Commit 2715894a authored by Andy Yates's avatar Andy Yates
Browse files

Minor changes to the schema from an entire schema redump.

Modified the enum on object_xref from 72->73 patch c and the redump
re-did some data. Such as choosing a different encoding for some very
small values. All changes are small though.
parent 589c8c6c
1 IS_REPRESENTATIVE
4 HAS_CODING_POTENTIAL
\ No newline at end of file
4 HAS_CODING_POTENTIAL
1282 Genes were annotated by the Ensembl automatic analysis pipeline using either a GeneWise model from a human/vertebrate protein, a set of aligned human cDNAs followed by GenomeWise for ORF prediction or from Genscan exons supported by protein, cDNA and EST evidence. GeneWise models are further combined with available aligned cDNAs to annotate UTRs. ensembl transcript 1 web data 1 0 \N
1503 new description new label 0 0 \N
1504 updated description N 0 0 \N
8405 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 1 {'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GE\NCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8405 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 1 {'multi_name' => 'Ensembl genes, or Merged Ensembl and Havana genes','colour_key' => '[biotype]','caption' => 'Genes (Merged Ensembl/Havana) (GENCODE)','name' => 'Merged Ensembl and Havana genes (GENCODE)','label_key' => '[biotype]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'ensembl'}
8406 Sequences from various databases are matched to Ensembl transcripts using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. These are external references, or 'Xrefs'. DNA match 0 \N
8407 Alignment of human 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> Human EST (EST2genome) 0 {'type' => 'est'}
8408 Proteins from the <a rel="external" href="http://uniprot.org">UniProtKB Swiss-Prot</a> database, aligned to the genome by Havana. UniProt proteins 0 \N
27374 21716 76 99 45 75 0 41 0 0 0 \N \N
217249 21716 47 151 49 79 PF000001 41 87.1 8.2e-25 0 \N \N
242732 21716 80 160 71 101 0 41 0 3.2e-11 0 \N \N
242732 21716 80 160 71 101 0 41 0 0.000000000032 0 \N \N
217179 21717 1 94 49 79 PF000019 41 99.1 3.3e-28 0 \N \N
242734 21717 3 91 71 101 0 41 0 1.7e-15 0 \N \N
242734 21717 3 91 71 101 0 41 0 0.0000000000000017 0 \N \N
217309 21718 76 201 49 79 PF000019 41 118.9 8.9e-34 0 \N \N
242735 21718 1 185 71 101 0 41 0 3e-14 0 \N \N
242735 21718 1 185 71 101 0 41 0 0.00000000000003 0 \N \N
27378 21719 90 117 45 75 0 41 0 0 0 \N \N
83043 21719 21 41 44 74 0 41 2.37 0 0 \N \N
242736 21719 76 124 71 101 0 41 0 0.0017 0 \N \N
......@@ -29,16 +29,16 @@
116151 21723 377 389 42 72 0 41 1 0 0 \N \N
130095 21723 144 241 41 71 0 41 26.88 0 0 \N \N
130097 21723 78 138 41 71 0 41 19.623 0 0 \N \N
161506 21723 144 158 40 70 0 41 394 9.81e-06 0 \N \N
161508 21723 165 175 40 70 0 41 321 2.59e-05 0 \N \N
161510 21723 177 188 40 70 0 41 288 1.03e-06 0 \N \N
161512 21723 194 204 40 70 0 41 295 4.86e-05 0 \N \N
161514 21723 215 229 40 70 0 41 349 7e-07 0 \N \N
161516 21723 81 91 40 70 0 41 266 3.18e-05 0 \N \N
161518 21723 95 110 40 70 0 41 334 1.38e-07 0 \N \N
161506 21723 144 158 40 70 0 41 394 0.00000981 0 \N \N
161508 21723 165 175 40 70 0 41 321 0.0000259 0 \N \N
161510 21723 177 188 40 70 0 41 288 0.00000103 0 \N \N
161512 21723 194 204 40 70 0 41 295 0.0000486 0 \N \N
161514 21723 215 229 40 70 0 41 349 0.0000007 0 \N \N
161516 21723 81 91 40 70 0 41 266 0.0000318 0 \N \N
161518 21723 95 110 40 70 0 41 334 0.000000138 0 \N \N
161520 21723 111 120 40 70 0 41 225 0.0222 0 \N \N
161522 21723 124 136 40 70 0 41 341 1.82e-06 0 \N \N
161524 21723 83 103 40 70 0 41 565 7.11e-09 0 \N \N
161522 21723 124 136 40 70 0 41 341 0.00000182 0 \N \N
161524 21723 83 103 40 70 0 41 565 0.00000000711 0 \N \N
161526 21723 103 119 40 70 0 41 188 0.099 0 \N \N
217502 21723 83 138 49 79 58 41 98.9 6.4e-27 0 \N \N
217503 21723 146 228 49 79 79 41 150.9 1.5e-42 0 \N \N
......@@ -81,13 +81,13 @@
130107 21726 191 218 41 71 0 41 12.092 0 0 \N \N
130109 21726 219 247 41 71 0 41 11.281 0 0 \N \N
217476 21726 68 94 49 79 24 41 12.8 0.29 0 \N \N
217477 21726 100 122 49 79 24 41 25.3 9.2e-05 0 \N \N
217477 21726 100 122 49 79 24 41 25.3 0.000092 0 \N \N
217478 21726 129 151 49 79 24 41 19.7 0.0045 0 \N \N
217479 21726 158 180 49 79 24 41 19.2 0.0063 0 \N \N
217480 21726 193 215 49 79 24 41 22.9 0.00049 0 \N \N
217481 21726 221 244 49 79 24 41 24 0.00023 0 \N \N
242784 21726 80 124 71 101 0 41 0 1.5e-09 0 \N \N
242785 21726 205 245 71 101 0 41 0 7.5e-09 0 \N \N
242784 21726 80 124 71 101 0 41 0 0.0000000015 0 \N \N
242785 21726 205 245 71 101 0 41 0 0.0000000075 0 \N \N
242786 21726 58 85 71 101 0 41 0 0.0011 0 \N \N
34517 21727 1 26 43 73 0 41 0 0 0 \N \N
83063 21727 15 22 44 74 0 41 0.81 0 0 \N \N
......@@ -108,8 +108,8 @@
116159 21729 239 250 42 72 0 41 1 0 0 \N \N
130111 21729 6 256 41 71 0 41 55.446 0 0 \N \N
161528 21729 87 108 40 70 0 41 911 4.44e-16 0 \N \N
161530 21729 206 223 40 70 0 41 585 2.63e-10 0 \N \N
161532 21729 240 258 40 70 0 41 576 8.36e-12 0 \N \N
161530 21729 206 223 40 70 0 41 585 0.000000000263 0 \N \N
161532 21729 240 258 40 70 0 41 576 0.00000000000836 0 \N \N
161534 21729 290 311 40 70 0 41 833 4.44e-16 0 \N \N
217672 21729 55 341 49 79 373 41 576.3 1.3e-170 0 \N \N
242791 21729 4 365 71 101 0 41 0 8.4e-131 0 \N \N
......@@ -140,17 +140,17 @@
116161 21737 309 316 42 72 0 41 0 0 0 \N \N
116162 21737 643 655 42 72 0 41 0 0 0 \N \N
217810 21737 223 296 49 79 87 41 121 1.5e-33 0 \N \N
217811 21737 576 849 49 79 418 41 -74 8.5e-06 0 \N \N
217811 21737 576 849 49 79 418 41 -74 0.0000085 0 \N \N
242841 21737 573 848 71 101 0 41 0 3e-50 0 \N \N
242842 21737 216 351 71 101 0 41 0 1.2e-41 0 \N \N
27455 21738 193 213 45 75 0 41 0 0 0 \N \N
83094 21738 256 267 44 74 0 41 2.12 0 0 \N \N
130115 21738 14 116 41 71 0 41 8.924 0 0 \N \N
217326 21738 15 117 49 79 106 41 28 1.5e-05 0 \N \N
217326 21738 15 117 49 79 106 41 28 0.000015 0 \N \N
217327 21738 210 257 49 79 56 41 106 4.7e-29 0 \N \N
242845 21738 13 115 71 101 0 41 0 3e-17 0 \N \N
83095 21739 44 56 44 74 0 41 2.19 0 0 \N \N
130117 21739 144 201 41 71 0 41 9.695 0 0 \N \N
217297 21739 141 168 49 79 29 41 4.4 1.7 0 \N \N
217298 21739 176 204 49 79 29 41 12.7 0.15 0 \N \N
242846 21739 117 207 71 101 0 41 0 4e-10 0 \N \N
242846 21739 117 207 71 101 0 41 0 0.0000000004 0 \N \N
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