09-30 16:17:22',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (480,65,'Syntenies','<p>[ ] human chimpanzee synteny</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:17:27',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (481,65,'ProteinTrees and homologies','<p>GeneTrees (protein-coding) with new/updated genebuilds and assemblies</p>\r\n<ul>\r\n<li>Clustering using hcluster_sg</li>\r\n<li>Multiple sequence alignments using MCoffee or Mafft</li>\r\n<li>Phylogenetic reconstruction using TreeBeST</li>\r\n<li>Homology inference</li>\r\n<li>Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues)</li>\r\n<li>GeneTree stable ID mapping</li>\r\n</ul>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:17:49',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (482,65,'ncRNAtrees and homologies','<ul>\r\n<li>Classification based on Rfam model</li>\r\n<li>Multiple sequence alignments with infernal</li>\r\n<li>Phylogenetic reconstruction using RaxML</li>\r\n<li>Phylogenetic reconstruction using FastTree2 and RaxML-light for very big families</li>\r\n<li>Additional multiple sequence alignments with Prank (w/ genomic flanks)</li>\r\n<li>Additional phylogenetic reconstruction using PhyML and NJ</li>\r\n<li>Phylogenetic tree merging using TreeBeST</li>\r\n<li>Homology inference</li>\r\n</ul>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:18:17',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (483,65,'Protein Families','<p>Updated MCL families including all Ensembl transcript isoforms (including human non-reference haplotypes) and newest Uniprot Metazoa.</p>\r\n<ul>\r\n<li>Clustering by MCL</li>\r\n<li>Multiple Sequence Alignments with MAFFT</li>\r\n<li>Family stable ID mapping</li>\r\n</ul>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:19:46',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (484,65,'Compara dumps','<ul>\r\n<li>[ ] EMF dumps for 19 way PECAN multiple aligments</li>\r\n<li>[ ] BED files for 19 way GERP constrained elements</li>\r\n<li>[ ] EMF dumps for 12 way EPO multiple aligments</li>\r\n<li>[ ] EMF dumps for 6way EPO multiple alignments</li>\r\n<li>[ ] EMF dumps for 35 way low-coverage alignments</li>\r\n<li>[ ] BED files for 35 way low-coverage alignments</li>\r\n<li>[ ] EMF dumps for 6way EPO fish multiple alignments</li>\r\n<li>[ ] BED dumps for 6way EPO fish multiple alignments</li>\r\n<li>[ ] Data dumps for ProteinTrees</li>\r\n<li>[ ] Data dumps for ncRNAtrees</li>\r\n<li>[ ] OrthoXML dumps for ProteinTrees</li>\r\n<li>[ ] OrthoXML dumps for ncRNAtrees</li>\r\n<li>[ ] maybe PhyloXML dumps for ProteinTrees ?</li>\r\n<li>[ ] maybe PhyloXML dumps for ncRNAtrees ?</li>\r\n<li>[ ] Ancestral sequences for primates</li>\r\n</ul>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:20:22',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (485,65,'API/schema changes','<p>[ ] changes in the schema: adding a new \"header\" table for a tree root, moving general properties of the tree into that table (including protein_tree_stable_id)</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:21:39',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (486,65,'API/schema changes','<p>[ ] changes in the schema: adding tables for tree\'s properties and node\'s properties to make tag storage and extraction more efficient</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:22:01',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (487,65,'API/schema changes','<p>[ ] changes in the schema: keeping the super-tree structures in protein_tree_node (thus removing all the super_protein_tree_* tables)</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:22:20',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (488,65,'API/schema changes','<p>[ ] left_index and right_index now start from 1 for every tree. This should avoid the deadlocks on lr_index_offset</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:22:41',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (489,65,'API/schema changes','<p>[ ] clever usage of partitions for the peptide_align_features_* tables</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:22:57',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (490,65,'API/schema changes','<p>[ ] bugfix: Storing several lost_taxon_id for each node</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:23:13',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (491,65,'API/schema changes','<p>[ ] rationalise the use of tags in protein_tree_tag:</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:23:25',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (492,65,'API/schema changes','<p>[ ] Families and Homologies should consist of AlignedMembers, not of Member-Attribute pairs ??</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:23:42',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (493,65,'API/schema changes','<p>[ ] DnaFragRegion and SyntenyRegion should not be inheriting from NestedSet ??</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:23:55',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (494,65,'API/schema changes','<p>[ ] Having a base class \"AlignedMemberSet\" for Family, Homology, ProteinTree with methods like getAllMembers, getSimpleAlign, etc ??</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:24:07',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (495,65,'Web','<p>[ ] Statistics of protein trees and homologies on the web (either static files, or dynamic page + table)</p>\r\n<h3><a name=\"Intentionsforrelease65-Web\"></a></h3>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:24:27',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (496,65,'Web','<p>[ ] OrthoXML export function (for any gene tree)</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:24:40',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (497,65,'Web','<p>[ ] Tree support information (which ones of the 5 initial trees are supporting the current node) (+corresponding field in the schema)</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:24:53',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (498,65,'Web','<p>[ ] Information about lost taxa</p>','','declared','Compara','N','N','N','N','N','N','N','N/A',2,104596,'2011-09-30 16:25:06',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (499,65,'LRG variation','<p>Submitted variation data for genes DMD (LRG_199) and CYBB (LRG_53)</p>','','declared','Variation','N','N','N','N','N','N','N','N/A',2,104595,'2011-10-03 13:00:33',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (500,65,'Experiment View','<p>An Experiment view has been developed to improve access and visualisation of experimental meta data. This will include archive IDs and source projects used as input for the Human and Mouse Regulatory builds.</p>','','declared','Funcgen','N','N','N','N','N','N','N','N/A',2,1273,'2011-10-04 14:25:37',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (501,65,'Updated Drosophila melanogaster gene models','<p>\r\n<p class=\"p1\">FlyBase gene models based on release 5.39 (FB2011_07)</p>\r\n<p class=\"p1\">Regulation database will be updated</p>\r\n<p class=\"p1\">Variation database will be updated</p>\r\n</p>','','declared','EnsemblGenomes','N','Y','Y','N','Y','N','N','new',2,98587,'2011-10-04 14:26:23',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (502,65,'Updated Drosophila melanogaster Regulation database','<p>Regulation database updated to reflect new gene models.</p>','','declared','EnsemblGenomes','N','Y','Y','N','Y','N','N','new',2,98587,'2011-10-04 14:47:15',NULL,NULL,1);
+INSERT INTO `changelog` VALUES (503,65,'Updated Drosophila melanogaster Variation database','<p>Variation database updated to reflect transcript model changes.</p>','','declared','EnsemblGenomes','N','Y','Y','N','N','N','N','new',2,98587,'2011-10-04 14:48:29',NULL,NULL,1);
--
-- Table structure for table `changelog_species`
@@ -3848,6 +3938,67 @@ INSERT INTO `changelog_species` VALUES (413,27);
INSERT INTO `changelog_species` VALUES (414,21);
INSERT INTO `changelog_species` VALUES (414,27);
INSERT INTO `changelog_species` VALUES (416,21);
+INSERT INTO `changelog_species` VALUES (421,8);
+INSERT INTO `changelog_species` VALUES (426,27);
+INSERT INTO `changelog_species` VALUES (427,34);
+INSERT INTO `changelog_species` VALUES (428,21);
+INSERT INTO `changelog_species` VALUES (433,33);
+INSERT INTO `changelog_species` VALUES (434,21);
+INSERT INTO `changelog_species` VALUES (435,1);
+INSERT INTO `changelog_species` VALUES (435,22);
+INSERT INTO `changelog_species` VALUES (435,31);
+INSERT INTO `changelog_species` VALUES (435,51);
+INSERT INTO `changelog_species` VALUES (435,52);
+INSERT INTO `changelog_species` VALUES (438,0);
+INSERT INTO `changelog_species` VALUES (442,2);
+INSERT INTO `changelog_species` VALUES (442,27);
+INSERT INTO `changelog_species` VALUES (442,34);
+INSERT INTO `changelog_species` VALUES (443,55);
+INSERT INTO `changelog_species` VALUES (444,39);
+INSERT INTO `changelog_species` VALUES (445,39);
+INSERT INTO `changelog_species` VALUES (446,39);
+INSERT INTO `changelog_species` VALUES (447,39);
+INSERT INTO `changelog_species` VALUES (448,21);
+INSERT INTO `changelog_species` VALUES (449,27);
+INSERT INTO `changelog_species` VALUES (451,21);
+INSERT INTO `changelog_species` VALUES (452,10);
+INSERT INTO `changelog_species` VALUES (453,10);
+INSERT INTO `changelog_species` VALUES (454,56);
+INSERT INTO `changelog_species` VALUES (455,5);
+INSERT INTO `changelog_species` VALUES (455,21);
+INSERT INTO `changelog_species` VALUES (455,27);
+INSERT INTO `changelog_species` VALUES (455,42);
+INSERT INTO `changelog_species` VALUES (456,21);
+INSERT INTO `changelog_species` VALUES (457,21);
+INSERT INTO `changelog_species` VALUES (458,21);
+INSERT INTO `changelog_species` VALUES (459,34);
+INSERT INTO `changelog_species` VALUES (460,21);
+INSERT INTO `changelog_species` VALUES (461,27);
+INSERT INTO `changelog_species` VALUES (467,34);
+INSERT INTO `changelog_species` VALUES (467,35);
+INSERT INTO `changelog_species` VALUES (468,21);
+INSERT INTO `changelog_species` VALUES (469,21);
+INSERT INTO `changelog_species` VALUES (470,21);
+INSERT INTO `changelog_species` VALUES (471,21);
+INSERT INTO `changelog_species` VALUES (472,21);
+INSERT INTO `changelog_species` VALUES (473,10);
+INSERT INTO `changelog_species` VALUES (474,21);
+INSERT INTO `changelog_species` VALUES (475,3);
+INSERT INTO `changelog_species` VALUES (475,10);
+INSERT INTO `changelog_species` VALUES (475,13);
+INSERT INTO `changelog_species` VALUES (475,21);
+INSERT INTO `changelog_species` VALUES (475,27);
+INSERT INTO `changelog_species` VALUES (475,38);
+INSERT INTO `changelog_species` VALUES (476,13);
+INSERT INTO `changelog_species` VALUES (479,10);
+INSERT INTO `changelog_species` VALUES (479,21);
+INSERT INTO `changelog_species` VALUES (479,27);
+INSERT INTO `changelog_species` VALUES (499,21);
+INSERT INTO `changelog_species` VALUES (500,21);
+INSERT INTO `changelog_species` VALUES (500,27);
+INSERT INTO `changelog_species` VALUES (501,13);
+INSERT INTO `changelog_species` VALUES (502,13);
+INSERT INTO `changelog_species` VALUES (503,13);
--
-- Table structure for table `db`
@@ -3874,6 +4025,379 @@ SET character_set_client = @saved_cs_client;
--
-- ORDER BY: `db_id`
+INSERT INTO `db` VALUES (1,21,0,'coreexpressionest','59',37,'d','ens-staging2');
+INSERT INTO `db` VALUES (2,21,0,'coreexpressiongnf','59',37,'d','ens-staging2');
+INSERT INTO `db` VALUES (3,21,0,'variation','60',37,'e','ens-staging1');
+INSERT INTO `db` VALUES (4,50,0,'otherfeatures','60',41,'q','ens-staging2');
+INSERT INTO `db` VALUES (5,13,0,'variation','60',525,'b','ens-staging1');
+INSERT INTO `db` VALUES (6,29,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (7,24,0,'core','60',1,'c','ens-staging1');
+INSERT INTO `db` VALUES (8,37,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (9,21,0,'core','60',37,'e','ens-staging1');
+INSERT INTO `db` VALUES (10,5,0,'core','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (11,33,0,'core','60',1,'h','ens-staging2');
+INSERT INTO `db` VALUES (12,2,0,'funcgen','60',4,'i','ens-staging1');
+INSERT INTO `db` VALUES (13,42,0,'funcgen','60',9,'d','ens-staging2');
+INSERT INTO `db` VALUES (14,47,0,'core','60',1,'i','ens-staging2');
+INSERT INTO `db` VALUES (15,4,0,'otherfeatures','60',321,'b','ens-staging1');
+INSERT INTO `db` VALUES (16,43,0,'otherfeatures','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (17,44,0,'core','60',4,'n','ens-staging2');
+INSERT INTO `db` VALUES (18,46,0,'core','60',8,'e','ens-staging2');
+INSERT INTO `db` VALUES (19,21,0,'cdna','60',37,'e','ens-staging1');
+INSERT INTO `db` VALUES (20,22,0,'core','60',3,'c','ens-staging1');
+INSERT INTO `db` VALUES (21,40,0,'core','60',1,'h','ens-staging2');
+INSERT INTO `db` VALUES (22,32,0,'core','60',1,'l','ens-staging2');
+INSERT INTO `db` VALUES (23,38,0,'core','60',34,'b','ens-staging2');
+INSERT INTO `db` VALUES (24,2,0,'core','60',4,'i','ens-staging1');
+INSERT INTO `db` VALUES (25,30,0,'otherfeatures','60',1,'n','ens-staging2');
+INSERT INTO `db` VALUES (26,4,0,'core','60',321,'b','ens-staging1');
+INSERT INTO `db` VALUES (27,9,0,'core','60',2,'k','ens-staging1');
+INSERT INTO `db` VALUES (28,32,0,'otherfeatures','60',1,'l','ens-staging2');
+INSERT INTO `db` VALUES (29,21,0,'coreexpressionest','60',37,'e','ens-staging2');
+INSERT INTO `db` VALUES (30,7,0,'core','60',1,'d','ens-staging1');
+INSERT INTO `db` VALUES (31,25,0,'core','60',1,'e','ens-staging2');
+INSERT INTO `db` VALUES (32,45,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (33,27,0,'vega','60',37,'m','ens-staging2');
+INSERT INTO `db` VALUES (34,5,0,'otherfeatures','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (35,15,0,'variation','60',2,'g','ens-staging1');
+INSERT INTO `db` VALUES (36,3,0,'funcgen','60',210,'b','ens-staging1');
+INSERT INTO `db` VALUES (37,34,0,'core','60',21,'o','ens-staging2');
+INSERT INTO `db` VALUES (38,21,0,'vega','60',37,'e','ens-staging1');
+INSERT INTO `db` VALUES (39,18,0,'variation','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (40,50,0,'funcgen','60',41,'q','ens-staging2');
+INSERT INTO `db` VALUES (41,10,0,'core','60',9,'','ens-staging1');
+INSERT INTO `db` VALUES (42,11,0,'core','60',2,'d','ens-staging1');
+INSERT INTO `db` VALUES (43,9,0,'otherfeatures','60',2,'k','ens-staging1');
+INSERT INTO `db` VALUES (44,42,0,'variation','60',9,'d','ens-staging2');
+INSERT INTO `db` VALUES (45,19,0,'core','60',1,'m','ens-staging1');
+INSERT INTO `db` VALUES (46,39,0,'core','60',2,'b','ens-staging1');
+INSERT INTO `db` VALUES (47,43,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (48,13,0,'core','60',525,'b','ens-staging1');
+INSERT INTO `db` VALUES (49,50,0,'core','60',41,'q','ens-staging2');
+INSERT INTO `db` VALUES (50,21,0,'coreexpressionatlas','60',37,'e','ens-staging2');
+INSERT INTO `db` VALUES (51,8,0,'funcgen','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (52,27,0,'variation','60',37,'m','ens-staging2');
+INSERT INTO `db` VALUES (53,39,0,'funcgen','60',2,'b','ens-staging1');
+INSERT INTO `db` VALUES (54,49,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (55,51,0,'core','60',1,'','ens-staging1');
+INSERT INTO `db` VALUES (56,36,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (57,5,0,'funcgen','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (58,42,0,'core','60',9,'d','ens-staging2');
+INSERT INTO `db` VALUES (59,43,0,'variation','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (60,21,0,'funcgen','60',37,'e','ens-staging1');
+INSERT INTO `db` VALUES (61,2,0,'otherfeatures','60',4,'i','ens-staging1');
+INSERT INTO `db` VALUES (62,20,0,'core','60',3,'c','ens-staging1');
+INSERT INTO `db` VALUES (63,20,0,'otherfeatures','60',3,'c','ens-staging1');
+INSERT INTO `db` VALUES (64,21,0,'otherfeatures','60',37,'e','ens-staging1');
+INSERT INTO `db` VALUES (65,23,0,'otherfeatures','60',10,'o','ens-staging1');
+INSERT INTO `db` VALUES (66,35,0,'variation','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (67,38,0,'otherfeatures','60',34,'b','ens-staging2');
+INSERT INTO `db` VALUES (68,30,0,'funcgen','60',1,'n','ens-staging2');
+INSERT INTO `db` VALUES (69,27,0,'core','60',37,'m','ens-staging2');
+INSERT INTO `db` VALUES (70,18,0,'funcgen','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (71,10,0,'funcgen','60',9,'','ens-staging1');
+INSERT INTO `db` VALUES (72,31,0,'core','60',3,'','ens-staging2');
+INSERT INTO `db` VALUES (73,46,0,'variation','60',8,'e','ens-staging2');
+INSERT INTO `db` VALUES (74,3,0,'core','60',210,'b','ens-staging1');
+INSERT INTO `db` VALUES (75,39,0,'variation','60',2,'b','ens-staging1');
+INSERT INTO `db` VALUES (76,10,0,'coreexpressionest','60',9,'','ens-staging1');
+INSERT INTO `db` VALUES (77,34,0,'variation','60',21,'o','ens-staging2');
+INSERT INTO `db` VALUES (78,15,0,'otherfeatures','60',2,'g','ens-staging1');
+INSERT INTO `db` VALUES (79,19,0,'otherfeatures','60',1,'m','ens-staging1');
+INSERT INTO `db` VALUES (80,16,0,'core','60',1,'h','ens-staging1');
+INSERT INTO `db` VALUES (81,46,0,'otherfeatures','60',8,'e','ens-staging2');
+INSERT INTO `db` VALUES (82,1,0,'core','60',1,'d','ens-staging1');
+INSERT INTO `db` VALUES (83,35,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (84,23,0,'core','60',10,'o','ens-staging1');
+INSERT INTO `db` VALUES (85,48,0,'core','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (86,17,0,'core','60',1,'i','ens-staging1');
+INSERT INTO `db` VALUES (87,28,0,'core','60',1,'j','ens-staging2');
+INSERT INTO `db` VALUES (88,18,0,'otherfeatures','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (89,42,0,'otherfeatures','60',9,'d','ens-staging2');
+INSERT INTO `db` VALUES (90,15,0,'core','60',2,'g','ens-staging1');
+INSERT INTO `db` VALUES (91,44,0,'otherfeatures','60',4,'n','ens-staging2');
+INSERT INTO `db` VALUES (92,35,0,'otherfeatures','60',1,'f','ens-staging2');
+INSERT INTO `db` VALUES (93,31,0,'otherfeatures','60',3,'','ens-staging2');
+INSERT INTO `db` VALUES (94,13,0,'otherfeatures','60',525,'b','ens-staging1');
+INSERT INTO `db` VALUES (95,30,0,'variation','60',1,'n','ens-staging2');
+INSERT INTO `db` VALUES (96,5,0,'variation','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (97,30,0,'core','60',1,'n','ens-staging2');
+INSERT INTO `db` VALUES (98,10,0,'otherfeatures','60',9,'','ens-staging1');
+INSERT INTO `db` VALUES (99,38,0,'variation','60',34,'b','ens-staging2');
+INSERT INTO `db` VALUES (100,6,0,'core','60',3,'d','ens-staging1');
+INSERT INTO `db` VALUES (101,2,0,'variation','60',4,'i','ens-staging1');
+INSERT INTO `db` VALUES (102,8,0,'core','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (103,13,0,'funcgen','60',525,'b','ens-staging1');
+INSERT INTO `db` VALUES (104,12,0,'core','60',1,'f','ens-staging1');
+INSERT INTO `db` VALUES (105,8,0,'otherfeatures','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (106,26,0,'core','60',5,'l','ens-staging2');
+INSERT INTO `db` VALUES (107,34,0,'otherfeatures','60',21,'o','ens-staging2');
+INSERT INTO `db` VALUES (108,38,0,'funcgen','60',34,'b','ens-staging2');
+INSERT INTO `db` VALUES (109,6,0,'otherfeatures','60',3,'d','ens-staging1');
+INSERT INTO `db` VALUES (110,34,0,'funcgen','60',21,'o','ens-staging2');
+INSERT INTO `db` VALUES (111,18,0,'core','60',2,'p','ens-staging1');
+INSERT INTO `db` VALUES (112,27,0,'funcgen','60',37,'m','ens-staging2');
+INSERT INTO `db` VALUES (113,14,0,'core','60',1,'j','ens-staging1');
+INSERT INTO `db` VALUES (114,41,0,'core','60',1,'j','ens-staging2');
+INSERT INTO `db` VALUES (115,23,0,'funcgen','60',10,'o','ens-staging1');
+INSERT INTO `db` VALUES (116,51,0,'otherfeatures','60',1,'','ens-staging1');
+INSERT INTO `db` VALUES (117,27,0,'otherfeatures','60',37,'m','ens-staging2');
+INSERT INTO `db` VALUES (118,27,0,'cdna','60',37,'m','ens-staging2');
+INSERT INTO `db` VALUES (119,39,0,'otherfeatures','60',2,'b','ens-staging1');
+INSERT INTO `db` VALUES (120,1,0,'otherfeatures','60',1,'d','ens-staging1');
+INSERT INTO `db` VALUES (121,10,0,'variation','60',9,'','ens-staging1');
+INSERT INTO `db` VALUES (122,4,0,'otherfeatures','61',321,'c','ens-staging1');
+INSERT INTO `db` VALUES (123,18,0,'funcgen','61',2,'q','ens-staging1');
+INSERT INTO `db` VALUES (124,39,0,'funcgen','61',2,'c','ens-staging1');
+INSERT INTO `db` VALUES (125,27,0,'variation','61',37,'n','ens-staging2');
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+INSERT INTO `db` VALUES (664,4,1,'core','65',321,'','ens-staging1');
+INSERT INTO `db` VALUES (665,19,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (666,30,1,'funcgen','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (667,46,1,'otherfeatures','65',8,'','ens-staging2');
+INSERT INTO `db` VALUES (668,56,1,'core','65',7,'','ens-staging2');
+INSERT INTO `db` VALUES (669,38,1,'funcgen','65',34,'','ens-staging2');
+INSERT INTO `db` VALUES (670,18,1,'core','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (671,19,1,'otherfeatures','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (672,15,1,'otherfeatures','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (673,53,1,'otherfeatures','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (674,35,1,'variation','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (675,50,1,'funcgen','65',42,'','ens-staging2');
+INSERT INTO `db` VALUES (676,14,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (677,5,1,'funcgen','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (678,42,1,'funcgen','65',9,'','ens-staging2');
+INSERT INTO `db` VALUES (679,8,1,'otherfeatures','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (680,10,1,'otherfeatures','65',9,'','ens-staging1');
+INSERT INTO `db` VALUES (681,43,1,'otherfeatures','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (682,27,1,'variation','65',37,'','ens-staging2');
+INSERT INTO `db` VALUES (683,30,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (684,15,1,'core','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (685,23,1,'funcgen','65',10,'','ens-staging1');
+INSERT INTO `db` VALUES (686,48,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (687,37,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (688,38,1,'core','65',34,'','ens-staging2');
+INSERT INTO `db` VALUES (689,2,1,'core','65',31,'','ens-staging1');
+INSERT INTO `db` VALUES (690,32,1,'otherfeatures','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (691,30,1,'variation','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (692,43,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (693,3,1,'core','65',220,'','ens-staging1');
+INSERT INTO `db` VALUES (694,41,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (695,11,1,'core','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (696,2,1,'variation','65',31,'','ens-staging1');
+INSERT INTO `db` VALUES (697,44,1,'otherfeatures','65',4,'','ens-staging2');
+INSERT INTO `db` VALUES (698,53,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (699,26,1,'variation','65',5,'','ens-staging2');
+INSERT INTO `db` VALUES (700,20,1,'core','65',31,'','ens-staging1');
+INSERT INTO `db` VALUES (701,30,1,'otherfeatures','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (702,42,1,'otherfeatures','65',9,'','ens-staging2');
+INSERT INTO `db` VALUES (703,46,1,'core','65',8,'','ens-staging2');
+INSERT INTO `db` VALUES (704,2,1,'funcgen','65',31,'','ens-staging1');
+INSERT INTO `db` VALUES (705,35,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (706,42,1,'core','65',9,'','ens-staging2');
+INSERT INTO `db` VALUES (708,32,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (709,18,1,'variation','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (710,20,1,'otherfeatures','65',31,'','ens-staging1');
+INSERT INTO `db` VALUES (711,25,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (712,10,1,'funcgen','65',9,'','ens-staging1');
+INSERT INTO `db` VALUES (713,5,1,'otherfeatures','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (714,10,1,'variation','65',9,'','ens-staging1');
+INSERT INTO `db` VALUES (715,47,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (716,27,1,'otherfeatures','65',37,'','ens-staging2');
+INSERT INTO `db` VALUES (717,44,1,'core','65',4,'','ens-staging2');
+INSERT INTO `db` VALUES (718,42,1,'variation','65',9,'','ens-staging2');
+INSERT INTO `db` VALUES (719,50,1,'otherfeatures','65',42,'','ens-staging2');
+INSERT INTO `db` VALUES (720,4,1,'otherfeatures','65',321,'','ens-staging1');
+INSERT INTO `db` VALUES (721,5,1,'variation','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (722,27,1,'vega','65',37,'','ens-staging2');
+INSERT INTO `db` VALUES (723,9,1,'otherfeatures','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (724,17,1,'variation','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (725,24,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (726,51,1,'otherfeatures','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (727,28,1,'otherfeatures','65',2,'','ens-staging2');
+INSERT INTO `db` VALUES (728,6,1,'otherfeatures','65',3,'','ens-staging1');
+INSERT INTO `db` VALUES (729,36,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (730,34,1,'funcgen','65',21,'','ens-staging2');
+INSERT INTO `db` VALUES (731,16,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (732,15,1,'variation','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (733,12,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (734,21,1,'rnaseq','65',37,'','ens-staging1');
+INSERT INTO `db` VALUES (735,1,1,'otherfeatures','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (736,40,1,'core','65',1,'','ens-staging2');
+INSERT INTO `db` VALUES (737,26,1,'core','65',5,'','ens-staging2');
+INSERT INTO `db` VALUES (738,8,1,'funcgen','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (739,55,1,'core','65',7,'','ens-staging2');
+INSERT INTO `db` VALUES (740,55,1,'otherfeatures','65',7,'','ens-staging2');
+INSERT INTO `db` VALUES (741,23,1,'core','65',10,'','ens-staging1');
+INSERT INTO `db` VALUES (742,46,1,'variation','65',8,'','ens-staging2');
+INSERT INTO `db` VALUES (743,38,1,'otherfeatures','65',34,'','ens-staging2');
+INSERT INTO `db` VALUES (744,1,1,'core','65',2,'','ens-staging1');
+INSERT INTO `db` VALUES (746,33,1,'otherfeatures','65',3,'','ens-staging2');
+INSERT INTO `db` VALUES (747,33,1,'core','65',3,'','ens-staging2');
+INSERT INTO `db` VALUES (748,51,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (749,34,1,'core','65',214,'','ens-staging2');
+INSERT INTO `db` VALUES (750,22,1,'core','65',3,'','ens-staging1');
+INSERT INTO `db` VALUES (754,34,1,'otherfeatures','65',214,'','ens-staging2');
+INSERT INTO `db` VALUES (755,21,1,'vega','65',37,'','ens-staging1');
+INSERT INTO `db` VALUES (756,52,1,'core','65',21,'','ens-staging2');
+INSERT INTO `db` VALUES (757,10,1,'core','65',9,'','ens-staging1');
+INSERT INTO `db` VALUES (758,39,1,'otherfeatures','65',4,'','ens-staging2');
+INSERT INTO `db` VALUES (759,39,1,'core','65',4,'','ens-staging2');
+INSERT INTO `db` VALUES (760,52,1,'otherfeatures','65',21,'','ens-staging2');
+INSERT INTO `db` VALUES (761,57,1,'core','65',1,'','ens-staging1');
+INSERT INTO `db` VALUES (762,31,1,'otherfeatures','65',3,'','ens-staging2');
+INSERT INTO `db` VALUES (763,31,1,'core','65',3,'','ens-staging2');
--
-- Table structure for table `master_attrib_type`
@@ -4405,7 +5046,6 @@ SET character_set_client = @saved_cs_client;
--
-- ORDER BY: `external_db_id`
-INSERT INTO `master_external_db` VALUES (0,'Kyoto_University',NULL,'KNOWN',5,'Kyoto University','MISC',NULL,NULL,NULL,1,NULL,'2011-08-25 08:02:58',NULL,NULL);
INSERT INTO `master_external_db` VALUES (210,'Anopheles_symbol',NULL,'KNOWN',50,'Anopheles symbol','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (211,'VB_Community_Symbol',NULL,'KNOWN',50,'VB Community Symbol','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (212,'VB_External_Description','1','PRED',50,'VB External Description','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
@@ -4449,6 +5089,7 @@ INSERT INTO `master_external_db` VALUES (883,'FlyReactome',NULL,'KNOWNXREF',5,'F
INSERT INTO `master_external_db` VALUES (890,'DEDb',NULL,'KNOWNXREF',5,'Drosophila melanogaster Exon Database','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (900,'GKB',NULL,'XREF',5,'GKB','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (1000,'GO',NULL,'XREF',5,'GO','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (1001,'GO_REF',NULL,'KNOWN',5,'GO Reference Collection','LIT',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (1100,'HGNC',NULL,'KNOWNXREF',100,'HGNC Symbol','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (1200,'Interpro',NULL,'XREF',5,'InterPro','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (1300,'EntrezGene',NULL,'KNOWNXREF',250,'EntrezGene','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
@@ -4602,6 +5243,7 @@ INSERT INTO `master_external_db` VALUES (9600,'Trace_archive',NULL,'XREF',40,'Tr
INSERT INTO `master_external_db` VALUES (9700,'CioSav_est',NULL,'XREF',40,'Ciona savignyi EST','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (9800,'kyotograil_2004',NULL,'PRED',30,'Ciona intestinalis Kyotograil 2004 predictions','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (9900,'kyotograil_2005',NULL,'PRED',30,'Ciona intestinalis Kyotograil 2005 predictions','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (9950,'Kyoto_University',NULL,'KNOWN',5,'Kyoto University','MISC',NULL,NULL,NULL,1,NULL,'2011-08-25 08:02:58',NULL,NULL);
INSERT INTO `master_external_db` VALUES (10000,'wormbase_id',NULL,'XREF',30,'Generic exdb for worbase id of any type for feature table','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (10100,'EPD',NULL,'KNOWNXREF',5,'Eukaryotic Promoter Database (Bucher)','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (10200,'GPCR',NULL,'KNOWNXREF',5,'The G protein-coupled receptor database','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
@@ -4747,6 +5389,50 @@ INSERT INTO `master_external_db` VALUES (20347,'PGD','1','KNOWNXREF',0,'Pythium
INSERT INTO `master_external_db` VALUES (20348,'PGD_GENE','1','KNOWNXREF',0,'Pythium genome database','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (20349,'PGD_TRANSCRIPT','1','KNOWNXREF',0,'Pythium genome database','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (20350,'RegulonDb_Operon',NULL,'KNOWNXREF',0,'RegulonDb','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20351,'BROAD_N_crassa_GENE','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20352,'BROAD_N_crassa_TRANSCRIPT','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20353,'BROAD_N_crassa','1','KNOWNXREF',0,'Broad Institute','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20354,'BROAD_U_maydis','1','KNOWNXREF',0,'Broad Institute','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20355,'BROAD_U_maydis_GENE','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20356,'BROAD_U_maydis_TRANSCRIPT','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20357,'BROAD_P_triticina','1','KNOWNXREF',0,'Broad Institute','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20358,'BROAD_P_triticina_GENE','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20359,'BROAD_P_triticina_TRANSCRIPT','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20360,'SpBase','1','KNOWNXREF',0,'SpBase','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20361,'PHIbase','3.2','XREF',50,'PHI-base','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20362,'necha_jgi_v2.0_gene','2','KNOWNXREF',0,'Nectria JGI gene','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20363,'necha_jgi_v2.0_transcript','2','KNOWNXREF',0,'Nectria JGI transcript','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20364,'necha_jgi_v2.0','2','KNOWNXREF',0,'Nectria JGI','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20365,'tuber_genoscope_gene','1','KNOWNXREF',0,'Tuber Genome Browser','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20366,'tuber_genoscope_transcript','2','KNOWNXREF',0,'Tuber Genome Browser','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20367,'tuber_genoscope','2','KNOWNXREF',0,'Tuber Genome Browser','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20368,'Mycgr3_jgi_v2.0_gene','2','KNOWNXREF',0,'Mycosphaerella JGI gene','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20369,'Mycgr3_jgi_v2.0_transcript','2','KNOWNXREF',0,'Mycosphaerella JGI transcript','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20370,'Mycgr3_jgi_v2.0','2','KNOWNXREF',0,'Mycosphaerella JGI','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20371,'BROAD_P_NODORUM','1','KNOWNXREF',0,'Broad Phaeosphaeria nodorum','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20372,'BROAD_P_NODORUM_GENE','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20373,'BROAD_P_NODORUM_TRANSCRIPT','1','KNOWNXREF',0,'Broad Institute','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20375,'PomBase',NULL,'KNOWN',0,'PomBase ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20376,'PomBase_GENE',NULL,'KNOWNXREF',0,'PomBase Gene ID','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20377,'PomBase_TRANSCRIPT',NULL,'KNOWNXREF',0,'PomBase Transcript ID','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20378,'PomBase_TRANSLATION',NULL,'KNOWNXREF',0,'PomBase Translation ID','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20379,'SPO',NULL,'KNOWNXREF',0,'SPO ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20380,'CBS',NULL,'KNOWNXREF',0,'CBS Server','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20381,'COG',NULL,'KNOWNXREF',0,'Cluster of Orthologous Groups (NCBI)','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20382,'CGD',NULL,'KNOWN',0,'Candida Genome Database','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20383,'ProSite',NULL,'XREF',0,'ProSite ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20384,'PFAM',NULL,'XREF',0,'PFAM ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20385,'SMART',NULL,'XREF',0,'SMART ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20386,'SPD',NULL,'KNOWNXREF',0,'SPD ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20387,'KOG',NULL,'KNOWNXREF',0,'KOG ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20388,'PBO',NULL,'KNOWNXREF',0,'PomBase Ontology ID','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20389,'FYPO',NULL,'KNOWNXREF',0,'Fission Yeast Phenotype Ontology','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20390,'MOD',NULL,'KNOWNXREF',0,'PSI-MOD, Post Translational Modification Ontology','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20391,'AGD_GENE','1','KNOWNXREF',0,'Ashbya Genome Database','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20392,'AGD_TRANSCRIPT','1','KNOWNXREF',0,'Ashbya Genome Database','PRIMARY_DB_SYNONYM',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20393,'AGD','1','KNOWNXREF',0,'Ashbya Genome Database','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20394,'FYPO_GENE','1','KNOWNXREF',0,'Fission Yeast Phenotype Ontology','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
+INSERT INTO `master_external_db` VALUES (20395,'FYPO_TRANSCRIPT','1','KNOWNXREF',0,'Fission Yeast Phenotype Ontology','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (50000,'BGI_EST_Cluster',NULL,'XREF',0,'EST Cluster (BGI Indica)','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (50005,'EC_NUMBER',NULL,'XREF',0,'Enzyme EC Number','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
INSERT INTO `master_external_db` VALUES (50010,'FSTs',NULL,'XREF',0,'Flanking Sequence Tag (FST)','MISC',NULL,NULL,NULL,1,NULL,NULL,NULL,NULL);
@@ -4809,6 +5495,9 @@ INSERT INTO `master_external_db` VALUES (50630,'PFAM','24','XREF',0,'PFAM','MISC
INSERT INTO `master_external_db` VALUES (50631,'PFAM','25','XREF',0,'PFAM','MISC',NULL,NULL,'Pfam release 25, from Vega',1,5132,'2011-08-01 13:44:42',NULL,NULL);
INSERT INTO `master_external_db` VALUES (50632,'PFAM','26','XREF',0,'PFAM','MISC',NULL,NULL,'Pfam release 26, from Vega',1,5132,'2011-08-01 13:45:34',NULL,NULL);
INSERT INTO `master_external_db` VALUES (50633,'GRC_human_primary_assembly',NULL,'XREF',0,'GRC human primary assembly','MISC',NULL,NULL,'Primary assembly of the human genome from the GRC',1,NULL,'2011-08-05 15:04:52',NULL,NULL);
+INSERT INTO `master_external_db` VALUES (50634,'Ens_Ga_gene',NULL,'XREF',5,'Ensembl Stickleback Gene','MISC',NULL,NULL,NULL,1,5132,'2011-09-11 10:34:42',NULL,NULL);
+INSERT INTO `master_external_db` VALUES (50635,'Ens_Ga_transcript',NULL,'XREF',170,'Ensembl Stickleback Transcript','MISC',NULL,NULL,NULL,1,5132,'2011-09-11 10:37:49',NULL,NULL);
+INSERT INTO `master_external_db` VALUES (50636,'Ens_Ga_translation',NULL,'XREF',5,'Ensembl Stickleback Translation','MISC',NULL,NULL,NULL,0,5132,'2011-09-11 10:38:53',NULL,NULL);
--
-- Table structure for table `master_misc_set`
@@ -5021,14 +5710,14 @@ INSERT INTO `meta_key` VALUES (60,'sample.transcript_text',0,0,'core,otherfeatur
INSERT INTO `meta_key` VALUES (61,'schema_version',0,1,'cdna,core,funcgen,otherfeatures,rnaseq,variation,vega',NULL,'The version of the schema in this database.',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (62,'simple_featurebuild.level',1,1,'cdna,core,otherfeatures,vega',NULL,NULL,NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (63,'species.alias',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'An alias for the species name, will be read by the Registry and may be used when getting adaptors using $registry->get_adpator(...)',NULL,NULL,NULL,NULL);
-INSERT INTO `meta_key` VALUES (64,'species.classification',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `meta_key` VALUES (65,'species.common_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `meta_key` VALUES (64,'species.classification',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'Full classification for every level, from our copy of NCBI taxonomy database',NULL,NULL,NULL,NULL);
+INSERT INTO `meta_key` VALUES (65,'species.common_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'Usually genbank common name, from ncbi taxonomy database',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (66,'species.description',0,0,'core,otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `meta_key` VALUES (67,'species.ensembl_alias_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `meta_key` VALUES (67,'species.ensembl_alias_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'Used by web for dropdown menu',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (68,'species.ensembl_common_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (69,'species.stable_id_prefix',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (70,'species.system_name',0,1,'funcgen',NULL,NULL,NULL,NULL,NULL,NULL);
-INSERT INTO `meta_key` VALUES (71,'species.taxonomy_id',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
+INSERT INTO `meta_key` VALUES (71,'species.taxonomy_id',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'Taxonomy ID from NCBI taxonomy database. Usually provided by INSDC who provides assembly.',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (72,'species.three_letter_code',0,0,'otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (73,'transcriptbuild.level',1,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,NULL,NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (74,'xref.timestamp',0,1,'cdna,core,otherfeatures',NULL,NULL,NULL,NULL,NULL,NULL);
@@ -5036,7 +5725,7 @@ INSERT INTO `meta_key` VALUES (75,'species.production_name',0,1,'cdna,core,other
INSERT INTO `meta_key` VALUES (76,'schema_type',0,1,'cdna,core,funcgen,otherfeatures,rnaseq,variation,vega',NULL,'The type of schema in this database, e.g., \'core\' in a Core database or \'variation\' in a Variation database.',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (77,'genebuild.vega_merge_db',0,0,'core','homo_sapiens,mus_musculus,danio_rerio','Database name for Vega database used for GENCODE gene merge',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (78,'genebuild.projection_source_db',0,1,'core','choloepus_hoffmanni,dasypus_novemcinctus,dipodomys_ordii,echinops_telfairi,erinaceus_europaeus,felis_catus,gorilla_gorilla,macropus_eugenii,microcebus_murinus,ochotona_princeps,otolemur_garnettii,pan_troglodytes,pongo_abelii,procavia_capensis,pteropus_vampyrus,sorex_araneus,spermophilus_tridecemlineatus,tarsius_syrichta,tupaia_belangeri,tursiops_truncatus,vicugna_pacos','Database name for Reference database used for the low_coverage projection build. The reference database is usually human.',NULL,NULL,NULL,NULL);
-INSERT INTO `meta_key` VALUES (79,'species.scientific_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'The full name of the species, e.g., \'Homo sapiens\'',NULL,NULL,NULL,NULL);
+INSERT INTO `meta_key` VALUES (79,'species.scientific_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'From NCBI taxonomy db, string directly associated to taxonomy ID, can be trinomial',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (80,'species.short_name',0,1,'cdna,core,otherfeatures,rnaseq,vega',NULL,'A name which is short enough to be used in space constraint areas',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (81,'genebuild.havana_datafreeze_date',0,1,'core,vega','homo_sapiens,mus_musculus,danio_rerio','Date of Havana annotation data freeze',NULL,NULL,NULL,NULL);
INSERT INTO `meta_key` VALUES (83,'removed_evidence_flag.uniprot_dbversion',0,1,'core',NULL,'Uniprot database used to flag transcripts whose transcript_supporting_feature has been removed from Uniprot',NULL,NULL,NULL,NULL);
@@ -5086,7 +5775,6 @@ INSERT INTO `meta_key_species` VALUES (78,24);
INSERT INTO `meta_key_species` VALUES (78,25);
INSERT INTO `meta_key_species` VALUES (78,28);
INSERT INTO `meta_key_species` VALUES (78,29);
-INSERT INTO `meta_key_species` VALUES (78,33);
INSERT INTO `meta_key_species` VALUES (78,34);
INSERT INTO `meta_key_species` VALUES (78,36);
INSERT INTO `meta_key_species` VALUES (78,37);
@@ -5096,6 +5784,7 @@ INSERT INTO `meta_key_species` VALUES (78,45);
INSERT INTO `meta_key_species` VALUES (78,47);
INSERT INTO `meta_key_species` VALUES (78,48);
INSERT INTO `meta_key_species` VALUES (78,49);
+INSERT INTO `meta_key_species` VALUES (78,57);
INSERT INTO `meta_key_species` VALUES (81,10);
INSERT INTO `meta_key_species` VALUES (81,21);
INSERT INTO `meta_key_species` VALUES (81,27);
@@ -5205,8 +5894,9 @@ INSERT INTO `species` VALUES (53,'nomascus_leucogenys','Northern white-cheeked g
INSERT INTO `species` VALUES (54,'oreochromus_niloticus','Nile tilapia','Tilapia',NULL,NULL,1,5132,'2011-05-17 07:48:33',NULL,NULL);
INSERT INTO `species` VALUES (55,'petromyzon_marinus','sea lamprey','Lamprey',NULL,NULL,1,97245,'2011-06-24 13:02:56',NULL,NULL);
INSERT INTO `species` VALUES (56,'sarcophilus_harrisii','Tasmanian devil','Tasmanian devil',NULL,NULL,1,97245,'2011-07-05 11:47:00',NULL,NULL);
-INSERT INTO `species` VALUES (57,'gadus_morhua','Atlantic cod','Atlantic cod',NULL,NULL,1,5132,'2011-08-15 15:33:07',NULL,NULL);
+INSERT INTO `species` VALUES (57,'gadus_morhua','Atlantic cod','Atlantic cod','8049',NULL,1,5132,'2011-08-15 15:33:07',NULL,NULL);
INSERT INTO `species` VALUES (58,'mustela_putorius_furo','Domestic ferret','Ferret',NULL,NULL,1,101214,'2011-08-17 14:50:17',NULL,NULL);
+INSERT INTO `species` VALUES (59,'','','',NULL,NULL,1,NULL,NULL,NULL,NULL);
--
-- Table structure for table `species_backup`
@@ -5278,7 +5968,7 @@ INSERT INTO `web_data` VALUES (21,'{\'colour_key\' => \'rna\',\'default\' => {\'
INSERT INTO `web_data` VALUES (22,'{\'additional_renderers\' => [\'histogram\',\'Variable height\'],\'colour_key\' => \'intron_support\',\'type\' => \'rnaseq\',\'zmenu\' => \'Supporting_alignment\'}',NULL,NULL,NULL,NULL);
INSERT INTO `web_data` VALUES (24,'{\'show_strands\' => \'1\'}',NULL,NULL,NULL,NULL);
INSERT INTO `web_data` VALUES (25,'{\'default\' => {\'contigviewbottom\' => \'stack\'},\'type\' => \'rna\'}',NULL,NULL,NULL,NULL);
-INSERT INTO `web_data` VALUES (27,'{\'colour_key\' => \'[logic_name]_[biotype]\',\'default\' => {\'MultiBottom\' => \'collapsed_label\',\'MultiTop\' => \'gene_label\',\'alignsliceviewbottom\' => \'as_collapsed_label\',\'contigviewbottom\' => \'transcript_label\',\'contigviewtop\' => \'gene_label\',\'cytoview\' => \'gene_label\'},\'label_key\' => \'projected [biotype]\'}',NULL,NULL,NULL,NULL);
+INSERT INTO `web_data` VALUES (27,'{\'colour_key\' => \'[logic_name]_[biotype]\',\'default\' => {\'MultiBottom\' => \'collapsed_label\',\'MultiTop\' => \'gene_label\',\'alignsliceviewbottom\' => \'as_collapsed_label\',\'contigviewbottom\' => \'transcript_label\',\'contigviewtop\' => \'gene_label\',\'cytoview\' => \'gene_label\'},\'key\' => \'ensembl\',\'label_key\' => \'projected [biotype]\',\'name\' => \'Ensembl\'}',NULL,NULL,5132,'2011-10-03 13:29:37');
INSERT INTO `web_data` VALUES (31,'{\'default\' => {\'contigviewbottom\' => \'stack\'},\'key\' => \'tetraodon_cdna\',\'name\' => \'Tetraodon cDNA\',\'type\' => \'cdna\'}',NULL,NULL,NULL,NULL);
INSERT INTO `web_data` VALUES (32,'{\'default\' => {\'contigviewbottom\' => \'stack\'},\'gene\' => {\'do_not_display\' => \'1\'},\'type\' => \'cdna\'}',NULL,NULL,NULL,NULL);
INSERT INTO `web_data` VALUES (33,'{\'caption\' => \'LRG gene\',\'colour_key\' => \'rna_[status]\',\'default\' => {\'MultiBottom\' => \'collapsed_label\',\'MultiTop\' => \'gene_label\',\'alignsliceviewbottom\' => \'as_collapsed_label\',\'contigviewbottom\' => \'transcript_label\',\'contigviewtop\' => \'gene_label\',\'cytoview\' => \'gene_label\'},\'label_key\' => \'[text_label] [display_label]\',\'multi_name\' => \'LRG genes\',\'name\' => \'LRG Genes\'}',NULL,NULL,NULL,NULL);
@@ -5313,6 +6003,7 @@ INSERT INTO `web_data` VALUES (69,'{\'caption\' => \'Assembly patch lincRNA gene
INSERT INTO `web_data` VALUES (70,'{\'caption\' => \'Assembly patch Ig gene\',\'colour_key\' => \'[biotype]\',\'default\' => {\'MultiBottom\' => \'collapsed_label\',\'MultiTop\' => \'gene_label\',\'alignsliceviewbottom\' => \'as_collapsed_label\',\'contigviewbottom\' => \'transcript_label\',\'contigviewtop\' => \'gene_label\',\'cytoview\' => \'gene_label\'},\'key\' => \'merged_ig_genes\',\'label_key\' => \'[biotype]\',\'multi_name\' => \'Assembly patch IG genes\',\'name\' => \'Assembly patch Ig/T-cell receptor genes\'}',NULL,'2011-08-08 14:53:20',NULL,NULL);
INSERT INTO `web_data` VALUES (71,'{\'caption\' => \'Assembly patch ncRNA gene\',\'colour_key\' => \'rna\',\'default\' => {\'MultiBottom\' => \'collapsed_label\',\'MultiTop\' => \'gene_label\',\'alignsliceviewbottom\' => \'as_collapsed_label\',\'contigviewbottom\' => \'transcript_label\',\'contigviewtop\' => \'gene_label\',\'cytoview\' => \'gene_label\'},\'label_key\' => \'[biotype]\',\'multi_name\' => \'Assembly patch ncRNA genes\',\'name\' => \'Assembly patch ncRNA genes\'}',NULL,'2011-08-08 14:59:18',NULL,NULL);
INSERT INTO `web_data` VALUES (72,'{\'caption\' => \'Assembly patch ncRNA pseudogene\',\'colour_key\' => \'rna\',\'default\' => {\'MultiBottom\' => \'collapsed_label\',\'MultiTop\' => \'gene_label\',\'alignsliceviewbottom\' => \'as_collapsed_label\',\'contigviewbottom\' => \'transcript_label\',\'contigviewtop\' => \'gene_label\',\'cytoview\' => \'gene_label\'},\'label_key\' => \'[biotype]\',\'multi_name\' => \'Assembly patch ncRNA pseudogenes\',\'name\' => \'Assembly patch ncRNA pseudogenes\'}',NULL,'2011-08-09 10:39:05',NULL,NULL);
+INSERT INTO `web_data` VALUES (73,'{\'default\' => {\'contigviewbottom\' => \'simple\'}, \'colour_key\' => \'reference\', zmenu => \'AltSeqAlignment\'}',NULL,'2011-09-21 17:14:21',NULL,NULL);
/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
@@ -5320,4 +6011,4 @@ INSERT INTO `web_data` VALUES (72,'{\'caption\' => \'Assembly patch ncRNA pseudo
/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
--- Dump completed on 2011-09-07 13:07:51
+-- Dump completed on 2011-10-11 9:11:12