From 69c8e18c6e4f4adc39e1702f102913cf3e410b84 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 16 Nov 2010 14:04:54 +0000
Subject: [PATCH] Remove files no longer used.
---
misc-scripts/external_db/README | 113 ------
.../external_db/convert_external_dbs.pl | 73 ----
misc-scripts/external_db/external_dbs.txt | 337 ------------------
.../load_additional_human_affy_xrefs.pl | 83 -----
.../load_additional_human_gkb_xrefs.pl | 88 -----
.../external_db/update_external_dbs.pl | 324 -----------------
6 files changed, 1018 deletions(-)
delete mode 100644 misc-scripts/external_db/README
delete mode 100644 misc-scripts/external_db/convert_external_dbs.pl
delete mode 100644 misc-scripts/external_db/external_dbs.txt
delete mode 100644 misc-scripts/external_db/load_additional_human_affy_xrefs.pl
delete mode 100644 misc-scripts/external_db/load_additional_human_gkb_xrefs.pl
delete mode 100644 misc-scripts/external_db/update_external_dbs.pl
diff --git a/misc-scripts/external_db/README b/misc-scripts/external_db/README
deleted file mode 100644
index 37a5f0ff55..0000000000
--- a/misc-scripts/external_db/README
+++ /dev/null
@@ -1,113 +0,0 @@
-EXTERNAL_DB UPDATES
-===================
-
-
-DESCRIPTION
------------
-
-The external_db table contains a list of all external databases which are
-referenced by ensembl. Specifically this table is used by the xref table
-which contains lists of external database identifiers.
-
-Foremerly all EnsEMBL core databases had their own external_db tables
-and used an enumeration of db_names. This was difficult to maintain and
-required schema updates every release. The new system requires that
-every ensembl database contains the exact same external_db table, which
-ensures consistancy across all databases and makes it easier to test.
-
-MASTER EXTERNAL_DB LIST
------------------------
-
-The master list of external databases is stored in the file:
-
-${ENSEMBL_HOME}/ensembl/misc-scripts/external_db/external_dbs.txt
-
-This file contains a tab-seperated list of values which are loaded into
-the external_db tables. In order the columns are:
- 'external_db_id', 'db_name', 'release', 'status',
-'db_primary_acc_linkable', 'display_label_linkable', 'priority',
-'db_display_name', 'type', 'secondary_db_name', 'secondary_db_table',
-'description'
-
-- external_db_id -- internal identifier for this entry, primary key
-- release -- is currently not used by the software and is always set to 1
-- status -- must be one of 'KNOWNXREF','KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO'.
-This is used by the webcode to determine which genes/transcripts can be considered
-to be known or unknown etc.
-- dbprimary_acc_linkable -- used by the webcode to indicate if the linkable
-element is the internal name in the database (e.g. HGNC_curated_gene)
-- display_label_linkable -- used by the webcode to indicate if the linkable
-element is the name of the database (e.g. WikiGene )
-- priority -- used for the website to indicate priority of display in page
-( the higher the number, the closer to the top of the page)
-- db_display_name -- name to be displayed in the website might be different
-to name of database (e.g. HGNC Symbol rather than HGNC)
-- type -- indicates kind of information the xref database offers (e.g. ALT_GENE
-is used in OTTG to indicate that this external database produces alternative gene from Vega)
-- secondary_db_name -- not used at the moment (requested by functional genomics team)
-- secondary_db_table -- not used at the moment (requested by functiona genomics team)
-- description -- free column to describe the external database
-
-...
-12300 HGNC_curated_gene 1 KNOWNXREF 1 0 5 HGNC (curated) MISC \N \N
-12305 HGNC_automatic_gene 1 KNOWNXREF 1 0 5 HGNC (automatic) MISC \N \N
-12310 Clone_based_vega_gene 1 KNOWNXREF 1 0 5 Clone-based (Vega) MISC \N \N
-12315 Clone_based_ensembl_gene 1 XREF 1 0 5 Clone-based (Ensembl) MISC \N \N
-12400 HGNC_curated_transcript 1 KNOWNXREF 1 0 5 HGNC (curated) MISC \N \N
-...
-
-
-UPDATE PROCEDURE
-----------------
-
-The following describes the steps necessary to update the external_db table
-
-
-(1) Add new external database(s) if the appropriate database(s) are not in the
-master list:
- (a) Add a row to the external_dbs.txt file. The columns must be tab
- seperated and the external_db identifier must be unique. The
- db_release should be set to 1 and the status should reflect the
- how xrefs from this external database are used by web.
-
- For example a new external_db 'Celera_gene' could be added as the
- following:
-
- 400 Celera_Gene 1 PRED 1 0 5 Celera gene MISC \N \N
-
- (b) Commit the external_dbs.txt file using cvs commit. This is to
- ensure that nobody else who may also be updating the file will use
- the same identifier that you chose (in the example ID 400).
-
-
-
-
-(2) Propagate the contents of the file to all of the core style databases
-(core|cdna|vega|otherfeatures). To update all of the core style databases
-for release 56:
-
-perl update_external_dbs.pl -host ens-staging -file external_dbs.txt \
- -user ensadmin -pass secret -release 56
-
-To update the human core database:
-
-perl update_external_dbs.pl -host ens-staging -file external_dbs.txt \
- -user ensadmin -pass secret -dbnames homo_sapiens_core_56_37a
-
-Upon executing the script it will display a list of dbs that the updates
-will be applied and you will have to type 'yes' at a confirmation.
-
-If the databases to be updated contain rows that are not in the file,
-a warning will be given and the database in question skipped.
-
-The flag -nonreleasemode it is used when we we want to load the master
-database (use in combination with -master): e.g. we want to create a new
-database with all the external_db from the file
-
-The flag -force is used to update the databases even there is a difference
-between the master file and the databases. This should only be used when
-we are sure the data in the database is wrong/not necessary and we want to
-overwrite it with the information in the external_db.txt file.
-
-In Ensembl, the release coordinator is responsible for running this script
-during the release process.
diff --git a/misc-scripts/external_db/convert_external_dbs.pl b/misc-scripts/external_db/convert_external_dbs.pl
deleted file mode 100644
index 89660e7997..0000000000
--- a/misc-scripts/external_db/convert_external_dbs.pl
+++ /dev/null
@@ -1,73 +0,0 @@
-use strict;
-use warnings;
-use DBI;
-
-my $user = 'ecs2dadmin';
-my $host = 'ecs2d';
-my $pass = 'TyhRv';
-my $dbname = shift;
-
-my $dbh = DBI->connect("DBI:mysql:host=$host;dbname=$dbname;", $user, $pass,
- {RaiseError => 1});
-
-#
-# Store the old external_db table in a hash
-#
-my $sth = $dbh->prepare('SELECT external_db_id, db_name
- FROM external_db');
-
-print STDERR "READING OLD EXTERNAL DB\n";
-$sth->execute();
-my %old_ext_db = map {$_->[0], $_->[1]} @{$sth->fetchall_arrayref};
-$sth->finish();
-
-
-#
-# drop the existing external_db table and replace it with the new table
-#
-print STDERR "REPLACING OLD EXTERNAL DB\n";
-
-`cat external_db.sql | mysql -h $host -u $user -p$pass $dbname`;
-
-#
-# Store the new external_db table in a hash
-#
-print STDERR "READING NEW EXTERNAL DB\n";
-$sth->execute();
-my %new_ext_db = map {$_->[1], $_->[0]} @{$sth->fetchall_arrayref};
-$sth->finish();
-
-#
-# update each row in the xref table
-#
-print STDERR "UPDATING XREF TABLE\n";
-$sth = $dbh->prepare('SELECT external_db_id, xref_id FROM xref');
-my($external_db_id, $xref_id);
-$sth->execute();
-$sth->bind_columns(\$external_db_id, \$xref_id);
-
-my $update_sth =
- $dbh->prepare('UPDATE xref SET external_db_id = ? WHERE xref_id = ?');
-
-my $count = 0;
-
-while($sth->fetch()) {
- my $dbname = $old_ext_db{$external_db_id};
- my $id = $new_ext_db{$dbname};
- if($id) {
- $update_sth->execute($id, $xref_id);
- $count++;
- if($count % 1_000 == 0) {
- print STDERR '.';
- }
- } else {
- warn("Could not convert ext_id=[$external_db_id] dbname=[$dbname]\n");
- }
-}
-
-$sth->finish();
-
-$dbh->disconnect();
-
-print STDERR "COMPLETE. Converted $count xrefs.\n";
-
diff --git a/misc-scripts/external_db/external_dbs.txt b/misc-scripts/external_db/external_dbs.txt
deleted file mode 100644
index 85fa39b350..0000000000
--- a/misc-scripts/external_db/external_dbs.txt
+++ /dev/null
@@ -1,337 +0,0 @@
-210 Anopheles_symbol NULL KNOWN 1 0 50 Anopheles symbol MISC NULL NULL NULL
-211 VB_Community_Symbol NULL KNOWN 1 0 50 VB Community Symbol MISC NULL NULL NULL
-300 BRIGGSAE_HYBRID NULL KNOWNXREF 1 0 5 Briggsae Hybrid MISC NULL NULL NULL
-400 Celera_Gene NULL PRED 1 0 5 Celera gene MISC NULL NULL NULL
-410 Celera_Pep NULL PRED 1 0 5 Celera peptide MISC NULL NULL NULL
-420 Celera_Trans NULL PRED 1 0 5 Celera transcript MISC NULL NULL NULL
-600 DROS_ORTH NULL ORTH 1 0 5 DROS ORTH MISC NULL NULL NULL
-700 EMBL NULL KNOWNXREF 1 0 5 European Nucleotide Archive (was EMBL) MISC NULL NULL NULL
-701 EMBL_predicted NULL PRED 1 0 4 Predicted European Nucleotide Archive (was EMBL) MISC NULL NULL NULL
-800 flybase_gene_id NULL KNOWNXREF 1 0 5 Flybase Gene MISC NULL NULL NULL
-801 flybase_translation_id NULL KNOWNXREF 1 0 5 Flybase translation ID MISC NULL NULL NULL
-802 flybase_gff NULL KNOWNXREF 1 0 5 Flybase GFF MISC NULL NULL NULL
-803 flybase_polypeptide_id NULL KNOWNXREF 1 0 5 Flybase Polypeptide ID MISC NULL NULL NULL
-804 flybase_annotation_id NULL KNOWNXREF 1 0 5 Flybase Annotation ID MISC NULL NULL NULL
-805 flybase_symbol NULL KNOWNXREF 1 0 50 Flybase Symbol MISC NULL NULL NULL
-806 flybase_synonym NULL KNOWNXREF 1 0 5 Flybase Synonym MISC NULL NULL NULL
-807 flybase_name NULL KNOWNXREF 1 0 5 Flybase Name MISC NULL NULL NULL
-808 flybase_transcript_id NULL KNOWNXREF 1 0 5 Flybase transcript ID MISC NULL NULL NULL
-810 gadfly_gene_cgid NULL XREF 1 0 10 Gadfly gene CGID MISC NULL NULL NULL
-811 gadfly_transcript_cgid NULL XREF 1 0 10 Gadfly transcript CGID MISC NULL NULL NULL
-812 gadfly_translation_cgid NULL XREF 1 0 10 Gadfly translation CGID MISC NULL NULL NULL
-821 FlyBaseName_gene NULL KNOWN 1 0 5 FlyBaseName gene MISC NULL NULL NULL
-824 FlyBaseName_translation NULL KNOWN 1 0 5 FlyBaseName translation MISC NULL NULL NULL
-825 FlyBaseName_transcript NULL XREF 1 0 50 FlyBaseName transcript MISC NULL NULL NULL
-826 FlyBaseCGID_gene NULL XREF 1 0 5 FlyBaseCGID gene MISC NULL NULL NULL
-827 FlyBaseCGID_transcript NULL XREF 1 0 50 FlyBaseCGID transcript MISC NULL NULL NULL
-828 FlyBaseCGID_translation NULL XREF 1 0 50 FlyBaseCGID translation MISC NULL NULL NULL
-880 BDGP_insitu_expr NULL KNOWNXREF 1 0 5 Berkeley Drosophila Genome Project in situ Gene Expression Database (embryogenesis) MISC NULL NULL NULL
-882 FlyGrid NULL KNOWNXREF 1 0 5 FlyGRID Interaction Data, The General Repository for Interaction Datasets MISC NULL NULL NULL
-883 FlyReactome NULL KNOWNXREF 1 0 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC NULL NULL NULL
-890 DEDb NULL KNOWNXREF 1 0 5 Drosophila melanogaster Exon Database MISC NULL NULL NULL
-900 GKB NULL XREF 1 0 5 GKB MISC NULL NULL NULL
-1000 GO NULL XREF 1 0 5 GO MISC NULL NULL NULL
-250 ImmunoDB 1 KNOWN 1 0 50 ImmunoDB MISC NULL NULL NULL
-1100 HGNC NULL KNOWNXREF 1 1 100 HGNC Symbol PRIMARY_DB_SYNONYM NULL NULL NULL
-1200 Interpro NULL XREF 1 0 5 InterPro MISC NULL NULL NULL
-1300 EntrezGene NULL KNOWNXREF 1 0 10 EntrezGene MISC NULL NULL NULL
-1400 MGI NULL KNOWNXREF 1 1 50 MGI Symbol MISC NULL NULL NULL
-1500 MIM NULL KNOWNXREF 1 0 5 MIM MISC NULL NULL NULL
-1510 MIM_GENE NULL KNOWNXREF 1 0 5 MIM gene MISC NULL NULL NULL
-1520 MIM_MORBID NULL KNOWNXREF 1 0 5 MIM disease MISC NULL NULL NULL
-1600 PDB NULL KNOWNXREF 1 0 5 PDB MISC NULL NULL NULL
-1700 protein_id NULL KNOWNXREF 1 0 5 Protein ID MISC NULL NULL NULL
-1701 protein_id_predicted NULL PRED 1 0 4 Predicted Protein ID MISC NULL NULL NULL
-1800 RefSeq_dna NULL KNOWN 1 0 25 RefSeq DNA MISC NULL NULL NULL
-214 VB_Community_Annotation 1 KNOWN 1 0 50 VB Community Annotation MISC NULL NULL NULL
-1805 RefSeq_dna_predicted NULL PRED 1 0 15 RefSeq DNA predicted MISC NULL NULL NULL
-1810 RefSeq_peptide NULL KNOWN 1 0 26 RefSeq peptide MISC NULL NULL NULL
-213 VB_RNA_Description 1 PRED 1 0 50 VB RNA Description MISC NULL NULL NULL
-1815 RefSeq_peptide_predicted NULL PRED 1 0 16 RefSeq peptide predicted MISC NULL NULL NULL
-1820 RefSeq_rna NULL KNOWN 1 0 24 RefSeq RNA MISC NULL NULL NULL
-1825 RefSeq_rna_predicted NULL PRED 1 0 14 RefSeq RNA predicted MISC NULL NULL NULL
-1830 RefSeq_genomic NULL KNOWN 1 0 23 RefSeq Genomic MISC NULL NULL NULL
-1900 Sanger_Hver1_2_1 NULL XREF 1 0 5 Sanger Hver 121 MISC NULL NULL NULL
-1901 Sanger_Hver1_3_1 NULL XREF 1 0 5 Sanger Hver 131 MISC NULL NULL NULL
-1902 SNGR_Hver NULL XREF 1 0 5 Sanger Hver MISC NULL NULL NULL
-1910 Sanger_Mver1_1_1 NULL XREF 1 0 5 Sanger Hver 111 MISC NULL NULL NULL
-2000 Uniprot/SPTREMBL NULL KNOWN 1 0 20 UniProtKB/TrEMBL MISC NULL NULL NULL
-2001 Uniprot/SPTREMBL_predicted NULL PRED 1 0 15 Predicted UniProtKB/TrEMBL MISC NULL NULL NULL
-2010 prediction_SPTREMBL NULL XREF 1 1 10 Prediction UniProtKB/TrEMBL MISC NULL NULL NULL
-2100 Superfamily NULL KNOWNXREF 1 0 5 Superfamily MISC NULL NULL NULL
-2200 Uniprot/SWISSPROT NULL KNOWN 1 1 30 UniProtKB/Swiss-Prot MISC NULL NULL NULL
-2201 Uniprot/SWISSPROT_predicted NULL PRED 1 1 15 Predicted UniProtKB/Swiss-Prot MISC NULL NULL NULL
-2202 Uniprot/Varsplic NULL KNOWN 1 1 15 UniprotKB/SpliceVariant MISC NULL NULL NULL
-2250 UniProtKB_all NULL XREF 1 0 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC NULL NULL NULL
-2300 Vega_gene NULL KNOWNXREF 1 0 5 Vega gene MISC NULL NULL NULL
-2305 Vega_gene_like NULL XREF 1 0 5 Vega gene like MISC NULL NULL NULL
-2310 Vega_transcript NULL KNOWNXREF 1 0 5 Vega transcript MISC NULL NULL NULL
-2315 Vega_transcript_like NULL XREF 1 0 5 Vega transcript like MISC NULL NULL NULL
-2320 Vega_translation NULL KNOWNXREF 1 0 5 Vega translation MISC NULL NULL NULL
-2400 wormbase_gene NULL KNOWN 1 0 5 Wormbase Gene MISC NULL NULL NULL
-2410 wormbase_transcript NULL KNOWN 1 0 5 Wormbase Transcript MISC NULL NULL NULL
-2420 wormpep_id NULL KNOWN 1 0 5 Wormpep ID MISC NULL NULL NULL
-2430 wormbase_pseudogene NULL PSEUDO 1 0 5 Wormbase Pseudogene MISC NULL NULL NULL
-2440 wormbase_locus NULL KNOWN 1 0 5 Wormbase Locus MISC NULL NULL NULL
-2510 ZFIN_ID NULL KNOWNXREF 1 1 5 ZFIN PRIMARY_DB_SYNONYM NULL NULL NULL
-2530 ZFIN_xpat NULL KNOWNXREF 1 0 4 ZFIN expression patterns MISC NULL NULL NULL
-2600 GeneDB NULL KNOWN 1 0 5 GeneDB MISC NULL NULL NULL
-2601 cint_jgi_v1 NULL KNOWN 1 0 10 JGI Gene ID (JGI 1.0) MISC NULL NULL NULL
-2602 cint_jgi_v2 NULL KNOWN 1 0 5 JGI Gene ID (JGI 2.0) MISC NULL NULL NULL
-2610 cint_aniseed_v1 NULL KNOWN 1 0 5 ANISEED (JGI 1.0) MISC NULL NULL NULL
-2611 cint_aniseed_v2 NULL KNOWN 1 0 5 ANISEED (JGI 2.0) MISC NULL NULL NULL
-2700 Ens_Hs_gene NULL XREF 1 0 5 Ensembl Human Gene MISC NULL NULL NULL
-2710 Ens_Hs_transcript NULL XREF 1 0 5 Ensembl Human Transcript MISC NULL NULL NULL
-2720 Ens_Hs_translation NULL XREF 1 0 5 Ensembl Human Translation MISC NULL NULL NULL
-2800 RGD NULL KNOWNXREF 1 1 50 RGD Symbol MISC NULL NULL NULL
-2900 Genoscope_pred_gene NULL XREF 1 0 38 Genoscope pred gene MISC NULL NULL NULL
-2910 Genoscope_pred_transcript NULL XREF 1 0 39 Genoscope pred transcript MISC NULL NULL NULL
-2920 Genoscope_annotated_gene NULL KNOWN 1 0 40 Genoscope annotated gene MISC NULL NULL NULL
-2930 Genoscope_pred_translation NULL XREF 1 0 40 Genoscope pred translation MISC NULL NULL NULL
-2940 Genoscope_ann_transcript NULL KNOWN 1 0 40 Genoscope annotated transcript MISC NULL NULL NULL
-2950 Genoscope_ann_translation NULL KNOWN 1 0 40 Genoscope annotated translation MISC NULL NULL NULL
-3300 miRBase NULL KNOWNXREF 1 0 1 miRBase MISC NULL NULL NULL
-3310 miRBase_predicted NULL XREF 1 0 1 miRBase predicted MISC NULL NULL NULL
-3400 SGD NULL KNOWN 1 1 50 SGD MISC NULL NULL NULL
-3500 IPI NULL KNOWN 1 0 5 IPI MISC NULL NULL NULL
-3800 CCDS NULL KNOWN 1 0 50 CCDS MISC NULL NULL NULL
-3900 PUBMED NULL KNOWN 1 0 5 Sequence Publications LIT NULL NULL NULL
-4000 MEDLINE NULL KNOWN 1 0 5 MEDLINE LIT NULL NULL NULL
-4100 UniGene NULL KNOWN 1 0 5 UniGene MISC NULL NULL NULL
-212 VB_External_Description 1 PRED 1 0 50 VB External Description MISC NULL NULL NULL
-4200 RFAM NULL XREF 1 0 5 RFAM MISC NULL NULL NULL
-4400 Xenopus_Jamboree NULL KNOWN 1 0 1 Jamboree MISC NULL NULL NULL
-4500 Tiffin NULL XREF 1 0 1 Tiffin DNA motifs MISC NULL NULL NULL
-4600 OTTG NULL XREF 1 0 1 Havana gene ALT_GENE NULL NULL NULL
-4610 OTTT NULL XREF 1 0 1 Havana transcript ALT_TRANS NULL NULL NULL
-4620 OTTP NULL XREF 1 0 1 Havana translation MISC NULL NULL NULL
-4650 shares_CDS_with NULL XREF 1 0 1 transcript having same CDS ALT_TRANS NULL NULL NULL
-4660 shares_CDS_with_ENST NULL XREF 1 0 1 Imported HAVANA transcripts (Shares CDS with ENST) ALT_TRANS NULL NULL NULL
-4670 shares_CDS_with_OTTT NULL XREF 1 0 1 Havana transcript having same CDS ALT_TRANS NULL NULL NULL
-4680 shares_CDS_and_UTR_with_OTTT NULL XREF 1 0 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS NULL NULL NULL
-4690 ENSG NULL XREF 1 0 1 Ensembl gene ALT_GENE NULL NULL NULL
-4700 Medaka NULL XREF 1 0 1 Medaka Genome Project MISC NULL NULL NULL
-4800 ENST NULL XREF 1 0 1 Ensembl transcript having exact match with Havana ALT_TRANS NULL NULL NULL
-4810 ENST_ident NULL XREF 1 0 1 Ensembl transcript having exact match with Havana ALT_TRANS NULL NULL NULL
-4820 ENST_CDS NULL XREF 1 0 1 Ensembl transcript sharing CDS with Havana ALT_TRANS NULL NULL NULL
-4900 TCAG NULL KNOWN 1 0 75 TCAG Chr 7 Annotation MISC NULL NULL NULL
-5000 Ens_Mm_gene NULL XREF 1 0 40 Ensembl Mouse Gene MISC NULL NULL NULL
-5010 Ens_Mm_transcript NULL XREF 1 0 40 Ensembl Mouse Transcript MISC NULL NULL NULL
-5020 Ens_Mm_translation NULL XREF 1 0 40 Ensembl Mouse Translation MISC NULL NULL NULL
-5100 IMGT_HLA NULL KNOWN 1 0 7 IMGT/HLA MISC NULL NULL NULL
-5200 Oxford_FGU_Md_gene NULL PRED 1 0 1 Oxford Ponting Group Monodelphis predictions gene id ALT_TRANS NULL NULL NULL
-5300 Oxford_FGU_Md_tscript NULL PRED 1 0 1 Oxford Ponting Group Monodelphis predictions transcript id ALT_TRANS NULL NULL NULL
-5400 Oxford_FGU_Oa_gene NULL PRED 1 0 1 Oxford Ponting Group Platypus predictions gene id ALT_TRANS NULL NULL NULL
-5500 Oxford_FGU_Oa_tscript NULL PRED 1 0 1 Oxford Ponting Group Platypus predictions transcript id ALT_TRANS NULL NULL NULL
-5700 Ens_Cf_gene NULL XREF 1 0 5 Ensembl Dog Gene MISC NULL NULL NULL
-5710 Ens_Cf_transcript NULL XREF 1 0 5 Ensembl Dog Transcript MISC NULL NULL NULL
-5720 Ens_Cf_translation NULL XREF 1 0 5 Ensembl Dog Translation MISC NULL NULL NULL
-5800 Ens_Dr_gene NULL XREF 1 0 5 Ensembl Zebrafish Gene MISC NULL NULL NULL
-5810 Ens_Dr_transcript NULL XREF 1 0 5 Ensembl Zebrafish Transcript MISC NULL NULL NULL
-5820 Ens_Dr_translation NULL XREF 1 0 5 Ensembl Zebrafish Translation MISC NULL NULL NULL
-5900 Ens_Md_gene NULL XREF 1 0 5 Ensembl Monodelphis Gene MISC NULL NULL NULL
-6100 Havana_gene NULL XREF 1 0 100 Havana gene ID MISC NULL NULL NULL
-6200 Ens_Rn_gene NULL XREF 1 0 5 Ensembl Rat Gene MISC NULL NULL NULL
-6300 Ens_Ol_gene NULL XREF 1 0 5 Ensembl Medaka Gene MISC NULL NULL NULL
-6400 Ens_Gg_gene NULL XREF 1 0 40 Ensembl Chicken Gene MISC NULL NULL NULL
-6410 Ens_Gg_transcript NULL XREF 1 0 40 Ensembl Chicken Transcript MISC NULL NULL NULL
-6420 Ens_Gg_translation NULL XREF 1 0 40 Ensembl Chicken Translation MISC NULL NULL NULL
-6500 IMCB_Tr_gene NULL XREF 1 0 40 IMCB Fugu Gene MISC NULL NULL NULL
-6600 Ens_Ag_gene NULL XREF 1 0 5 Ensembl Mosquito Gene MISC NULL NULL NULL
-6630 Ens_Am_gene NULL XREF 1 0 5 Ensembl Bee Gene MISC NULL NULL NULL
-6660 Ens_Ce_gene NULL XREF 1 0 5 Ensembl Worm Gene MISC NULL NULL NULL
-6690 Ens_Dm_gene NULL XREF 1 0 5 Ensembl FruitFly Gene MISC NULL NULL NULL
-6720 Ens_Fr_gene NULL XREF 1 0 5 Ensembl Fugu Gene MISC NULL NULL NULL
-6750 Ens_Pt_gene NULL XREF 1 0 5 Ensembl Chimpanzee Gene MISC NULL NULL NULL
-6780 Ens_Rn_gene NULL XREF 1 0 5 Ensembl Rat Gene MISC NULL NULL NULL
-6810 Ens_Tn_gene NULL XREF 1 0 5 Ensembl PufferFish Gene MISC NULL NULL NULL
-6820 Ens_Tr_transcript NULL XREF 1 0 40 Ensembl Fugu Transcript MISC NULL NULL NULL
-7120 Ens_Aa_translation NULL XREF 1 0 40 Ensembl Aedes Translation MISC NULL NULL NULL
-7159 AedesGenBank NULL PRED 1 0 30 Aedes GenBank MISC NULL NULL NULL
-7160 Aedes_ManualAnnotation NULL PRED 1 0 30 Aedes ManualAnnotation MISC NULL NULL NULL
-7170 Ixodes_ManualAnnotation NULL PRED 1 0 30 Ixodes ManualAnnotation MISC NULL NULL NULL
-7200 IMGT/LIGM_DB NULL XREF 1 1 10 IMGT/LIGM-DB MISC NULL NULL NULL
-7201 IMGT/GENE_DB NULL KNOWN 1 0 40 IMGT/GENE-DB MISC NULL NULL NULL
-8000 Vega_mouse_transcript NULL XREF 1 0 5 Vega mouse transcript MISC NULL NULL NULL
-8100 Platypus_olfactory_receptor NULL XREF 1 0 40 Platypus olfactory receptor gene MISC NULL NULL NULL
-8200 PRF NULL XREF 1 0 5 PRF MISC NULL NULL NULL
-8300 PIR NULL XREF 1 0 5 PIR MISC NULL NULL NULL
-8400 TetNig_cdna NULL XREF 1 0 40 Genoscope tetraodon cDNA MISC NULL NULL NULL
-8500 GasAcu_cdna NULL XREF 1 0 40 Stickleback cDNA MISC NULL NULL NULL
-8600 OrnAna_454_cdna NULL XREF 1 0 40 Platypus 454 cDNA MISC NULL NULL NULL
-8700 TakRub_cdna NULL XREF 1 0 40 Takifugu cDNA MISC NULL NULL NULL
-8800 CioInt_est NULL XREF 1 0 40 Ciona intestinalis EST MISC NULL NULL NULL
-8900 CioInt_cdna NULL XREF 1 0 40 Ciona intestinalis cDNA MISC NULL NULL NULL
-9000 CaeEle_est NULL XREF 1 0 40 C Elegans EST MISC NULL NULL NULL
-9100 XenTro_Gurdon_EST NULL XREF 1 0 40 Xenopus Gurdon EST Clusters MISC NULL NULL NULL
-9110 XenTro_cdna NULL XREF 1 0 40 Xenopus Tropicalis cDNA MISC NULL NULL NULL
-9120 XenLae_cdna NULL XREF 1 0 40 Xenopus Laevis cDNA MISC NULL NULL NULL
-9200 TakRub_est NULL XREF 1 0 40 Takifugu EST MISC NULL NULL NULL
-9210 TakRub_annotation NULL XREF 1 0 40 Takifugu gene annotation MISC NULL NULL NULL
-9220 TakRub_seleno_annotation NULL XREF 1 0 40 Takifugu selenoprotein annotation MISC NULL NULL NULL
-9400 TetNig_mouse_econtig NULL XREF 1 0 40 Genoscope mouse exofish econtig MISC NULL NULL NULL
-9410 TetNig_fugu_econtig NULL XREF 1 0 40 Genoscope fugu exofish econtig MISC NULL NULL NULL
-9420 TetNig_human_econtig NULL XREF 1 0 40 Genoscope human exofish econtig MISC NULL NULL NULL
-9430 TetNig_human_IPI_econtig NULL XREF 1 0 40 Genoscope human IPI exofish econtig MISC NULL NULL NULL
-9440 TetNig_mouse_IPI_econtig NULL XREF 1 0 40 Genoscope mouse IPI exofish econtig MISC NULL NULL NULL
-9450 TetNig_rat_econtig NULL XREF 1 0 40 Genoscope rat exofish econtig MISC NULL NULL NULL
-9460 TetNig_chick_econtig NULL XREF 1 0 40 Genoscope chicken exofish econtig MISC NULL NULL NULL
-9500 OryLat_est NULL XREF 1 0 40 Medaka EST MISC NULL NULL NULL
-9600 Trace_archive NULL XREF 1 0 40 Trace Archive id MISC NULL NULL NULL
-9700 CioSav_est NULL XREF 1 0 40 Ciona savignyi EST MISC NULL NULL NULL
-9800 kyotograil_2004 NULL PRED 1 0 30 Ciona intestinalis Kyotograil 2004 predictions MISC NULL NULL NULL
-9900 kyotograil_2005 NULL PRED 1 0 30 Ciona intestinalis Kyotograil 2005 predictions MISC NULL NULL NULL
-10000 wormbase_id NULL XREF 1 0 30 Generic exdb for worbase id of any type for feature table MISC NULL NULL NULL
-10100 EPD NULL KNOWNXREF 1 0 5 Eukaryotic Promoter Database (Bucher) MISC NULL NULL NULL
-10200 GPCR NULL KNOWNXREF 1 0 5 The G protein-coupled receptor database MISC NULL NULL NULL
-10300 MEROPS NULL KNOWNXREF 1 0 5 MEROPS - the Peptidase Database MISC NULL NULL NULL
-10500 TransFac NULL KNOWNXREF 1 0 5 TransFac, database of transcription factors and their binding sites MISC NULL NULL NULL
-10600 modCB_gene NULL KNOWNXREF 1 0 5 Caenorhabditis briggsae, InParanoid model organism database MISC NULL NULL NULL
-10700 modCE_gene NULL KNOWNXREF 1 0 5 Caenorhabditis elegans, InParanoid model organism database MISC NULL NULL NULL
-10800 modDD_gene NULL KNOWNXREF 1 0 5 Dictyostelium discoideum, InParanoid model organism database MISC NULL NULL NULL
-10900 GI NULL XREF 1 0 5 GenInfo Identifier, a sequence identification number for a nucleotide sequence MISC NULL NULL NULL
-11000 UCSC NULL KNOWNXREF 1 0 100 UCSC Stable ID MISC NULL NULL NULL
-11100 Culex_ncRNA NULL XREF 1 0 70 Culex ncRNAs MISC NULL NULL NULL
-12300 HGNC_curated_gene NULL KNOWNXREF 1 0 5 HGNC (curated) MISC NULL NULL NULL
-12305 HGNC_automatic_gene NULL KNOWNXREF 1 0 5 HGNC (automatic) MISC NULL NULL NULL
-12310 Clone_based_vega_gene NULL KNOWNXREF 1 0 5 Clone-based (Vega) MISC NULL NULL NULL
-12315 Clone_based_ensembl_gene NULL XREF 1 0 5 Clone-based (Ensembl) MISC NULL NULL NULL
-12400 HGNC_curated_transcript NULL KNOWNXREF 1 0 5 HGNC (curated) MISC NULL NULL NULL
-12405 HGNC_automatic_transcript NULL KNOWNXREF 1 0 5 HGNC (automatic) MISC NULL NULL NULL
-12410 Clone_based_vega_transcript NULL KNOWNXREF 1 0 5 Clone-based (Vega) MISC NULL NULL NULL
-12415 Clone_based_ensembl_transcript NULL XREF 1 0 5 Clone-based (Ensembl) MISC NULL NULL NULL
-12500 DBASS3 NULL XREF 1 0 50 DataBase of Aberrant 3' Splice Sites MISC NULL NULL NULL
-12505 DBASS5 NULL XREF 1 0 50 DataBase of Aberrant 5' Splice Sites MISC NULL NULL NULL
-12510 HPA NULL XREF 1 0 50 Human Protein Atlas MISC NULL NULL NULL
-12550 MGI_curated_gene NULL KNOWNXREF 1 0 5 MGI (curated) MISC NULL NULL NULL
-12555 MGI_automatic_gene NULL KNOWNXREF 1 0 5 MGI (automatic) MISC NULL NULL NULL
-12560 MGI_curated_transcript NULL KNOWNXREF 1 0 5 MGI (curated) MISC NULL NULL NULL
-12565 MGI_automatic_transcript NULL KNOWNXREF 1 0 5 MGI (automatic) MISC NULL NULL NULL
-12600 WikiGene NULL XREF 0 1 50 WikiGene MISC NULL NULL NULL
-12601 Tgut_symbol NULL KNOWNXREF 0 0 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM NULL NULL NULL
-12610 Fantom NULL XREF 0 1 50 Fantom MISC NULL NULL NULL
-12620 Duck_consortium NULL XREF 0 0 0 Duck consortium MISC NULL NULL NULL
-12630 BGI_duck_transcriptome NULL XREF 0 0 0 Beijing Genomics Institute (BGI) duck transcriptome MISC NULL NULL NULL
-12700 goslim_goa NULL XREF 1 0 5 GOSlim GOA MISC NULL NULL NULL
-12710 WTSI_gorilla_transcriptome NULL XREF 0 0 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC NULL NULL NULL
-12720 WTSI_zebrafish_transcriptome NULL XREF 0 0 0 Wellcome Trust Sanger Institute (WTSI) zebrafish transcriptome MISC NULL NULL NULL
-20005 UniParc NULL KNOWNXREF 1 0 0 UniParc PRIMARY_DB_SYNONYM NULL NULL NULL
-20008 BRENDA NULL KNOWNXREF 1 0 0 BRENDA PRIMARY_DB_SYNONYM NULL NULL NULL
-20009 BioCyc NULL KNOWNXREF 1 0 0 BioCyc PRIMARY_DB_SYNONYM NULL NULL NULL
-20010 BuruList NULL KNOWNXREF 1 0 0 BuruList PRIMARY_DB_SYNONYM NULL NULL NULL
-20013 EchoBASE NULL KNOWNXREF 1 0 0 EchoBASE PRIMARY_DB_SYNONYM NULL NULL NULL
-20014 EcoGene NULL KNOWNXREF 1 0 0 EcoGene PRIMARY_DB_SYNONYM NULL NULL NULL
-20017 GeneDB_Spombe NULL KNOWNXREF 1 0 0 GeneDB_Spombe PRIMARY_DB_SYNONYM NULL NULL NULL
-20025 Leproma NULL KNOWNXREF 1 0 0 Leproma PRIMARY_DB_SYNONYM NULL NULL NULL
-20031 2DBase_Ecoli NULL KNOWNXREF 1 0 0 2DBase-Ecoli PRIMARY_DB_SYNONYM NULL NULL NULL
-20038 SagaList NULL KNOWNXREF 1 0 0 SagaList PRIMARY_DB_SYNONYM NULL NULL NULL
-20040 SubtiList NULL KNOWNXREF 1 0 0 SubtiList PRIMARY_DB_SYNONYM NULL NULL NULL
-20042 TIGR NULL KNOWNXREF 1 0 0 TIGR PRIMARY_DB_SYNONYM NULL NULL NULL
-20043 TubercuList NULL KNOWNXREF 1 0 0 TubercuList PRIMARY_DB_SYNONYM NULL NULL NULL
-20046 ArrayExpress NULL KNOWNXREF 1 0 0 ArrayExpress PRIMARY_DB_SYNONYM NULL NULL NULL
-20050 GermOnline NULL KNOWNXREF 1 0 0 GermOnline PRIMARY_DB_SYNONYM NULL NULL NULL
-20059 DIP NULL KNOWNXREF 1 0 0 DIP PRIMARY_DB_SYNONYM NULL NULL NULL
-20061 DisProt NULL KNOWNXREF 1 0 0 DisProt PRIMARY_DB_SYNONYM NULL NULL NULL
-20062 DrugBank NULL KNOWNXREF 1 0 0 DrugBank PRIMARY_DB_SYNONYM NULL NULL NULL
-20065 GlycoSuiteDB NULL KNOWNXREF 1 0 0 GlycoSuiteDB PRIMARY_DB_SYNONYM NULL NULL NULL
-20066 HAMAP NULL KNOWNXREF 1 0 0 HAMAP PRIMARY_DB_SYNONYM NULL NULL NULL
-20067 HOGENOM NULL KNOWNXREF 1 0 0 HOGENOM PRIMARY_DB_SYNONYM NULL NULL NULL
-20071 HSSP NULL KNOWNXREF 1 0 0 HSSP PRIMARY_DB_SYNONYM NULL NULL NULL
-20072 IntAct NULL KNOWNXREF 1 0 0 IntAct PRIMARY_DB_SYNONYM NULL NULL NULL
-20074 KEGG NULL KNOWNXREF 1 0 0 KEGG PRIMARY_DB_SYNONYM NULL NULL NULL
-20078 PDBsum NULL KNOWNXREF 1 0 0 PDBsum PRIMARY_DB_SYNONYM NULL NULL NULL
-20082 PeroxiBase NULL KNOWNXREF 1 0 0 PeroxiBase PRIMARY_DB_SYNONYM NULL NULL NULL
-20083 PhosSite NULL KNOWNXREF 1 0 0 PhosSite PRIMARY_DB_SYNONYM NULL NULL NULL
-20084 PptaseDB NULL KNOWNXREF 1 0 0 PptaseDB PRIMARY_DB_SYNONYM NULL NULL NULL
-20085 REBASE NULL KNOWNXREF 1 0 0 REBASE PRIMARY_DB_SYNONYM NULL NULL NULL
-20088 Reactome NULL KNOWNXREF 1 0 0 Reactome PRIMARY_DB_SYNONYM NULL NULL NULL
-20090 SWISS_2DPAGE NULL KNOWNXREF 1 0 0 SWISS-2DPAGE PRIMARY_DB_SYNONYM NULL NULL NULL
-20097 RegulonDb_Transcript NULL KNOWNXREF 1 0 0 RegulonDb PRIMARY_DB_SYNONYM NULL NULL NULL
-20099 RegulonDb_Gene NULL KNOWNXREF 1 0 0 RegulonDb PRIMARY_DB_SYNONYM NULL NULL NULL
-20101 IntEnz NULL KNOWNXREF 1 0 0 EnzymeCommission PRIMARY_DB_SYNONYM NULL NULL NULL
-20102 ArrayExpressExperiment NULL KNOWNXREF 1 0 0 ArrayExpressExperiment PRIMARY_DB_SYNONYM NULL NULL NULL
-20200 EMBLBANK_GENE NULL KNOWNXREF 0 0 0 European Nucleotide Archive PRIMARY_DB_SYNONYM NULL NULL NULL
-20201 GeneDB_SPombe_transcript NULL KNOWNXREF 0 0 0 GeneDB_SPombe PRIMARY_DB_SYNONYM NULL NULL NULL
-20202 EBACTERIA_GENE NULL KNOWNXREF 0 0 0 e!Bacteria PRIMARY_DB_SYNONYM NULL NULL NULL
-20203 EBACTERIA_TRANSCRIPT NULL KNOWNXREF 0 0 0 e!Bacteria PRIMARY_DB_SYNONYM NULL NULL NULL
-20204 EPROTIST_GENE NULL KNOWNXREF 0 0 0 e!Protists PRIMARY_DB_SYNONYM NULL NULL NULL
-20205 EPROTIST_TRANSCRIPT NULL KNOWNXREF 0 0 0 e!Protists PRIMARY_DB_SYNONYM NULL NULL NULL
-20207 EFUNGI_GENE NULL KNOWNXREF 0 0 0 e!Fungi PRIMARY_DB_SYNONYM NULL NULL NULL
-20208 EFUNGI_TRANSCRIPT NULL KNOWNXREF 0 0 0 e!Fungi PRIMARY_DB_SYNONYM NULL NULL NULL
-20209 EMBLBANK_TRANSCRIPT NULL KNOWNXREF 0 0 0 European Nucleotide Archive PRIMARY_DB_SYNONYM NULL NULL NULL
-20210 GeneDB_SPombe_gene NULL KNOWNXREF 0 0 0 GeneDB_SPombe PRIMARY_DB_SYNONYM NULL NULL NULL
-20301 RNAMMER NULL KNOWNXREF 1 0 0 RNAmmer MISC NULL NULL NULL
-20302 TRNASCAN_SE NULL KNOWNXREF 1 0 0 tRNAScan-SE MISC NULL NULL NULL
-20303 dictyBase NULL KNOWNXREF 1 0 0 DictyBase PRIMARY_DB_SYNONYM NULL NULL NULL
-20304 dictyBase_gene NULL KNOWNXREF 1 0 0 DictyBase PRIMARY_DB_SYNONYM NULL NULL NULL
-20305 dictyBase_transcript NULL KNOWNXREF 1 0 0 DictyBase PRIMARY_DB_SYNONYM NULL NULL NULL
-20306 ASPGD NULL KNOWNXREF 1 0 0 AspGD PRIMARY_DB_SYNONYM NULL NULL NULL
-20307 ASPGD_GENE NULL KNOWNXREF 1 0 0 AspGD PRIMARY_DB_SYNONYM NULL NULL NULL
-20308 ASPGD_TRANSCRIPT NULL KNOWNXREF 1 0 0 AspGD PRIMARY_DB_SYNONYM NULL NULL NULL
-20309 CADRE NULL KNOWNXREF 1 0 0 CADRE PRIMARY_DB_SYNONYM NULL NULL NULL
-20310 CADRE_GENE NULL KNOWNXREF 1 0 0 CADRE PRIMARY_DB_SYNONYM NULL NULL NULL
-20311 CADRE_TRANSCRIPT NULL KNOWNXREF 1 0 0 CADRE PRIMARY_DB_SYNONYM NULL NULL NULL
-20312 SGD_GENE NULL KNOWNXREF 1 0 0 SGD PRIMARY_DB_SYNONYM NULL NULL NULL
-20313 SGD_TRANSCRIPT NULL KNOWNXREF 1 0 0 SGD PRIMARY_DB_SYNONYM NULL NULL NULL
-20214 phatr_jgi_v2_bd NULL KNOWNXREF 1 0 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM NULL NULL NULL
-20215 phatr_jgi_v2 NULL KNOWNXREF 1 0 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20216 phatr_jgi_v2_bd_gene NULL KNOWNXREF 1 0 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM NULL NULL NULL
-20217 phatr_jgi_v2_gene NULL KNOWNXREF 1 0 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20218 phatr_jgi_v2_bd_transcript NULL KNOWNXREF 1 0 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM NULL NULL NULL
-20219 phatr_jgi_v2_transcript NULL KNOWNXREF 1 0 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20220 thaps_jgi_v2_bd NULL KNOWNXREF 1 0 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM NULL NULL NULL
-20221 thaps_jgi_v2 NULL KNOWNXREF 1 0 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20222 thaps_jgi_v2_gene NULL KNOWNXREF 1 0 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20223 thaps_jgi_v2_bd_gene NULL KNOWNXREF 1 0 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM NULL NULL NULL
-20224 thaps_jgi_v2_gene NULL KNOWNXREF 1 0 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20225 thaps_jgi_v2_bd_transcript NULL KNOWNXREF 1 0 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM NULL NULL NULL
-20226 thaps_jgi_v2_transcript NULL KNOWNXREF 1 0 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM NULL NULL NULL
-20227 Diatom_EST_Cluster NULL XREF 1 0 0 ENS EST Cluster (Diatom ESTDB) MISC NULL NULL NULL
-50000 BGI_EST_Cluster NULL XREF 1 0 0 EST Cluster (BGI Indica) MISC NULL NULL NULL
-50005 EC_NUMBER NULL XREF 1 0 0 Enzyme EC Number MISC NULL NULL NULL
-50010 FSTs NULL XREF 1 0 0 Flanking Sequence Tag (FST) MISC NULL NULL NULL
-50015 gene_name NULL KNOWNXREF 1 0 0 Gene Name MISC NULL NULL NULL
-50020 Gramene_Pathway NULL XREF 1 0 0 Gramene Pathway MISC NULL NULL NULL
-50030 Gramene_GenesDB NULL KNOWNXREF 1 0 100 Gramene Curated Gene MISC NULL NULL NULL
-50035 Gramene_MarkersDB NULL XREF 1 0 0 Gramene MISC NULL NULL NULL
-50040 Gramene_MarkersDB_mRNA NULL XREF 1 0 0 GenBank mRNA (Gramene) MISC NULL NULL NULL
-50050 Gramene_MarkersDB_EST NULL XREF 1 0 0 GenBank EST (Gramene) MISC NULL NULL NULL
-50060 IRGSP_Gene NULL XREF 1 0 0 IRGSP/RAP Gene MISC NULL NULL NULL
-50065 KOME NULL KNOWNXREF 1 0 0 Full Length cDNA (KOME) MISC NULL NULL NULL
-50070 miRNA_Accession NULL XREF 1 0 0 miRNA miRBase accession MISC NULL NULL NULL
-50080 miRNA_Registry NULL XREF 1 0 1 miRNA Registry MISC NULL NULL NULL
-50090 NASC_GENE_ID NULL XREF 1 0 1 NASC Gene ID MISC NULL NULL NULL
-50100 NASC_TRANSCRIPT_ID NULL XREF 1 0 1 NASC Transcript ID MISC NULL NULL NULL
-50110 PlantGDB_PUT NULL XREF 1 0 1 PlantGDB Transcript MISC NULL NULL NULL
-50120 RAP_Gene NULL XREF 1 0 0 IRGSP/RAP Gene MISC NULL NULL NULL
-50130 siRNA_Sunkar NULL XREF 1 0 0 siRNA ID from Sunkar et. al. 2005 NAR 33(14):4443-54 MISC NULL NULL NULL
-50140 TIGR_LOCUS NULL XREF 0 1 1 MSU/TIGR Locus MISC NULL NULL NULL
-50150 TIGR_LOCUS_MODEL NULL XREF 0 1 0 MSU/TIGR Locus (Model) MISC NULL NULL NULL
-50160 TAIR_LOCUS NULL XREF 1 0 8 TAIR Locus MISC NULL NULL NULL
-50170 TAIR_LOCUS_MODEL NULL XREF 1 0 8 TAIR Locus (Model) MISC NULL NULL NULL
-50180 TIGR_GeneIndex NULL XREF 1 0 0 Gene Index MISC NULL NULL NULL
-50185 TO NULL XREF 1 0 0 Plant Trait Ontology MISC NULL NULL NULL
-50190 PO NULL XREF 1 0 0 Plant Structure Ontology MISC NULL NULL NULL
-50195 PO_to_gene NULL XREF 1 0 0 Plant Structure Ontology MISC NULL NULL NULL
-50196 GO_to_gene NULL XREF 1 0 0 Gene Ontology MISC NULL NULL NULL
-50200 GRO NULL XREF 1 0 0 Plant Growth Stage MISC NULL NULL NULL
-50510 AFFY_RICE NULL XREF 1 0 1 Affymx GeneChip Rice ARRAY NULL NULL NULL
-50520 AFFY_ATH1 NULL XREF 1 0 1 Affymx GeneChip ATH1 ARRAY NULL NULL NULL
-50530 AFFY_Vitis_Vinifera NULL XREF 1 0 1 Affymx GeneChip Vitis vinifera ARRAY NULL NULL NULL
-50540 AFFY_Poplar NULL XREF 1 0 1 Affymx GeneChip Poplar ARRAY NULL NULL NULL
-50541 LRG NULL KNOWN 1 0 10 Locus Reference Genomic MISC NULL NULL NULL
-50542 ENS_LRG_gene NULL KNOWN 1 0 10 LRG display in Ensembl MISC NULL NULL NULL
-50543 ENS_LRG_transcript NULL KNOWN 1 0 10 LRG display in Ensembl MISC NULL NULL NULL
-20228 CADRE_Afum_A1163 NULL KNOWNXREF 1 0 0 CADRE PRIMARY_DB_SYNONYM NULL NULL NULL
-50600 IKMCs_KOs NULL XREF 1 0 10 International Knockout Mouse Consortium Knockouts MISC NULL NULL Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse
-50601 IKMCs_ES_cells_available NULL XREF 1 0 10 International Knockout Mouse Consortium Knockouts (ES cells available) MISC NULL NULL Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (ES cells available)
-50602 IKMCs_Mice_available NULL XREF 1 0 10 International Knockout Mouse Consortium Knockouts (Mice available) MISC NULL NULL Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (Mice available)
-50603 IKMCs_No_products_available_yet NULL XREF 1 0 10 International Knockout Mouse Consortium Knockouts (No products available yet) MISC NULL NULL Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (No products available yet)
-50604 IKMCs_Vector_available NULL XREF 1 0 10 International Knockout Mouse Consortium Knockouts (Vector available) MISC NULL NULL Mouse lines produced as part of a high throughput strategy by the International Knockout Mouse Consortium to knock out every protein coding gene in mouse (Vector available)
-5901 Ens_Md_transcript NULL XREF 1 0 5 Ensembl Monodelphis Transcript MISC NULL NULL NULL
-832 InteractiveFly NULL KNOWNXREF 0 1 5 The Interactive Fly gene MISC NULL NULL NULL
-829 BioGRID NULL KNOWNXREF 1 0 5 BioGRID Interaction data, The General Repository for Interaction Datasets gene MISC NULL NULL NULL
-7180 VB_Community_Annotation NULL KNOWN 1 0 30 VB Community Annotation MISC NULL NULL NULL
-831 GenomeRNAi NULL KNOWNXREF 1 0 5 GenomeRNAi, a database for cell-based RNAi phenotypes gene MISC NULL NULL NULL
-830 FlyExpress NULL KNOWNXREF 1 0 5 FlyExpress, expression patterns of developmentally relevant genes in Drosophila embryogenesis gene MISC NULL NULL NULL
-833 MitoDrome NULL KNOWNXREF 1 0 5 Nuclear genes encoding proteins targeted to the mitochondrion gene MISC NULL NULL NULL
diff --git a/misc-scripts/external_db/load_additional_human_affy_xrefs.pl b/misc-scripts/external_db/load_additional_human_affy_xrefs.pl
deleted file mode 100644
index af8ef92eb6..0000000000
--- a/misc-scripts/external_db/load_additional_human_affy_xrefs.pl
+++ /dev/null
@@ -1,83 +0,0 @@
-#Contact: Emmanuel Mongin (mongin@ebi.ac.uk)
-
-use strict;
-use DBI;
-use Getopt::Long;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
-use Bio::EnsEMBL::DBEntry;
-use Bio::SeqIO;
-
-
-
-my ( $host, $dbuser, $dbname, $dbpass, $port, $filename );
-
-my %map;
-
-GetOptions( "host=s", \$host,
- "user=s", \$dbuser,
- "pass=s", \$dbpass,
- "port=i", \$port,
- "dbname=s", \$dbname,
- "file=s", \$filename
- );
-
-if( ! $filename ) {
- usage()
-}
-
-print STDERR "Connecting to $host, $dbname\n";
-
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- '-host' => $host,
- '-user' => $dbuser,
- '-dbname' => $dbname,
- '-pass' => $dbpass,
- '-port' => $port
- );
-
-my $adaptor = $db->get_DBEntryAdaptor();
-
-print STDERR "Loading expression data\n";
-
-open (AFFY, $filename ) || die "Can't open AFFY file";
-
-while (<AFFY>) {
- chomp;
- my ($transl_id,$db1,$id) = split;
-
- if ($id ne "NULL") {
- my $dbentry = Bio::EnsEMBL::DBEntry->new
- ( -adaptor => $adaptor,
- -primary_id => $id,
- -display_id => $id,
- -version => 1,
- -release => 1,
- -dbname => $db1);
- $dbentry->status("XREF");
- print "$transl_id\t$db1\t$id\n";
- $adaptor->store($dbentry,$transl_id,"Translation");
- }
-}
-
-close(AFFY);
-
-
-sub usage {
- print STDERR <<HELP
-
-Usage: perl load_additional_human_affy_xrefs.pl
- -host db connection detail
- -user
- -pass
- -port
- -dbname
- -file filename
- File with xrefs to upload
-
-HELP
-;
-
- exit();
-}
diff --git a/misc-scripts/external_db/load_additional_human_gkb_xrefs.pl b/misc-scripts/external_db/load_additional_human_gkb_xrefs.pl
deleted file mode 100644
index 63e99527c9..0000000000
--- a/misc-scripts/external_db/load_additional_human_gkb_xrefs.pl
+++ /dev/null
@@ -1,88 +0,0 @@
-#Contact: Emmanuel Mongin (mongin@ebi.ac.uk)
-
-use strict;
-use DBI;
-use Getopt::Long;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
-use Bio::EnsEMBL::DBEntry;
-use Bio::SeqIO;
-
-
-
-my ( $host, $dbuser, $dbname, $dbpass, $port, $filename );
-
-my %map;
-
-GetOptions( "host=s", \$host,
- "user=s", \$dbuser,
- "pass=s", \$dbpass,
- "port=i", \$port,
- "dbname=s", \$dbname,
- "file=s", \$filename
- );
-
-if( ! $filename ) {
- usage()
-}
-
-print STDERR "Connecting to $host, $dbname\n";
-
-
-my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
- '-host' => $host,
- '-user' => $dbuser,
- '-dbname' => $dbname,
- '-pass' => $dbpass,
- '-port' => $port
- );
-
-my $adaptor = $db->get_DBEntryAdaptor();
-
-print STDERR "Loading GKB mapping\n";
-open (GKB, $filename ) || die "Can't open GKB file";
-
-my $sth =
- $db->prepare("SELECT o.ensembl_id
- FROM object_xref o, xref x
- WHERE x.dbprimary_acc = ? AND x.xref_id = o.xref_id");
-my $db1 = "GKB";
-
-
-while (<GKB>) {
- chomp;
- my ($sp,$id) = split;
-
- $sth->execute($sp);
- while (my $transl_id = $sth->fetchrow) {
- my $dbentry = Bio::EnsEMBL::DBEntry->new
- ( -adaptor => $adaptor,
- -primary_id => $id,
- -display_id => $id,
- -version => 1,
- -release => 1,
- -dbname => $db1);
- $dbentry->status("XREF");
- print STDERR "$transl_id\t$db1\t$id\n";
-
- $adaptor->store($dbentry,$transl_id,"Translation");
- }
-}
-
-sub usage {
- print STDERR <<HELP
-
-Usage: perl load_additional_human_gkb_xrefs.pl
- -host db connection detail
- -user
- -pass
- -port
- -dbname
- -file filename
- File with xrefs to upload
-
-HELP
-;
-
- exit();
-}
diff --git a/misc-scripts/external_db/update_external_dbs.pl b/misc-scripts/external_db/update_external_dbs.pl
deleted file mode 100644
index 2e9ea3a6bb..0000000000
--- a/misc-scripts/external_db/update_external_dbs.pl
+++ /dev/null
@@ -1,324 +0,0 @@
-#!/usr/local/ensembl/bin/perl -w
-
-#
-# updates the external db tables on all of the core databases on a given host
-#
-
-use strict;
-
-use Getopt::Long;
-use DBI;
-use IO::File;
-
-my ( $host, $user, $pass, $port, @dbnames,
- $file, $release_num, $master, $nonreleasemode, $force );
-
-GetOptions( "dbhost|host=s", \$host,
- "dbuser|user=s", \$user,
- "dbpass|pass=s", \$pass,
- "dbport|port=i", \$port,
- "file=s", \$file,
- "dbnames=s@", \@dbnames,
- "release_num=i", \$release_num,
- "master=s", \$master,
- "nonreleasemode", \$nonreleasemode,
- "force", \$force );
-
-$port ||= 3306;
-
-$file ||= "external_dbs.txt";
-
-usage("[DIE] Need a host") if(!$host);
-
-#release num XOR dbname are required.
-usage( "[DIE] Need either both a release number and "
- . "database names or neither" )
- if ( ( $release_num && @dbnames ) || ( !$release_num && !@dbnames ) );
-
-if(!$nonreleasemode){
- # master database is required
- usage("[DIE] Master database required") if (!$master);
-}
-
-my $dsn = "DBI:mysql:host=$host;port=$port";
-
-my $db = DBI->connect( $dsn, $user, $pass, {RaiseError => 1} );
-
-if($release_num) {
- @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
-
- #
- # filter out all non-core databases
- #
- @dbnames = grep {/^[a-zA-Z]+\_[a-zA-Z]+\_(core|est|estgene|vega|otherfeatures|cdna)\_${release_num}\_\d+[A-Za-z]?$/} @dbnames;
-}
-
-my @field_names = qw(external_db_id db_name release status dbprimary_acc_linkable display_label_linkable priority db_display_name type);
-
-my @types = qw(ARRAY ALT_TRANS MISC LIT PRIMARY_DB_SYNONYM ALT_GENE);
-
-#
-# make sure the user wishes to continue
-#
-print STDERR "Please make sure you've updated $file from CVS!\n";
-print STDERR
- "The following databases will have their external_db tables "
- . "updated if necessary:\n ";
-print join( "\n ", @dbnames );
-print "\nContinue with update (yes/no)> ";
-
-my $input = lc(<STDIN>);
-chomp($input);
-if ($input ne 'yes') {
- print "external_db conversion aborted\n";
- exit();
-}
-
-#
-# read all of the new external_db entries from the file
-#
-my $fh = IO::File->new();
-$fh->open($file) or die("Could not open input file $file");
-my @rows;
-my %bad_lines;
-
-while (my $row = <$fh>) {
- chomp($row);
- next if ($row =~ /^#/); # skip comments
- next if ($row =~ /^$/); # and blank lines
- next if ($row =~ /^\s+$/); # and whitespace-only lines
- my @a = split(/\t/, $row);
- push @rows, {
- 'external_db_id' => $a[0],
- 'db_name' => $a[1],
- 'release' => $a[2],
- 'status' => $a[3],
- 'dbprimary_acc_linkable' => $a[4],
- 'display_label_linkable' => $a[5],
- 'priority' => $a[6],
- 'db_display_name' => $a[7],
- 'type' => $a[8] };
-
- if ( $a[1] =~ /-/ ) {
- print STDERR "Database name "
- . $a[1]
- . " contains '-' characters "
- . "which will break Mart, "
- . "please replace them with '_' until Mart is fixed\n";
- exit(1);
- }
-
- # do some formatting checks
- my $blank;
- for (my $i=0; $i < scalar(@a); $i++) {
- if ($a[$i] eq '') {
- $bad_lines{$row} = $field_names[$i] . " - field blank - check all tabs/spaces in line";
- }
- }
-
- if ($a[1] =~ /\s/) {
- $bad_lines{$row} = "db_name field appears to contain spaces";
- }
- if ($a[1] =~ /^$/) {
- $bad_lines{$row} = "db_name field appears to be missing";
- }
- if ($a[1] =~ /^\s+$/) {
- $bad_lines{$row} = "db_name field appears to be blank";
- }
- if ($a[1] =~ /^\d+$/) {
- $bad_lines{$row} = "db_name field appears to be numeric - check formatting";
- }
-
- my $type_ok;
- foreach my $type (@types) {
- $type_ok = 1 if ($a[8] eq $type);
- }
- $bad_lines{$row} = "type field is " . $a[8] . ", not one of the recognised types" if (!$type_ok);
-
-}
-$fh->close();
-
-if (%bad_lines) {
- print STDERR "Cannot parse the following line(s) from $file; check that all fields are present and are separated by one tab (not spaces). \n";
- print STDERR "Name of problem field, and the error is printed in brackets first\n\n";
- foreach my $row (keys %bad_lines) {
- print STDERR "[". $bad_lines{$row} . "]" . " $row\n";
- }
- exit(1);
-}
-
-# Load into master database
- if(!$nonreleasemode){
- load_database($db, $master, @rows);
- }
- # Check each other database in turn
- # Load if no extra rows in db that aren't in master
- # Warn and skip if there are
-
- foreach my $dbname (@dbnames) {
-
- print STDERR "Looking at $dbname ... \n";
- if ($force || $nonreleasemode) {
-
- print STDERR "Forcing overwrite of external_db table in "
- . "$dbname from $file\n";
- load_database( $db, $dbname, @rows );
-
- } elsif (compare_external_db($db, $master, $dbname)) {
-
- print STDERR "$dbname has no additional rows. "
- . "Overwriting external_db table from $file\n";
- load_database( $db, $dbname, @rows );
-
- } else {
-
- print STDERR "$dbname has extra rows "
- . "that are not in $file, skipping\n";
-
- }
-
- }
-
-print STDERR "Updates complete\n";
-
-
-
-sub load_database {
- my ($db, $dbname, @rows) = @_;
-
- $db->do("USE $dbname");
-
- # Save all existing release information from the table.
- my $sth = $db->prepare(
- qq( SELECT external_db_id, db_release
- FROM external_db) );
- $sth->execute();
-
- my %saved_release;
- while ( my ( $id, $release ) = $sth->fetchrow_array() ) {
- if ( defined($release) && $release ne '1' ) {
- $saved_release{$id} = $release;
- }
- }
- $sth->finish();
-
- # Delete the existing table
- $sth = $db->prepare('DELETE FROM external_db');
- $sth->execute();
- $sth->finish();
-
- # Populate the table with data from the file (using the saved release
- # information)
- $sth = $db->prepare(
- qq( INSERT INTO external_db (
- external_db_id,
- db_name,
- db_release,
- status,
- dbprimary_acc_linkable,
- display_label_linkable,
- priority,
- db_display_name,
- type) VALUES (?,?,?,?,?,?,?,?,?)) );
-
- foreach my $row (@rows) {
- my $id = $row->{'external_db_id'};
-
- $sth->execute( $id,
- $row->{'db_name'}, (
- exists( $saved_release{$id} )
- ? $saved_release{$id}
- : $row->{'release'}
- ),
- $row->{'status'},
- $row->{'dbprimary_acc_linkable'},
- $row->{'display_label_linkable'},
- $row->{'priority'},
- $row->{'db_display_name'},
- $row->{'type'} );
- }
-
- $sth->finish();
-}
-
-
-# return true if the tables are the same, undef if not
-sub compare_external_db {
-
- my ($db, $master, $dbname) = @_;
-
- my $same = 1;
-
- # check each row in $dbname against each row in $master
- # only compare ID and name since we're only aiming to catch extra rows in $dbname
- $db->do("use $dbname");
-
- my $sth = $db->prepare(qq {SELECT d.external_db_id, d.db_name
- FROM $dbname.external_db d
- LEFT JOIN $master.external_db m
- ON (d.external_db_id=m.external_db_id AND d.db_name=m.db_name)
- WHERE m.external_db_id IS NULL OR m.db_name IS NULL });
- $sth->execute();
-
- while (my ($id, $external_db_name) = $sth->fetchrow_array) {
- print "$dbname has external_db entry for $external_db_name (ID $id) which is not present in $master\n";
- $same = undef;
-
- }
-
- $sth->finish();
-
- return $same;
-
-}
-
-sub usage {
- my $error = shift;
-
- print STDERR <<EOF;
- $error
-
- Usage: $0 options
-
- -host hostname
- -user username
- -pass password
- -port port_of_server optional
- -master the name of the master database to load the file into
- -force force update, even if there are rows in the database
- that are not in the file
- -release the release of the database to update used to match
- database names, e.g. 13
- -file the path of the file containing the insert statements
- of the entries of the external_db table. Default is
- 'external_dbs.txt'
- -dbnames the names of the database to update. If not provided
- all of the core databases matching the release arg
- will be updated. Either -dbnames or -release must
- be specified, but not both. Multiple dbnames can be
- provided.
- -nonreleasemode Does not require master schema and forces the update.
-
-
- Examples:
-
- # Update two databases
-
- ./update_external_dbs.pl -host ecs1c -file external_dbs.txt \\
- -user ensadmin -pass secret -master master_schema_14 \\
- -dbnames homo_sapiens_core_14_33 -dbnames mus_musculus_core_14_30
-
- # Update all Core databases for release 14
-
- ./update_external_dbs.pl -host ens-staging -file external_dbs.txt \\
- -user ensadmin -pass secret -release 42 -master master_schema_42
-
- If the databases to be updated contain rows that are not in the file,
- a warning will be given and the database in question skipped, unless
- -force is used.
-
- This program will not overwrite the db_release column of any table.
-
-EOF
- exit;
-} ## end sub usage
--
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