diff --git a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
index dde56c6a945f89460935ae7123494c954c291ea6..f55479f04b23f6b07b795f3dd7882f4baa51e51d 100644
--- a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:21 2019
+-- Created on Fri Nov 1 15:18:23 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/circ/core/external_db.txt b/modules/t/test-genome-DBs/circ/core/external_db.txt
index 80f2ac6bd4f63a417c7ce3f9a33b84ea816c971f..197d1856b9b140156dc6337d10456ac85453b6ff 100644
--- a/modules/t/test-genome-DBs/circ/core/external_db.txt
+++ b/modules/t/test-genome-DBs/circ/core/external_db.txt
@@ -1,310 +1,310 @@
-210 Anopheles_symbol \N KNOWN 50 Anopheles symbol MISC \N \N \N
-211 VB_Community_Symbol \N KNOWN 50 VB Community Symbol MISC \N \N \N
+210 Anopheles_symbol KNOWN 50 Anopheles symbol MISC \N \N \N
+211 VB_Community_Symbol KNOWN 50 VB Community Symbol MISC \N \N \N
212 VB_External_Description 1 PRED 50 VB External Description MISC \N \N \N
213 VB_RNA_Description 1 PRED 50 VB RNA Description MISC \N \N \N
-230 Ribosomal_Protein_Gene_Database Dec.2010 XREF 50 Ribosomal Protein Gene DB MISC \N \N \N
+230 Ribosomal_Protein_Gene_Data Dec.2010 XREF 50 Ribosomal Protein Gene DB MISC \N \N \N
250 ImmunoDB 1 KNOWN 50 ImmunoDB MISC \N \N \N
-300 BRIGGSAE_HYBRID \N KNOWNXREF 5 Briggsae Hybrid MISC \N \N \N
-400 Celera_Gene \N PRED 5 Celera gene MISC \N \N \N
-410 Celera_Pep \N PRED 5 Celera peptide MISC \N \N \N
-420 Celera_Trans \N PRED 5 Celera transcript MISC \N \N \N
-600 DROS_ORTH \N ORTH 5 DROS ORTH MISC \N \N \N
-700 EMBL \N KNOWNXREF 5 European Nucleotide Archive MISC \N \N \N
-701 EMBL_predicted \N PRED 119 Predicted European Nucleotide Archive MISC \N \N \N
-800 flybase_gene_id \N KNOWNXREF 5 Flybase Gene MISC \N \N \N
-801 flybase_translation_id \N KNOWNXREF 5 Flybase translation ID MISC \N \N \N
-802 flybase_gff \N KNOWNXREF 5 Flybase GFF MISC \N \N \N
-803 flybase_polypeptide_id \N KNOWNXREF 5 Flybase Polypeptide ID MISC \N \N \N
-804 flybase_annotation_id \N KNOWNXREF 5 Flybase Annotation ID MISC \N \N \N
-805 flybase_symbol \N KNOWNXREF 50 Flybase Symbol MISC \N \N \N
-806 flybase_synonym \N KNOWNXREF 5 Flybase Synonym MISC \N \N \N
-807 flybase_name \N KNOWNXREF 5 Flybase Name MISC \N \N \N
-808 flybase_transcript_id \N KNOWNXREF 299 Flybase transcript ID MISC \N \N \N
-810 gadfly_gene_cgid \N XREF 10 Gadfly gene CGID MISC \N \N \N
-811 gadfly_transcript_cgid \N XREF 10 Gadfly transcript CGID MISC \N \N \N
-812 gadfly_translation_cgid \N XREF 10 Gadfly translation CGID MISC \N \N \N
-821 FlyBaseName_gene \N KNOWN 5 FlyBase gene name MISC \N \N \N
-824 FlyBaseName_translation \N KNOWN 5 FlyBase translation name MISC \N \N \N
-825 FlyBaseName_transcript \N XREF 50 FlyBase transcript name MISC \N \N \N
-826 FlyBaseCGID_gene \N XREF 5 FlyBase gene CGID MISC \N \N \N
-827 FlyBaseCGID_transcript \N XREF 50 FlyBase transcript CGID MISC \N \N \N
-828 FlyBaseCGID_translation \N XREF 50 FlyBase translation CGID MISC \N \N \N
-829 BioGRID \N KNOWNXREF 5 BioGRID Interaction data, The General Repository for Interaction Datasets MISC \N \N \N
-830 FlyExpress \N KNOWNXREF 5 FlyExpress, expression patterns of developmentally relevant genes in Drosophila embryogenesis MISC \N \N \N
-831 GenomeRNAi \N KNOWNXREF 5 GenomeRNAi, a database for cell-based RNAi phenotypes MISC \N \N \N
-832 InteractiveFly \N KNOWNXREF 5 The Interactive Fly MISC \N \N \N
-833 MitoDrome \N KNOWNXREF 5 Nuclear genes encoding proteins targeted to the mitochondrion MISC \N \N \N
-880 BDGP_insitu_expr \N KNOWNXREF 5 Berkeley Drosophila Genome Project in situ Gene Expression Database (embryogenesis) MISC \N \N \N
-882 FlyGrid \N KNOWNXREF 5 FlyGRID Interaction Data, The General Repository for Interaction Datasets MISC \N \N \N
-883 FlyReactome \N KNOWNXREF 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC \N \N \N
-890 DEDb \N KNOWNXREF 5 Drosophila melanogaster Exon Database MISC \N \N \N
-900 GKB \N XREF 5 GKB MISC \N \N \N
-1000 GO \N XREF 5 GO MISC \N \N \N
-1001 GO_REF \N KNOWN 5 GO Reference Collection LIT \N \N \N
-1100 HGNC \N KNOWNXREF 100 HGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
-1200 Interpro \N XREF 5 InterPro MISC \N \N \N
-1300 EntrezGene \N KNOWNXREF 250 EntrezGene MISC \N \N \N
-1400 MGI \N KNOWNXREF 270 MGI Symbol MISC \N \N \N
-1500 MIM \N KNOWNXREF 5 MIM MISC \N \N \N
-1510 MIM_GENE \N KNOWNXREF 5 MIM gene MISC \N \N \N
-1520 MIM_MORBID \N KNOWNXREF 150 MIM disease MISC \N \N \N
-1600 PDB \N KNOWNXREF 5 PDB MISC \N \N \N
-1700 protein_id \N KNOWNXREF 5 INSDC protein ID MISC \N \N \N
-1701 protein_id_predicted \N PRED 4 Predicted INSDC Protein ID MISC \N \N \N
-1800 RefSeq_dna \N KNOWN 200 RefSeq DNA MISC \N \N \N
-1801 RefSeq_mRNA \N KNOWN 200 RefSeq mRNA MISC \N \N \N
-1803 RefSeq_ncRNA \N KNOWN 200 RefSeq ncRNA MISC \N \N \N
-1805 RefSeq_dna_predicted \N PRED 199 RefSeq DNA predicted MISC \N \N \N
-1806 RefSeq_mRNA_predicted \N PRED 199 RefSeq mRNA predicted MISC \N \N \N
-1808 RefSeq_ncRNA_predicted \N PRED 199 RefSeq ncRNA predicted MISC \N \N \N
-1810 RefSeq_peptide \N KNOWN 210 RefSeq peptide MISC \N \N \N
-1815 RefSeq_peptide_predicted \N PRED 197 RefSeq peptide predicted MISC \N \N \N
-1820 RefSeq_rna \N KNOWN 230 RefSeq RNA MISC \N \N \N
-1825 RefSeq_rna_predicted \N PRED 195 RefSeq RNA predicted MISC \N \N \N
-1830 RefSeq_genomic \N KNOWN 193 RefSeq Genomic MISC \N \N \N
-1900 Sanger_Hver1_2_1 \N XREF 5 Sanger Hver 121 MISC \N \N \N
-1901 Sanger_Hver1_3_1 \N XREF 5 Sanger Hver 131 MISC \N \N \N
-1902 SNGR_Hver \N XREF 5 Sanger Hver MISC \N \N \N
-1910 Sanger_Mver1_1_1 \N XREF 5 Sanger Hver 111 MISC \N \N \N
-2000 Uniprot/SPTREMBL \N KNOWN 119 UniProtKB/TrEMBL MISC \N \N \N
-2001 Uniprot/SPTREMBL_predicted \N PRED 117 Predicted UniProtKB/TrEMBL MISC \N \N \N
-2010 prediction_SPTREMBL \N XREF 10 Prediction UniProtKB/TrEMBL MISC \N \N \N
-2100 Superfamily \N KNOWNXREF 5 Superfamily MISC \N \N \N
-2200 Uniprot/SWISSPROT \N KNOWN 220 UniProtKB/Swiss-Prot MISC \N \N \N
-2201 Uniprot/SWISSPROT_predicted \N PRED 15 Predicted UniProtKB/Swiss-Prot MISC \N \N \N
-2202 Uniprot/Varsplic \N KNOWN 15 UniProtKB/SpliceVariant MISC \N \N \N
-2250 UniProtKB_all \N XREF 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC \N \N \N
-2300 Vega_gene \N KNOWNXREF 5 Vega gene MISC \N \N \N
-2305 Vega_gene_like \N XREF 5 Vega gene like MISC \N \N \N
-2310 Vega_transcript \N KNOWNXREF 160 Vega transcript MISC \N \N \N
-2315 Vega_transcript_like \N XREF 5 Vega transcript like MISC \N \N \N
-2320 Vega_translation \N KNOWNXREF 5 Vega translation MISC \N \N \N
-2400 wormbase_gene \N KNOWN 5 WormBase Gene MISC \N \N \N
-2410 wormbase_transcript \N KNOWN 5 WormBase Transcript MISC \N \N \N
-2420 wormpep_id \N KNOWN 5 Wormpep ID MISC \N \N \N
-2430 wormbase_pseudogene \N PSEUDO 5 WormBase Pseudogene MISC \N \N \N
-2440 wormbase_locus \N KNOWN 5 WormBase Locus MISC \N \N \N
-2510 ZFIN_ID \N KNOWNXREF 260 ZFIN PRIMARY_DB_SYNONYM \N \N \N
-2530 ZFIN_xpat \N KNOWNXREF 4 ZFIN expression patterns MISC \N \N \N
-2600 GeneDB \N KNOWN 5 GeneDB MISC \N \N \N
-2601 cint_jgi_v1 \N KNOWN 10 JGI Gene ID (JGI 1.0) MISC \N \N \N
-2602 cint_jgi_v2 \N KNOWN 5 JGI Gene ID (JGI 2.0) MISC \N \N \N
-2610 cint_aniseed_v1 \N KNOWN 5 ANISEED (JGI 1.0) MISC \N \N \N
-2611 cint_aniseed_v2 \N KNOWN 5 ANISEED (JGI 2.0) MISC \N \N \N
-2700 Ens_Hs_gene \N XREF 5 Ensembl Human Gene MISC \N \N \N
-2710 Ens_Hs_transcript \N XREF 170 Ensembl Human Transcript MISC \N \N \N
-2720 Ens_Hs_translation \N XREF 5 Ensembl Human Translation MISC \N \N \N
-2800 RGD \N KNOWNXREF 50 RGD Symbol MISC \N \N \N
-2900 Genoscope_pred_gene \N XREF 38 Genoscope pred gene MISC \N \N \N
-2910 Genoscope_pred_transcript \N XREF 39 Genoscope pred transcript MISC \N \N \N
-2920 Genoscope_annotated_gene \N KNOWN 40 Genoscope annotated gene MISC \N \N \N
-2930 Genoscope_pred_translation \N XREF 40 Genoscope pred translation MISC \N \N \N
-2940 Genoscope_ann_transcript \N KNOWN 40 Genoscope annotated transcript MISC \N \N \N
-2950 Genoscope_ann_translation \N KNOWN 40 Genoscope annotated translation MISC \N \N \N
-3300 miRBase \N KNOWNXREF 180 miRBase MISC \N \N \N
-3310 miRBase_predicted \N XREF 1 miRBase predicted MISC \N \N \N
-3400 SGD \N KNOWN 50 SGD MISC \N \N \N
-3500 IPI \N KNOWN 5 IPI MISC \N \N \N
-3800 CCDS \N KNOWN 240 CCDS MISC \N \N \N
-3900 PUBMED \N KNOWN 5 Sequence Publications LIT \N \N \N
-4000 MEDLINE \N KNOWN 5 MEDLINE LIT \N \N \N
-4100 UniGene \N KNOWN 5 UniGene MISC \N \N \N
-4200 RFAM \N XREF 190 RFAM MISC \N \N \N
-4400 Xenopus_Jamboree \N KNOWN 1 Jamboree MISC \N \N \N
-4500 Tiffin \N XREF 1 Tiffin DNA motifs MISC \N \N \N
-4600 OTTG \N XREF 1 Havana gene ALT_GENE \N \N \N
-4610 OTTT \N XREF 1 Havana transcript ALT_TRANS \N \N \N
-4620 OTTP \N XREF 1 Havana translation MISC \N \N \N
-4650 shares_CDS_with \N XREF 1 transcript having same CDS ALT_TRANS \N \N \N
-4670 shares_CDS_with_OTTT \N XREF 1 Havana transcript having same CDS ALT_TRANS \N \N \N
-4680 shares_CDS_and_UTR_with_OTTT \N XREF 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS \N \N \N
-4690 ENSG \N XREF 1 Ensembl gene ALT_GENE \N \N \N
-4700 Medaka \N XREF 1 Medaka Genome Project MISC \N \N \N
-4800 ENST \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
-4810 ENST_ident \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
-4820 ENST_CDS \N XREF 1 Ensembl transcript sharing CDS with Havana ALT_TRANS \N \N \N
-4900 TCAG \N KNOWN 75 TCAG Chr 7 Annotation MISC \N \N \N
-5000 Ens_Mm_gene \N XREF 40 Ensembl Mouse Gene MISC \N \N \N
-5010 Ens_Mm_transcript \N XREF 40 Ensembl Mouse Transcript MISC \N \N \N
-5020 Ens_Mm_translation \N XREF 40 Ensembl Mouse Translation MISC \N \N \N
-5100 IMGT_HLA \N KNOWN 7 IMGT/HLA MISC \N \N \N
-5200 Oxford_FGU_Md_gene \N PRED 1 Oxford Ponting Group Monodelphis predictions gene id MISC \N \N \N
-5300 Oxford_FGU_Md_tscript \N PRED 1 Oxford Ponting Group Monodelphis predictions transcript id MISC \N \N Updated from alt_gene to misc due to user query
-5400 Oxford_FGU_Oa_gene \N PRED 1 Oxford Ponting Group Platypus predictions gene id MISC \N \N Updated from alt_gene to misc due to user query
-5500 Oxford_FGU_Oa_tscript \N PRED 1 Oxford Ponting Group Platypus predictions transcript id MISC \N \N \N
-5700 Ens_Cf_gene \N XREF 5 Ensembl Dog Gene MISC \N \N \N
-5710 Ens_Cf_transcript \N XREF 5 Ensembl Dog Transcript MISC \N \N \N
-5720 Ens_Cf_translation \N XREF 5 Ensembl Dog Translation MISC \N \N \N
-5800 Ens_Dr_gene \N XREF 5 Ensembl Zebrafish Gene MISC \N \N \N
-5810 Ens_Dr_transcript \N XREF 5 Ensembl Zebrafish Transcript MISC \N \N \N
-5820 Ens_Dr_translation \N XREF 5 Ensembl Zebrafish Translation MISC \N \N \N
-5900 Ens_Md_gene \N XREF 5 Ensembl Monodelphis Gene MISC \N \N \N
-5901 Ens_Md_transcript \N XREF 5 Ensembl Monodelphis Transcript MISC \N \N \N
-6100 Havana_gene \N XREF 100 Havana gene ID MISC \N \N \N
-6200 Ens_Rn_gene \N XREF 5 Ensembl Rat Gene MISC \N \N \N
-6300 Ens_Ol_gene \N XREF 5 Ensembl Medaka Gene MISC \N \N \N
-6400 Ens_Gg_gene \N XREF 40 Ensembl Chicken Gene MISC \N \N \N
-6410 Ens_Gg_transcript \N XREF 40 Ensembl Chicken Transcript MISC \N \N \N
-6420 Ens_Gg_translation \N XREF 40 Ensembl Chicken Translation MISC \N \N \N
-6500 IMCB_Tr_gene \N XREF 40 IMCB Fugu Gene MISC \N \N \N
-6600 Ens_Ag_gene \N XREF 5 Ensembl Mosquito Gene MISC \N \N \N
-6630 Ens_Am_gene \N XREF 5 Ensembl Bee Gene MISC \N \N \N
-6660 Ens_Ce_gene \N XREF 5 Ensembl Worm Gene MISC \N \N \N
-6690 Ens_Dm_gene \N XREF 5 Ensembl FruitFly Gene MISC \N \N \N
-6720 Ens_Fr_gene \N XREF 5 Ensembl Fugu Gene MISC \N \N \N
-6750 Ens_Pt_gene \N XREF 5 Ensembl Chimpanzee Gene MISC \N \N \N
-6810 Ens_Tn_gene \N XREF 5 Ensembl PufferFish Gene MISC \N \N \N
-6820 Ens_Tr_transcript \N XREF 40 Ensembl Fugu Transcript MISC \N \N \N
-6900 Ens_Ga_translation \N XREF 5 Ensembl Stickleback Translation MISC \N \N \N
-7120 Ens_Aa_translation \N XREF 40 Ensembl Aedes Translation MISC \N \N \N
-7159 AedesGenBank \N PRED 30 Aedes GenBank MISC \N \N \N
-7160 Aedes_ManualAnnotation \N PRED 30 Aedes ManualAnnotation MISC \N \N \N
-7170 Ixodes_ManualAnnotation \N PRED 30 Ixodes ManualAnnotation MISC \N \N \N
+300 BRIGGSAE_HYBRID KNOWNXREF 5 Briggsae Hybrid MISC \N \N \N
+400 Celera_Gene PRED 5 Celera gene MISC \N \N \N
+410 Celera_Pep PRED 5 Celera peptide MISC \N \N \N
+420 Celera_Trans PRED 5 Celera transcript MISC \N \N \N
+600 DROS_ORTH ORTH 5 DROS ORTH MISC \N \N \N
+700 EMBL KNOWNXREF 5 European Nucleotide Archive MISC \N \N \N
+701 EMBL_predicted PRED 119 Predicted European Nucleotide Archive MISC \N \N \N
+800 flybase_gene_id KNOWNXREF 5 Flybase Gene MISC \N \N \N
+801 flybase_translation_id KNOWNXREF 5 Flybase translation ID MISC \N \N \N
+802 flybase_gff KNOWNXREF 5 Flybase GFF MISC \N \N \N
+803 flybase_polypeptide_id KNOWNXREF 5 Flybase Polypeptide ID MISC \N \N \N
+804 flybase_annotation_id KNOWNXREF 5 Flybase Annotation ID MISC \N \N \N
+805 flybase_symbol KNOWNXREF 50 Flybase Symbol MISC \N \N \N
+806 flybase_synonym KNOWNXREF 5 Flybase Synonym MISC \N \N \N
+807 flybase_name KNOWNXREF 5 Flybase Name MISC \N \N \N
+808 flybase_transcript_id KNOWNXREF 299 Flybase transcript ID MISC \N \N \N
+810 gadfly_gene_cgid XREF 10 Gadfly gene CGID MISC \N \N \N
+811 gadfly_transcript_cgid XREF 10 Gadfly transcript CGID MISC \N \N \N
+812 gadfly_translation_cgid XREF 10 Gadfly translation CGID MISC \N \N \N
+821 FlyBaseName_gene KNOWN 5 FlyBase gene name MISC \N \N \N
+824 FlyBaseName_translation KNOWN 5 FlyBase translation name MISC \N \N \N
+825 FlyBaseName_transcript XREF 50 FlyBase transcript name MISC \N \N \N
+826 FlyBaseCGID_gene XREF 5 FlyBase gene CGID MISC \N \N \N
+827 FlyBaseCGID_transcript XREF 50 FlyBase transcript CGID MISC \N \N \N
+828 FlyBaseCGID_translation XREF 50 FlyBase translation CGID MISC \N \N \N
+829 BioGRID KNOWNXREF 5 BioGRID Interaction data, The General Repository for Interaction Datasets MISC \N \N \N
+830 FlyExpress KNOWNXREF 5 FlyExpress, expression patterns of developmentally relevant genes in Drosophila embryogenesis MISC \N \N \N
+831 GenomeRNAi KNOWNXREF 5 GenomeRNAi, a database for cell-based RNAi phenotypes MISC \N \N \N
+832 InteractiveFly KNOWNXREF 5 The Interactive Fly MISC \N \N \N
+833 MitoDrome KNOWNXREF 5 Nuclear genes encoding proteins targeted to the mitochondrion MISC \N \N \N
+880 BDGP_insitu_expr KNOWNXREF 5 Berkeley Drosophila Genome Project in situ Gene Expression Database (embryogenesis) MISC \N \N \N
+882 FlyGrid KNOWNXREF 5 FlyGRID Interaction Data, The General Repository for Interaction Datasets MISC \N \N \N
+883 FlyReactome KNOWNXREF 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC \N \N \N
+890 DEDb KNOWNXREF 5 Drosophila melanogaster Exon Database MISC \N \N \N
+900 GKB XREF 5 GKB MISC \N \N \N
+1000 GO XREF 5 GO MISC \N \N \N
+1001 GO_REF KNOWN 5 GO Reference Collection LIT \N \N \N
+1100 HGNC KNOWNXREF 100 HGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
+1200 Interpro XREF 5 InterPro MISC \N \N \N
+1300 EntrezGene KNOWNXREF 250 EntrezGene MISC \N \N \N
+1400 MGI KNOWNXREF 270 MGI Symbol MISC \N \N \N
+1500 MIM KNOWNXREF 5 MIM MISC \N \N \N
+1510 MIM_GENE KNOWNXREF 5 MIM gene MISC \N \N \N
+1520 MIM_MORBID KNOWNXREF 150 MIM disease MISC \N \N \N
+1600 PDB KNOWNXREF 5 PDB MISC \N \N \N
+1700 protein_id KNOWNXREF 5 INSDC protein ID MISC \N \N \N
+1701 protein_id_predicted PRED 4 Predicted INSDC Protein ID MISC \N \N \N
+1800 RefSeq_dna KNOWN 200 RefSeq DNA MISC \N \N \N
+1801 RefSeq_mRNA KNOWN 200 RefSeq mRNA MISC \N \N \N
+1803 RefSeq_ncRNA KNOWN 200 RefSeq ncRNA MISC \N \N \N
+1805 RefSeq_dna_predicted PRED 199 RefSeq DNA predicted MISC \N \N \N
+1806 RefSeq_mRNA_predicted PRED 199 RefSeq mRNA predicted MISC \N \N \N
+1808 RefSeq_ncRNA_predicted PRED 199 RefSeq ncRNA predicted MISC \N \N \N
+1810 RefSeq_peptide KNOWN 210 RefSeq peptide MISC \N \N \N
+1815 RefSeq_peptide_predicted PRED 197 RefSeq peptide predicted MISC \N \N \N
+1820 RefSeq_rna KNOWN 230 RefSeq RNA MISC \N \N \N
+1825 RefSeq_rna_predicted PRED 195 RefSeq RNA predicted MISC \N \N \N
+1830 RefSeq_genomic KNOWN 193 RefSeq Genomic MISC \N \N \N
+1900 Sanger_Hver1_2_1 XREF 5 Sanger Hver 121 MISC \N \N \N
+1901 Sanger_Hver1_3_1 XREF 5 Sanger Hver 131 MISC \N \N \N
+1902 SNGR_Hver XREF 5 Sanger Hver MISC \N \N \N
+1910 Sanger_Mver1_1_1 XREF 5 Sanger Hver 111 MISC \N \N \N
+2000 Uniprot/SPTREMBL KNOWN 119 UniProtKB/TrEMBL MISC \N \N \N
+2001 Uniprot/SPTREMBL_predicted PRED 117 Predicted UniProtKB/TrEMBL MISC \N \N \N
+2010 prediction_SPTREMBL XREF 10 Prediction UniProtKB/TrEMBL MISC \N \N \N
+2100 Superfamily KNOWNXREF 5 Superfamily MISC \N \N \N
+2200 Uniprot/SWISSPROT KNOWN 220 UniProtKB/Swiss-Prot MISC \N \N \N
+2201 Uniprot/SWISSPROT_predicted PRED 15 Predicted UniProtKB/Swiss-Prot MISC \N \N \N
+2202 Uniprot/Varsplic KNOWN 15 UniProtKB/SpliceVariant MISC \N \N \N
+2250 UniProtKB_all XREF 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC \N \N \N
+2300 Vega_gene KNOWNXREF 5 Vega gene MISC \N \N \N
+2305 Vega_gene_like XREF 5 Vega gene like MISC \N \N \N
+2310 Vega_transcript KNOWNXREF 160 Vega transcript MISC \N \N \N
+2315 Vega_transcript_like XREF 5 Vega transcript like MISC \N \N \N
+2320 Vega_translation KNOWNXREF 5 Vega translation MISC \N \N \N
+2400 wormbase_gene KNOWN 5 WormBase Gene MISC \N \N \N
+2410 wormbase_transcript KNOWN 5 WormBase Transcript MISC \N \N \N
+2420 wormpep_id KNOWN 5 Wormpep ID MISC \N \N \N
+2430 wormbase_pseudogene PSEUDO 5 WormBase Pseudogene MISC \N \N \N
+2440 wormbase_locus KNOWN 5 WormBase Locus MISC \N \N \N
+2510 ZFIN_ID KNOWNXREF 260 ZFIN PRIMARY_DB_SYNONYM \N \N \N
+2530 ZFIN_xpat KNOWNXREF 4 ZFIN expression patterns MISC \N \N \N
+2600 GeneDB KNOWN 5 GeneDB MISC \N \N \N
+2601 cint_jgi_v1 KNOWN 10 JGI Gene ID (JGI 1.0) MISC \N \N \N
+2602 cint_jgi_v2 KNOWN 5 JGI Gene ID (JGI 2.0) MISC \N \N \N
+2610 cint_aniseed_v1 KNOWN 5 ANISEED (JGI 1.0) MISC \N \N \N
+2611 cint_aniseed_v2 KNOWN 5 ANISEED (JGI 2.0) MISC \N \N \N
+2700 Ens_Hs_gene XREF 5 Ensembl Human Gene MISC \N \N \N
+2710 Ens_Hs_transcript XREF 170 Ensembl Human Transcript MISC \N \N \N
+2720 Ens_Hs_translation XREF 5 Ensembl Human Translation MISC \N \N \N
+2800 RGD KNOWNXREF 50 RGD Symbol MISC \N \N \N
+2900 Genoscope_pred_gene XREF 38 Genoscope pred gene MISC \N \N \N
+2910 Genoscope_pred_transcript XREF 39 Genoscope pred transcript MISC \N \N \N
+2920 Genoscope_annotated_gene KNOWN 40 Genoscope annotated gene MISC \N \N \N
+2930 Genoscope_pred_translation XREF 40 Genoscope pred translation MISC \N \N \N
+2940 Genoscope_ann_transcript KNOWN 40 Genoscope annotated transcript MISC \N \N \N
+2950 Genoscope_ann_translation KNOWN 40 Genoscope annotated translation MISC \N \N \N
+3300 miRBase KNOWNXREF 180 miRBase MISC \N \N \N
+3310 miRBase_predicted XREF 1 miRBase predicted MISC \N \N \N
+3400 SGD KNOWN 50 SGD MISC \N \N \N
+3500 IPI KNOWN 5 IPI MISC \N \N \N
+3800 CCDS KNOWN 240 CCDS MISC \N \N \N
+3900 PUBMED KNOWN 5 Sequence Publications LIT \N \N \N
+4000 MEDLINE KNOWN 5 MEDLINE LIT \N \N \N
+4100 UniGene KNOWN 5 UniGene MISC \N \N \N
+4200 RFAM XREF 190 RFAM MISC \N \N \N
+4400 Xenopus_Jamboree KNOWN 1 Jamboree MISC \N \N \N
+4500 Tiffin XREF 1 Tiffin DNA motifs MISC \N \N \N
+4600 OTTG XREF 1 Havana gene ALT_GENE \N \N \N
+4610 OTTT XREF 1 Havana transcript ALT_TRANS \N \N \N
+4620 OTTP XREF 1 Havana translation MISC \N \N \N
+4650 shares_CDS_with XREF 1 transcript having same CDS ALT_TRANS \N \N \N
+4670 shares_CDS_with_OTTT XREF 1 Havana transcript having same CDS ALT_TRANS \N \N \N
+4680 shares_CDS_and_UTR_with_OTT XREF 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS \N \N \N
+4690 ENSG XREF 1 Ensembl gene ALT_GENE \N \N \N
+4700 Medaka XREF 1 Medaka Genome Project MISC \N \N \N
+4800 ENST XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
+4810 ENST_ident XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
+4820 ENST_CDS XREF 1 Ensembl transcript sharing CDS with Havana ALT_TRANS \N \N \N
+4900 TCAG KNOWN 75 TCAG Chr 7 Annotation MISC \N \N \N
+5000 Ens_Mm_gene XREF 40 Ensembl Mouse Gene MISC \N \N \N
+5010 Ens_Mm_transcript XREF 40 Ensembl Mouse Transcript MISC \N \N \N
+5020 Ens_Mm_translation XREF 40 Ensembl Mouse Translation MISC \N \N \N
+5100 IMGT_HLA KNOWN 7 IMGT/HLA MISC \N \N \N
+5200 Oxford_FGU_Md_gene PRED 1 Oxford Ponting Group Monodelphis predictions gene id MISC \N \N \N
+5300 Oxford_FGU_Md_tscript PRED 1 Oxford Ponting Group Monodelphis predictions transcript id MISC \N \N Updated from alt_gene to misc due to user query
+5400 Oxford_FGU_Oa_gene PRED 1 Oxford Ponting Group Platypus predictions gene id MISC \N \N Updated from alt_gene to misc due to user query
+5500 Oxford_FGU_Oa_tscript PRED 1 Oxford Ponting Group Platypus predictions transcript id MISC \N \N \N
+5700 Ens_Cf_gene XREF 5 Ensembl Dog Gene MISC \N \N \N
+5710 Ens_Cf_transcript XREF 5 Ensembl Dog Transcript MISC \N \N \N
+5720 Ens_Cf_translation XREF 5 Ensembl Dog Translation MISC \N \N \N
+5800 Ens_Dr_gene XREF 5 Ensembl Zebrafish Gene MISC \N \N \N
+5810 Ens_Dr_transcript XREF 5 Ensembl Zebrafish Transcript MISC \N \N \N
+5820 Ens_Dr_translation XREF 5 Ensembl Zebrafish Translation MISC \N \N \N
+5900 Ens_Md_gene XREF 5 Ensembl Monodelphis Gene MISC \N \N \N
+5901 Ens_Md_transcript XREF 5 Ensembl Monodelphis Transcript MISC \N \N \N
+6100 Havana_gene XREF 100 Havana gene ID MISC \N \N \N
+6200 Ens_Rn_gene XREF 5 Ensembl Rat Gene MISC \N \N \N
+6300 Ens_Ol_gene XREF 5 Ensembl Medaka Gene MISC \N \N \N
+6400 Ens_Gg_gene XREF 40 Ensembl Chicken Gene MISC \N \N \N
+6410 Ens_Gg_transcript XREF 40 Ensembl Chicken Transcript MISC \N \N \N
+6420 Ens_Gg_translation XREF 40 Ensembl Chicken Translation MISC \N \N \N
+6500 IMCB_Tr_gene XREF 40 IMCB Fugu Gene MISC \N \N \N
+6600 Ens_Ag_gene XREF 5 Ensembl Mosquito Gene MISC \N \N \N
+6630 Ens_Am_gene XREF 5 Ensembl Bee Gene MISC \N \N \N
+6660 Ens_Ce_gene XREF 5 Ensembl Worm Gene MISC \N \N \N
+6690 Ens_Dm_gene XREF 5 Ensembl FruitFly Gene MISC \N \N \N
+6720 Ens_Fr_gene XREF 5 Ensembl Fugu Gene MISC \N \N \N
+6750 Ens_Pt_gene XREF 5 Ensembl Chimpanzee Gene MISC \N \N \N
+6810 Ens_Tn_gene XREF 5 Ensembl PufferFish Gene MISC \N \N \N
+6820 Ens_Tr_transcript XREF 40 Ensembl Fugu Transcript MISC \N \N \N
+6900 Ens_Ga_translation XREF 5 Ensembl Stickleback Translation MISC \N \N \N
+7120 Ens_Aa_translation XREF 40 Ensembl Aedes Translation MISC \N \N \N
+7159 AedesGenBank PRED 30 Aedes GenBank MISC \N \N \N
+7160 Aedes_ManualAnnotation PRED 30 Aedes ManualAnnotation MISC \N \N \N
+7170 Ixodes_ManualAnnotation PRED 30 Ixodes ManualAnnotation MISC \N \N \N
7180 VB_Community_Annotation 1 KNOWN 50 VB Community Annotation MISC \N \N \N
-7200 IMGT/LIGM_DB \N XREF 10 IMGT/LIGM-DB MISC \N \N \N
-7201 IMGT/GENE_DB \N KNOWN 40 IMGT/GENE-DB MISC \N \N \N
-7300 Ens_Mg_transcript \N XREF 40 Ensembl Turkey Transcript MISC \N \N \N
-7400 Ens_Tg_transcript \N XREF 40 Ensembl Zebrafinch Transcript MISC \N \N \N
-7500 Ens_St_transcript \N XREF 40 Ensembl Squirrel Transcript MISC \N \N \N
-7600 Ens_Fc_transcript \N XREF 40 Ensembl Cat Transcript MISC \N \N \N
-7620 Ens_Fc_translation \N XREF 40 Ensembl Cat Translation MISC \N \N \N
-8000 Vega_mouse_transcript \N XREF 5 Vega mouse transcript MISC \N \N \N
-8100 Platypus_olfactory_receptor \N XREF 40 Platypus olfactory receptor gene MISC \N \N \N
-8200 PRF \N XREF 5 PRF MISC \N \N \N
-8300 PIR \N XREF 5 PIR MISC \N \N \N
-8400 TetNig_cdna \N XREF 40 Genoscope tetraodon cDNA MISC \N \N \N
-8500 GasAcu_cdna \N XREF 40 Stickleback cDNA MISC \N \N \N
-8600 OrnAna_454_cdna \N XREF 40 Platypus 454 cDNA MISC \N \N \N
-8700 TakRub_cdna \N XREF 40 Takifugu cDNA MISC \N \N \N
-8800 CioInt_est \N XREF 40 Ciona intestinalis EST MISC \N \N \N
-8900 CioInt_cdna \N XREF 40 Ciona intestinalis cDNA MISC \N \N \N
-9000 CaeEle_est \N XREF 40 C Elegans EST MISC \N \N \N
-9100 XenTro_Gurdon_EST \N XREF 40 Xenopus Gurdon EST Clusters MISC \N \N \N
-9110 XenTro_cdna \N XREF 40 Xenopus Tropicalis cDNA MISC \N \N \N
-9120 XenLae_cdna \N XREF 40 Xenopus Laevis cDNA MISC \N \N \N
-9200 TakRub_est \N XREF 40 Takifugu EST MISC \N \N \N
-9210 TakRub_annotation \N XREF 40 Takifugu gene annotation MISC \N \N \N
-9220 TakRub_seleno_annotation \N XREF 40 Takifugu selenoprotein annotation MISC \N \N \N
-9400 TetNig_mouse_econtig \N XREF 40 Genoscope mouse exofish econtig MISC \N \N \N
-9410 TetNig_fugu_econtig \N XREF 40 Genoscope fugu exofish econtig MISC \N \N \N
-9420 TetNig_human_econtig \N XREF 40 Genoscope human exofish econtig MISC \N \N \N
-9430 TetNig_human_IPI_econtig \N XREF 40 Genoscope human IPI exofish econtig MISC \N \N \N
-9440 TetNig_mouse_IPI_econtig \N XREF 40 Genoscope mouse IPI exofish econtig MISC \N \N \N
-9450 TetNig_rat_econtig \N XREF 40 Genoscope rat exofish econtig MISC \N \N \N
-9460 TetNig_chick_econtig \N XREF 40 Genoscope chicken exofish econtig MISC \N \N \N
-9500 OryLat_est \N XREF 40 Medaka EST MISC \N \N \N
-9600 Trace_archive \N XREF 40 Trace Archive id MISC \N \N \N
-9700 CioSav_est \N XREF 40 Ciona savignyi EST MISC \N \N \N
-9800 kyotograil_2004 \N PRED 30 Ciona intestinalis Kyotograil 2004 predictions MISC \N \N \N
-9900 kyotograil_2005 \N PRED 30 Ciona intestinalis Kyotograil 2005 predictions MISC \N \N \N
-9950 Kyoto_University \N KNOWN 5 Kyoto University MISC \N \N \N
-10000 wormbase_id \N XREF 30 Generic exdb for WormBase id of any type for feature table MISC \N \N \N
-10100 EPD \N KNOWNXREF 5 Eukaryotic Promoter Database (Bucher) MISC \N \N \N
-10200 GPCR \N KNOWNXREF 5 The G protein-coupled receptor database MISC \N \N \N
-10300 MEROPS \N KNOWNXREF 5 MEROPS - the Peptidase Database MISC \N \N \N
-10500 TransFac \N KNOWNXREF 5 TransFac, database of transcription factors and their binding sites MISC \N \N \N
-10600 modCB_gene \N KNOWNXREF 5 Caenorhabditis briggsae, InParanoid model organism database MISC \N \N \N
-10700 modCE_gene \N KNOWNXREF 5 Caenorhabditis elegans, InParanoid model organism database MISC \N \N \N
-10800 modDD_gene \N KNOWNXREF 5 Dictyostelium discoideum, InParanoid model organism database MISC \N \N \N
-10900 GI \N XREF 5 GenInfo Identifier, a sequence identification number for a nucleotide sequence MISC \N \N \N
-11000 UCSC \N KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
-11100 Culex_ncRNA \N XREF 70 Culex ncRNAs MISC \N \N \N
-12300 HGNC_curated_gene \N KNOWNXREF 5 HGNC (curated) MISC \N \N \N
-12305 HGNC_automatic_gene \N KNOWNXREF 5 HGNC (automatic) MISC \N \N \N
-12310 Clone_based_vega_gene \N KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
-12315 Clone_based_ensembl_gene \N XREF 5 Clone-based (Ensembl) MISC \N \N \N
-12400 HGNC_curated_transcript \N KNOWNXREF 300 HGNC (curated) MISC \N \N \N
-12405 HGNC_automatic_transcript \N KNOWNXREF 290 HGNC (automatic) MISC \N \N \N
-12410 Clone_based_vega_transcript \N KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
-12415 Clone_based_ensembl_transcript \N XREF 5 Clone-based (Ensembl) MISC \N \N \N
-12500 DBASS3 \N XREF 50 DataBase of Aberrant 3' Splice Sites MISC \N \N \N
-12505 DBASS5 \N XREF 50 DataBase of Aberrant 5' Splice Sites MISC \N \N \N
-12510 HPA \N XREF 50 Human Protein Atlas MISC \N \N \N
-12550 MGI_curated_gene \N KNOWNXREF 5 MGI (curated) MISC \N \N \N
-12555 MGI_automatic_gene \N KNOWNXREF 5 MGI (automatic) MISC \N \N \N
-12560 MGI_curated_transcript \N KNOWNXREF 140 MGI (curated) MISC \N \N \N
-12565 MGI_automatic_transcript \N KNOWNXREF 279 MGI (automatic) MISC \N \N \N
-12600 WikiGene \N XREF 50 WikiGene MISC \N \N \N
-12601 Tgut_symbol \N KNOWNXREF 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM \N \N \N
-12610 Fantom \N XREF 50 Fantom MISC \N \N \N
-12620 Duck_consortium \N XREF 0 Duck consortium MISC \N \N \N
-12630 BGI_duck_transcriptome \N XREF 0 Beijing Genomics Institute (BGI) duck transcriptome MISC \N \N \N
-12700 goslim_goa \N XREF 5 GOSlim GOA MISC \N \N \N
-12701 goslim_generic \N XREF 5 GOSlim Generic MISC \N \N \N
-12710 WTSI_gorilla_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC \N \N \N
-12720 WTSI_zebrafish_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) zebrafish transcriptome MISC \N \N \N
-20005 UniParc \N KNOWNXREF 0 UniParc PRIMARY_DB_SYNONYM \N \N \N
-20008 BRENDA \N KNOWNXREF 0 BRENDA PRIMARY_DB_SYNONYM \N \N \N
-20009 BioCyc \N KNOWNXREF 0 BioCyc PRIMARY_DB_SYNONYM \N \N \N
-20010 BuruList \N KNOWNXREF 0 BuruList PRIMARY_DB_SYNONYM \N \N \N
-20013 EchoBASE \N KNOWNXREF 0 EchoBASE PRIMARY_DB_SYNONYM \N \N \N
-20014 EcoGene \N KNOWNXREF 0 EcoGene PRIMARY_DB_SYNONYM \N \N \N
-20017 GeneDB_Spombe \N KNOWNXREF 0 GeneDB_Spombe PRIMARY_DB_SYNONYM \N \N \N
-20025 Leproma \N KNOWNXREF 0 Leproma PRIMARY_DB_SYNONYM \N \N \N
-20031 2DBase_Ecoli \N KNOWNXREF 0 2DBase-Ecoli PRIMARY_DB_SYNONYM \N \N \N
-20038 SagaList \N KNOWNXREF 0 SagaList PRIMARY_DB_SYNONYM \N \N \N
-20040 SubtiList \N KNOWNXREF 0 SubtiList PRIMARY_DB_SYNONYM \N \N \N
-20042 TIGR \N KNOWNXREF 0 TIGR PRIMARY_DB_SYNONYM \N \N \N
-20043 TubercuList \N KNOWNXREF 0 TubercuList PRIMARY_DB_SYNONYM \N \N \N
-20046 ArrayExpress \N XREF 0 ArrayExpress MISC \N \N \N
-20050 GermOnline \N KNOWNXREF 0 GermOnline PRIMARY_DB_SYNONYM \N \N \N
-20059 DIP \N KNOWNXREF 0 DIP PRIMARY_DB_SYNONYM \N \N \N
-20061 DisProt \N KNOWNXREF 0 DisProt PRIMARY_DB_SYNONYM \N \N \N
-20062 DrugBank \N KNOWNXREF 0 DrugBank PRIMARY_DB_SYNONYM \N \N \N
-20065 GlycoSuiteDB \N KNOWNXREF 0 GlycoSuiteDB PRIMARY_DB_SYNONYM \N \N \N
-20066 HAMAP \N KNOWNXREF 0 HAMAP PRIMARY_DB_SYNONYM \N \N \N
-20067 HOGENOM \N KNOWNXREF 0 HOGENOM PRIMARY_DB_SYNONYM \N \N \N
-20071 HSSP \N KNOWNXREF 0 HSSP PRIMARY_DB_SYNONYM \N \N \N
-20072 IntAct \N KNOWNXREF 0 IntAct PRIMARY_DB_SYNONYM \N \N \N
-20074 KEGG \N KNOWNXREF 0 KEGG PRIMARY_DB_SYNONYM \N \N \N
-20078 PDBsum \N KNOWNXREF 0 PDBsum PRIMARY_DB_SYNONYM \N \N \N
-20082 PeroxiBase \N KNOWNXREF 0 PeroxiBase PRIMARY_DB_SYNONYM \N \N \N
-20083 PhosSite \N KNOWNXREF 0 PhosSite PRIMARY_DB_SYNONYM \N \N \N
-20084 PptaseDB \N KNOWNXREF 0 PptaseDB PRIMARY_DB_SYNONYM \N \N \N
-20085 REBASE \N KNOWNXREF 0 REBASE PRIMARY_DB_SYNONYM \N \N \N
-20088 Reactome \N KNOWNXREF 0 Reactome PRIMARY_DB_SYNONYM \N \N \N
-20090 SWISS_2DPAGE \N KNOWNXREF 0 SWISS-2DPAGE PRIMARY_DB_SYNONYM \N \N \N
-20097 RegulonDb_Transcript \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
-20099 RegulonDb_Gene \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
-20101 IntEnz \N KNOWNXREF 0 EnzymeCommission PRIMARY_DB_SYNONYM \N \N \N
-20102 ArrayExpressExperiment \N XREF 0 ArrayExpressExperiment MISC \N \N \N
-20200 EMBLBANK_GENE \N KNOWNXREF 117 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
-20201 GeneDB_SPombe_transcript \N KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
-20202 EBACTERIA_GENE \N KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
-20203 EBACTERIA_TRANSCRIPT \N KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
-20204 EPROTIST_GENE \N KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
-20205 EPROTIST_TRANSCRIPT \N KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
-20207 EFUNGI_GENE \N KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
-20208 EFUNGI_TRANSCRIPT \N KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
-20209 EMBLBANK_TRANSCRIPT \N KNOWNXREF 115 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
-20210 GeneDB_SPombe_gene \N KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
-20214 phatr_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20215 phatr_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20216 phatr_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20217 phatr_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20218 phatr_jgi_v2_bd_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20219 phatr_jgi_v2_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20220 thaps_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20221 thaps_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20222 thaps_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20223 thaps_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20225 thaps_jgi_v2_bd_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20226 thaps_jgi_v2_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20227 Diatom_EST_Cluster \N XREF 0 ENS EST Cluster (Diatom ESTDB) MISC \N \N \N
-20228 CADRE_Afum_A1163 \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20301 RNAMMER \N KNOWNXREF 0 RNAmmer MISC \N \N \N
-20302 TRNASCAN_SE \N KNOWNXREF 0 tRNAScan-SE MISC \N \N \N
-20303 dictyBase \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
-20304 dictyBase_gene \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
-20305 dictyBase_transcript \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
-20306 ASPGD \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
-20307 ASPGD_GENE \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
-20308 ASPGD_TRANSCRIPT \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
-20309 CADRE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20310 CADRE_GENE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20311 CADRE_TRANSCRIPT \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20312 SGD_GENE \N KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
-20313 SGD_TRANSCRIPT \N KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
+7200 IMGT/LIGM_DB XREF 10 IMGT/LIGM-DB MISC \N \N \N
+7201 IMGT/GENE_DB KNOWN 40 IMGT/GENE-DB MISC \N \N \N
+7300 Ens_Mg_transcript XREF 40 Ensembl Turkey Transcript MISC \N \N \N
+7400 Ens_Tg_transcript XREF 40 Ensembl Zebrafinch Transcript MISC \N \N \N
+7500 Ens_St_transcript XREF 40 Ensembl Squirrel Transcript MISC \N \N \N
+7600 Ens_Fc_transcript XREF 40 Ensembl Cat Transcript MISC \N \N \N
+7620 Ens_Fc_translation XREF 40 Ensembl Cat Translation MISC \N \N \N
+8000 Vega_mouse_transcript XREF 5 Vega mouse transcript MISC \N \N \N
+8100 Platypus_olfactory_receptor XREF 40 Platypus olfactory receptor gene MISC \N \N \N
+8200 PRF XREF 5 PRF MISC \N \N \N
+8300 PIR XREF 5 PIR MISC \N \N \N
+8400 TetNig_cdna XREF 40 Genoscope tetraodon cDNA MISC \N \N \N
+8500 GasAcu_cdna XREF 40 Stickleback cDNA MISC \N \N \N
+8600 OrnAna_454_cdna XREF 40 Platypus 454 cDNA MISC \N \N \N
+8700 TakRub_cdna XREF 40 Takifugu cDNA MISC \N \N \N
+8800 CioInt_est XREF 40 Ciona intestinalis EST MISC \N \N \N
+8900 CioInt_cdna XREF 40 Ciona intestinalis cDNA MISC \N \N \N
+9000 CaeEle_est XREF 40 C Elegans EST MISC \N \N \N
+9100 XenTro_Gurdon_EST XREF 40 Xenopus Gurdon EST Clusters MISC \N \N \N
+9110 XenTro_cdna XREF 40 Xenopus Tropicalis cDNA MISC \N \N \N
+9120 XenLae_cdna XREF 40 Xenopus Laevis cDNA MISC \N \N \N
+9200 TakRub_est XREF 40 Takifugu EST MISC \N \N \N
+9210 TakRub_annotation XREF 40 Takifugu gene annotation MISC \N \N \N
+9220 TakRub_seleno_annotation XREF 40 Takifugu selenoprotein annotation MISC \N \N \N
+9400 TetNig_mouse_econtig XREF 40 Genoscope mouse exofish econtig MISC \N \N \N
+9410 TetNig_fugu_econtig XREF 40 Genoscope fugu exofish econtig MISC \N \N \N
+9420 TetNig_human_econtig XREF 40 Genoscope human exofish econtig MISC \N \N \N
+9430 TetNig_human_IPI_econtig XREF 40 Genoscope human IPI exofish econtig MISC \N \N \N
+9440 TetNig_mouse_IPI_econtig XREF 40 Genoscope mouse IPI exofish econtig MISC \N \N \N
+9450 TetNig_rat_econtig XREF 40 Genoscope rat exofish econtig MISC \N \N \N
+9460 TetNig_chick_econtig XREF 40 Genoscope chicken exofish econtig MISC \N \N \N
+9500 OryLat_est XREF 40 Medaka EST MISC \N \N \N
+9600 Trace_archive XREF 40 Trace Archive id MISC \N \N \N
+9700 CioSav_est XREF 40 Ciona savignyi EST MISC \N \N \N
+9800 kyotograil_2004 PRED 30 Ciona intestinalis Kyotograil 2004 predictions MISC \N \N \N
+9900 kyotograil_2005 PRED 30 Ciona intestinalis Kyotograil 2005 predictions MISC \N \N \N
+9950 Kyoto_University KNOWN 5 Kyoto University MISC \N \N \N
+10000 wormbase_id XREF 30 Generic exdb for WormBase id of any type for feature table MISC \N \N \N
+10100 EPD KNOWNXREF 5 Eukaryotic Promoter Database (Bucher) MISC \N \N \N
+10200 GPCR KNOWNXREF 5 The G protein-coupled receptor database MISC \N \N \N
+10300 MEROPS KNOWNXREF 5 MEROPS - the Peptidase Database MISC \N \N \N
+10500 TransFac KNOWNXREF 5 TransFac, database of transcription factors and their binding sites MISC \N \N \N
+10600 modCB_gene KNOWNXREF 5 Caenorhabditis briggsae, InParanoid model organism database MISC \N \N \N
+10700 modCE_gene KNOWNXREF 5 Caenorhabditis elegans, InParanoid model organism database MISC \N \N \N
+10800 modDD_gene KNOWNXREF 5 Dictyostelium discoideum, InParanoid model organism database MISC \N \N \N
+10900 GI XREF 5 GenInfo Identifier, a sequence identification number for a nucleotide sequence MISC \N \N \N
+11000 UCSC KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
+11100 Culex_ncRNA XREF 70 Culex ncRNAs MISC \N \N \N
+12300 HGNC_curated_gene KNOWNXREF 5 HGNC (curated) MISC \N \N \N
+12305 HGNC_automatic_gene KNOWNXREF 5 HGNC (automatic) MISC \N \N \N
+12310 Clone_based_vega_gene KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
+12315 Clone_based_ensembl_gene XREF 5 Clone-based (Ensembl) MISC \N \N \N
+12400 HGNC_curated_transcript KNOWNXREF 300 HGNC (curated) MISC \N \N \N
+12405 HGNC_automatic_transcript KNOWNXREF 290 HGNC (automatic) MISC \N \N \N
+12410 Clone_based_vega_transcript KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
+12415 Clone_based_ensembl_transcr XREF 5 Clone-based (Ensembl) MISC \N \N \N
+12500 DBASS3 XREF 50 DataBase of Aberrant 3' Splice Sites MISC \N \N \N
+12505 DBASS5 XREF 50 DataBase of Aberrant 5' Splice Sites MISC \N \N \N
+12510 HPA XREF 50 Human Protein Atlas MISC \N \N \N
+12550 MGI_curated_gene KNOWNXREF 5 MGI (curated) MISC \N \N \N
+12555 MGI_automatic_gene KNOWNXREF 5 MGI (automatic) MISC \N \N \N
+12560 MGI_curated_transcript KNOWNXREF 140 MGI (curated) MISC \N \N \N
+12565 MGI_automatic_transcript KNOWNXREF 279 MGI (automatic) MISC \N \N \N
+12600 WikiGene XREF 50 WikiGene MISC \N \N \N
+12601 Tgut_symbol KNOWNXREF 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM \N \N \N
+12610 Fantom XREF 50 Fantom MISC \N \N \N
+12620 Duck_consortium XREF 0 Duck consortium MISC \N \N \N
+12630 BGI_duck_transcriptome XREF 0 Beijing Genomics Institute (BGI) duck transcriptome MISC \N \N \N
+12700 goslim_goa XREF 5 GOSlim GOA MISC \N \N \N
+12701 goslim_generic XREF 5 GOSlim Generic MISC \N \N \N
+12710 WTSI_gorilla_transcriptome XREF 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC \N \N \N
+12720 WTSI_zebrafish_transcriptom XREF 0 Wellcome Trust Sanger Institute (WTSI) zebrafish transcriptome MISC \N \N \N
+20005 UniParc KNOWNXREF 0 UniParc PRIMARY_DB_SYNONYM \N \N \N
+20008 BRENDA KNOWNXREF 0 BRENDA PRIMARY_DB_SYNONYM \N \N \N
+20009 BioCyc KNOWNXREF 0 BioCyc PRIMARY_DB_SYNONYM \N \N \N
+20010 BuruList KNOWNXREF 0 BuruList PRIMARY_DB_SYNONYM \N \N \N
+20013 EchoBASE KNOWNXREF 0 EchoBASE PRIMARY_DB_SYNONYM \N \N \N
+20014 EcoGene KNOWNXREF 0 EcoGene PRIMARY_DB_SYNONYM \N \N \N
+20017 GeneDB_Spombe KNOWNXREF 0 GeneDB_Spombe PRIMARY_DB_SYNONYM \N \N \N
+20025 Leproma KNOWNXREF 0 Leproma PRIMARY_DB_SYNONYM \N \N \N
+20031 2DBase_Ecoli KNOWNXREF 0 2DBase-Ecoli PRIMARY_DB_SYNONYM \N \N \N
+20038 SagaList KNOWNXREF 0 SagaList PRIMARY_DB_SYNONYM \N \N \N
+20040 SubtiList KNOWNXREF 0 SubtiList PRIMARY_DB_SYNONYM \N \N \N
+20042 TIGR KNOWNXREF 0 TIGR PRIMARY_DB_SYNONYM \N \N \N
+20043 TubercuList KNOWNXREF 0 TubercuList PRIMARY_DB_SYNONYM \N \N \N
+20046 ArrayExpress XREF 0 ArrayExpress MISC \N \N \N
+20050 GermOnline KNOWNXREF 0 GermOnline PRIMARY_DB_SYNONYM \N \N \N
+20059 DIP KNOWNXREF 0 DIP PRIMARY_DB_SYNONYM \N \N \N
+20061 DisProt KNOWNXREF 0 DisProt PRIMARY_DB_SYNONYM \N \N \N
+20062 DrugBank KNOWNXREF 0 DrugBank PRIMARY_DB_SYNONYM \N \N \N
+20065 GlycoSuiteDB KNOWNXREF 0 GlycoSuiteDB PRIMARY_DB_SYNONYM \N \N \N
+20066 HAMAP KNOWNXREF 0 HAMAP PRIMARY_DB_SYNONYM \N \N \N
+20067 HOGENOM KNOWNXREF 0 HOGENOM PRIMARY_DB_SYNONYM \N \N \N
+20071 HSSP KNOWNXREF 0 HSSP PRIMARY_DB_SYNONYM \N \N \N
+20072 IntAct KNOWNXREF 0 IntAct PRIMARY_DB_SYNONYM \N \N \N
+20074 KEGG KNOWNXREF 0 KEGG PRIMARY_DB_SYNONYM \N \N \N
+20078 PDBsum KNOWNXREF 0 PDBsum PRIMARY_DB_SYNONYM \N \N \N
+20082 PeroxiBase KNOWNXREF 0 PeroxiBase PRIMARY_DB_SYNONYM \N \N \N
+20083 PhosSite KNOWNXREF 0 PhosSite PRIMARY_DB_SYNONYM \N \N \N
+20084 PptaseDB KNOWNXREF 0 PptaseDB PRIMARY_DB_SYNONYM \N \N \N
+20085 REBASE KNOWNXREF 0 REBASE PRIMARY_DB_SYNONYM \N \N \N
+20088 Reactome KNOWNXREF 0 Reactome PRIMARY_DB_SYNONYM \N \N \N
+20090 SWISS_2DPAGE KNOWNXREF 0 SWISS-2DPAGE PRIMARY_DB_SYNONYM \N \N \N
+20097 RegulonDb_Transcript KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20099 RegulonDb_Gene KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20101 IntEnz KNOWNXREF 0 EnzymeCommission PRIMARY_DB_SYNONYM \N \N \N
+20102 ArrayExpressExperiment XREF 0 ArrayExpressExperiment MISC \N \N \N
+20200 EMBLBANK_GENE KNOWNXREF 117 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
+20201 GeneDB_SPombe_transcript KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
+20202 EBACTERIA_GENE KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
+20203 EBACTERIA_TRANSCRIPT KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
+20204 EPROTIST_GENE KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
+20205 EPROTIST_TRANSCRIPT KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
+20207 EFUNGI_GENE KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
+20208 EFUNGI_TRANSCRIPT KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
+20209 EMBLBANK_TRANSCRIPT KNOWNXREF 115 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
+20210 GeneDB_SPombe_gene KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
+20214 phatr_jgi_v2_bd KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20215 phatr_jgi_v2 KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20216 phatr_jgi_v2_bd_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20217 phatr_jgi_v2_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20218 phatr_jgi_v2_bd_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20219 phatr_jgi_v2_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20220 thaps_jgi_v2_bd KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20221 thaps_jgi_v2 KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20222 thaps_jgi_v2_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20223 thaps_jgi_v2_bd_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20225 thaps_jgi_v2_bd_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20226 thaps_jgi_v2_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20227 Diatom_EST_Cluster XREF 0 ENS EST Cluster (Diatom ESTDB) MISC \N \N \N
+20228 CADRE_Afum_A1163 KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20301 RNAMMER KNOWNXREF 0 RNAmmer MISC \N \N \N
+20302 TRNASCAN_SE KNOWNXREF 0 tRNAScan-SE MISC \N \N \N
+20303 dictyBase KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20304 dictyBase_gene KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20305 dictyBase_transcript KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20306 ASPGD KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20307 ASPGD_GENE KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20308 ASPGD_TRANSCRIPT KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20309 CADRE KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20310 CADRE_GENE KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20311 CADRE_TRANSCRIPT KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20312 SGD_GENE KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
+20313 SGD_TRANSCRIPT KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
20314 BROAD_PUCCINIA_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20315 BROAD_PUCCINIA_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20316 BROAD_PUCCINIA 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
@@ -315,7 +315,7 @@
20321 physo1_jgi_v1.1_gene 1.1 KNOWNXREF 0 JGI Gene ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
20322 physo1_jgi_v1.1_transcript 1.1 KNOWNXREF 0 JGI transcript ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
20323 BROAD_P_infestans_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20324 BROAD_P_infestans_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20324 BROAD_P_infestans_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20325 BROAD_P_infestans 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20326 BROAD_M_oryzae_GENE 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20327 BROAD_M_oryzae_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
@@ -330,18 +330,18 @@
20336 SCHISTODB_TRANSCRIPT 1 KNOWNXREF 0 SchistoDB PRIMARY_DB_SYNONYM \N \N \N
20337 BROAD_F_oxysporum 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20338 BROAD_F_oxysporum_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20339 BROAD_F_oxysporum_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20339 BROAD_F_oxysporum_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20340 BROAD_G_zeae 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20341 BROAD_G_zeae_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20342 BROAD_G_zeae_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20343 BROAD_G_moniliformis 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20344 BROAD_G_moniliformis_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20345 BROAD_G_moniliformis_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20345 BROAD_G_moniliformis_TRANSC 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20346 GeneDB_TRANSLATION 1 KNOWNXREF 0 GeneDB Translation ID PRIMARY_DB_SYNONYM \N \N \N
20347 PGD 1 KNOWNXREF 0 Pythium genome database MISC \N \N \N
20348 PGD_GENE 1 KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
20349 PGD_TRANSCRIPT 1 KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
-20350 RegulonDb_Operon \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20350 RegulonDb_Operon KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
20351 BROAD_N_crassa_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20352 BROAD_N_crassa_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20353 BROAD_N_crassa 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
@@ -350,7 +350,7 @@
20356 BROAD_U_maydis_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20357 BROAD_P_triticina 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20358 BROAD_P_triticina_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20359 BROAD_P_triticina_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20359 BROAD_P_triticina_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20360 SpBase 1 KNOWNXREF 0 SpBase MISC \N \N \N
20361 PHIbase 3.2 XREF 50 PHI-base MISC \N \N \N
20362 necha_jgi_v2.0_gene 2 KNOWNXREF 0 Nectria JGI gene PRIMARY_DB_SYNONYM \N \N \N
@@ -367,114 +367,114 @@
20373 BROAD_P_NODORUM_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20375 PomBase 1 KNOWN 0 PomBase MISC \N \N \N
20376 PomBase_GENE 1 KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
-20377 PomBase_TRANSCRIPT \N KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
+20377 PomBase_TRANSCRIPT KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
20378 PomBase_TRANSLATION 1 KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
-20379 SPO \N KNOWNXREF 0 SPO ID MISC \N \N \N
-20380 CBS \N KNOWNXREF 0 CBS Server MISC \N \N \N
-20381 COG \N KNOWNXREF 0 Cluster of Orthologous Groups (NCBI) MISC \N \N \N
-20382 CGD \N KNOWN 0 Candida Genome Database MISC \N \N \N
-20383 ProSite \N XREF 0 ProSite ID MISC \N \N \N
-20385 SMART \N XREF 0 SMART ID MISC \N \N \N
-20386 SPD \N KNOWNXREF 0 SPD ID MISC \N \N \N
-20387 KOG \N KNOWNXREF 0 KOG ID MISC \N \N \N
-20388 PBO \N KNOWNXREF 0 PomBase Ontology ID MISC \N \N \N
-20389 FYPO \N KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
-20390 MOD \N KNOWNXREF 0 PSI-MOD, Post Translational Modification Ontology MISC \N \N \N
+20379 SPO KNOWNXREF 0 SPO ID MISC \N \N \N
+20380 CBS KNOWNXREF 0 CBS Server MISC \N \N \N
+20381 COG KNOWNXREF 0 Cluster of Orthologous Groups (NCBI) MISC \N \N \N
+20382 CGD KNOWN 0 Candida Genome Database MISC \N \N \N
+20383 ProSite XREF 0 ProSite ID MISC \N \N \N
+20385 SMART XREF 0 SMART ID MISC \N \N \N
+20386 SPD KNOWNXREF 0 SPD ID MISC \N \N \N
+20387 KOG KNOWNXREF 0 KOG ID MISC \N \N \N
+20388 PBO KNOWNXREF 0 PomBase Ontology ID MISC \N \N \N
+20389 FYPO KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
+20390 MOD KNOWNXREF 0 PSI-MOD, Post Translational Modification Ontology MISC \N \N \N
20391 AGD_GENE 1 KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
20392 AGD_TRANSCRIPT 1 KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
20393 AGD 1 KNOWNXREF 0 Ashbya Genome Database MISC \N \N \N
20394 FYPO_GENE 1 KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
20395 FYPO_TRANSCRIPT 1 KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
-50000 BGI_EST_Cluster \N XREF 0 EST Cluster (BGI Indica) MISC \N \N \N
-50005 EC_NUMBER \N XREF 0 Enzyme EC Number MISC \N \N \N
-50010 FSTs \N XREF 0 Flanking Sequence Tag (FST) MISC \N \N \N
-50015 gene_name \N KNOWNXREF 0 Gene Name MISC \N \N \N
-50020 Gramene_Pathway \N XREF 0 Gramene Pathway MISC \N \N \N
-50030 Gramene_GenesDB \N KNOWNXREF 100 Gramene Curated Gene MISC \N \N \N
-50035 Gramene_MarkersDB \N XREF 0 Gramene MISC \N \N \N
-50040 Gramene_MarkersDB_mRNA \N XREF 0 GenBank mRNA (Gramene) MISC \N \N \N
-50050 Gramene_MarkersDB_EST \N XREF 0 GenBank EST (Gramene) MISC \N \N \N
-50060 IRGSP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
-50065 KOME \N KNOWNXREF 0 Full Length cDNA (KOME) MISC \N \N \N
-50070 miRNA_Accession \N XREF 0 miRNA miRBase accession MISC \N \N \N
-50080 miRNA_Registry \N XREF 1 miRNA Registry MISC \N \N \N
-50090 NASC_GENE_ID \N XREF 1 NASC Gene ID MISC \N \N \N
-50100 NASC_TRANSCRIPT_ID \N XREF 1 NASC Transcript ID MISC \N \N \N
-50110 PlantGDB_PUT \N XREF 1 PlantGDB Transcript MISC \N \N \N
-50120 RAP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
-50130 siRNA_Sunkar \N XREF 0 siRNA ID from Sunkar et. al. 2005 NAR 33(14):4443-54 MISC \N \N \N
-50140 TIGR_LOCUS \N XREF 1 MSU/TIGR Locus MISC \N \N \N
-50150 TIGR_LOCUS_MODEL \N XREF 0 MSU/TIGR Locus (Model) MISC \N \N \N
-50160 TAIR_LOCUS \N XREF 8 TAIR Locus MISC \N \N \N
-50170 TAIR_LOCUS_MODEL \N XREF 8 TAIR Locus (Model) MISC \N \N \N
-50180 TIGR_GeneIndex \N XREF 0 Gene Index MISC \N \N \N
-50185 TO \N XREF 0 Plant Trait Ontology MISC \N \N \N
-50190 PO \N XREF 0 Plant Structure Ontology MISC \N \N \N
-50195 PO_to_gene \N XREF 0 Plant Structure Ontology MISC \N \N \N
-50196 GO_to_gene \N XREF 0 Gene Ontology MISC \N \N \N
-50200 GRO \N XREF 0 Plant Growth Stage MISC \N \N \N
-50510 AFFY_RICE \N XREF 1 Affymx GeneChip Rice ARRAY \N \N \N
-50520 AFFY_ATH1 \N XREF 1 Affymx GeneChip ATH1 ARRAY \N \N \N
-50530 AFFY_Vitis_Vinifera \N XREF 1 Affymx GeneChip Vitis vinifera ARRAY \N \N \N
-50540 AFFY_Poplar \N XREF 1 Affymx GeneChip Poplar ARRAY \N \N \N
-50541 LRG \N KNOWN 10 Locus Reference Genomic MISC \N \N \N
-50542 ENS_LRG_gene \N KNOWN 10 LRG display in Ensembl MISC \N \N \N
-50543 ENS_LRG_transcript \N KNOWN 10 LRG display in Ensembl MISC \N \N \N
-50600 IKMCs_KOs \N XREF 10 International Knockout Mouse Consortium Knockouts MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (ES cells available) MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (Mice available) MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (No products available yet) MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (Vector available) MISC \N \N 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)
-50605 RFAM_gene_name \N KNOWNXREF 5 RFAM gene name MISC \N \N gene name from RFAM
-50606 miRBase_gene_name \N KNOWNXREF 5 miRBase gene name MISC \N \N gene name from miRBase
-50607 miRBase_trans_name \N KNOWNXREF 5 miRBase transcript name MISC \N \N transcript name from miRBase
-50608 RFAM_trans_name \N KNOWNXREF 5 RFAM transcript name MISC \N \N transcript name from RFAM
-50609 HGNC_trans_name \N KNOWNXREF 5 HGNC transcript name MISC \N \N transcript name from HGNC
-50610 MGI_trans_name \N KNOWNXREF 5 MGI transcript name MISC \N \N transcript name from MGI
-50611 ZFIN_ID_trans_name \N KNOWNXREF 5 ZFIN transcript name MISC \N \N transcript name from ZFIN
-50612 LampreyGenomeProject \N KNOWN 1 Lamprey Genome Project MISC \N \N \N
-50620 Illumina_Bodymap_transcriptome \N XREF 0 Illumina Bodymap transcriptome MISC \N \N \N
-50621 Uniprot_gn \N KNOWN 116 UniProtKB Gene Name MISC \N \N \N
-50622 GGSC \N KNOWNXREF 0 Gibbon Genome Sequencing Consortium MISC \N \N Gibbon Genome Sequencing Consortium
-50623 Broad Institute \N KNOWN 5 Broad Institute of MIT and Harvard MISC \N \N \N
-50624 PFAM \N XREF 0 PFAM MISC \N \N Pfam from Vega
-50625 SGSC \N KNOWN 5 Swine Genome Sequencing Consortium MISC \N \N \N
-50626 RIKEN \N KNOWN 5 Riken Institute MISC \N \N \N
-50627 SHSC \N KNOWNXREF 0 Tasmanian Devil Sequencing Consortium MISC \N \N Tasmanian Devil Genome Sequencing Consortium
+50000 BGI_EST_Cluster XREF 0 EST Cluster (BGI Indica) MISC \N \N \N
+50005 EC_NUMBER XREF 0 Enzyme EC Number MISC \N \N \N
+50010 FSTs XREF 0 Flanking Sequence Tag (FST) MISC \N \N \N
+50015 gene_name KNOWNXREF 0 Gene Name MISC \N \N \N
+50020 Gramene_Pathway XREF 0 Gramene Pathway MISC \N \N \N
+50030 Gramene_GenesDB KNOWNXREF 100 Gramene Curated Gene MISC \N \N \N
+50035 Gramene_MarkersDB XREF 0 Gramene MISC \N \N \N
+50040 Gramene_MarkersDB_mRNA XREF 0 GenBank mRNA (Gramene) MISC \N \N \N
+50050 Gramene_MarkersDB_EST XREF 0 GenBank EST (Gramene) MISC \N \N \N
+50060 IRGSP_Gene XREF 0 IRGSP/RAP Gene MISC \N \N \N
+50065 KOME KNOWNXREF 0 Full Length cDNA (KOME) MISC \N \N \N
+50070 miRNA_Accession XREF 0 miRNA miRBase accession MISC \N \N \N
+50080 miRNA_Registry XREF 1 miRNA Registry MISC \N \N \N
+50090 NASC_GENE_ID XREF 1 NASC Gene ID MISC \N \N \N
+50100 NASC_TRANSCRIPT_ID XREF 1 NASC Transcript ID MISC \N \N \N
+50110 PlantGDB_PUT XREF 1 PlantGDB Transcript MISC \N \N \N
+50120 RAP_Gene XREF 0 IRGSP/RAP Gene MISC \N \N \N
+50130 siRNA_Sunkar XREF 0 siRNA ID from Sunkar et. al. 2005 NAR 33(14):4443-54 MISC \N \N \N
+50140 TIGR_LOCUS XREF 1 MSU/TIGR Locus MISC \N \N \N
+50150 TIGR_LOCUS_MODEL XREF 0 MSU/TIGR Locus (Model) MISC \N \N \N
+50160 TAIR_LOCUS XREF 8 TAIR Locus MISC \N \N \N
+50170 TAIR_LOCUS_MODEL XREF 8 TAIR Locus (Model) MISC \N \N \N
+50180 TIGR_GeneIndex XREF 0 Gene Index MISC \N \N \N
+50185 TO XREF 0 Plant Trait Ontology MISC \N \N \N
+50190 PO XREF 0 Plant Structure Ontology MISC \N \N \N
+50195 PO_to_gene XREF 0 Plant Structure Ontology MISC \N \N \N
+50196 GO_to_gene XREF 0 Gene Ontology MISC \N \N \N
+50200 GRO XREF 0 Plant Growth Stage MISC \N \N \N
+50510 AFFY_RICE XREF 1 Affymx GeneChip Rice ARRAY \N \N \N
+50520 AFFY_ATH1 XREF 1 Affymx GeneChip ATH1 ARRAY \N \N \N
+50530 AFFY_Vitis_Vinifera XREF 1 Affymx GeneChip Vitis vinifera ARRAY \N \N \N
+50540 AFFY_Poplar XREF 1 Affymx GeneChip Poplar ARRAY \N \N \N
+50541 LRG KNOWN 10 Locus Reference Genomic MISC \N \N \N
+50542 ENS_LRG_gene KNOWN 10 LRG display in Ensembl MISC \N \N \N
+50543 ENS_LRG_transcript KNOWN 10 LRG display in Ensembl MISC \N \N \N
+50600 IKMCs_KOs XREF 10 International Knockout Mouse Consortium Knockouts MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (ES cells available) MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (Mice available) MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (No products available yet) MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (Vector available) MISC \N \N 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)
+50605 RFAM_gene_name KNOWNXREF 5 RFAM gene name MISC \N \N gene name from RFAM
+50606 miRBase_gene_name KNOWNXREF 5 miRBase gene name MISC \N \N gene name from miRBase
+50607 miRBase_trans_name KNOWNXREF 5 miRBase transcript name MISC \N \N transcript name from miRBase
+50608 RFAM_trans_name KNOWNXREF 5 RFAM transcript name MISC \N \N transcript name from RFAM
+50609 HGNC_trans_name KNOWNXREF 5 HGNC transcript name MISC \N \N transcript name from HGNC
+50610 MGI_trans_name KNOWNXREF 5 MGI transcript name MISC \N \N transcript name from MGI
+50611 ZFIN_ID_trans_name KNOWNXREF 5 ZFIN transcript name MISC \N \N transcript name from ZFIN
+50612 LampreyGenomeProject KNOWN 1 Lamprey Genome Project MISC \N \N \N
+50620 Illumina_Bodymap_transcript XREF 0 Illumina Bodymap transcriptome MISC \N \N \N
+50621 Uniprot_gn KNOWN 116 UniProtKB Gene Name MISC \N \N \N
+50622 GGSC KNOWNXREF 0 Gibbon Genome Sequencing Consortium MISC \N \N Gibbon Genome Sequencing Consortium
+50623 Broad Institute KNOWN 5 Broad Institute of MIT and Harvard MISC \N \N \N
+50624 PFAM XREF 0 PFAM MISC \N \N Pfam from Vega
+50625 SGSC KNOWN 5 Swine Genome Sequencing Consortium MISC \N \N \N
+50626 RIKEN KNOWN 5 Riken Institute MISC \N \N \N
+50627 SHSC KNOWNXREF 0 Tasmanian Devil Sequencing Consortium MISC \N \N Tasmanian Devil Genome Sequencing Consortium
50628 PFAM 22 XREF 0 PFAM MISC \N \N Pfam release 22, from Vega
50629 PFAM 23 XREF 0 PFAM MISC \N \N Pfam release 23, from Vega
50630 PFAM 24 XREF 0 PFAM MISC \N \N Pfam release 24, from Vega
50631 PFAM 25 XREF 0 PFAM MISC \N \N Pfam release 25, from Vega
50632 PFAM 26 XREF 0 PFAM MISC \N \N Pfam release 26, from Vega
-50633 GRC_primary_assembly \N XREF 0 GRC primary assembly MISC \N \N Primary assembly of this species genome from the GRC
-50634 Ens_Ga_gene \N XREF 5 Ensembl Stickleback Gene MISC \N \N \N
-50635 Ens_Ga_transcript \N XREF 170 Ensembl Stickleback Transcript MISC \N \N \N
-50637 CSAC \N KNOWN 5 Chimpanzee Sequencing and Analysis Consortium MISC \N \N \N
+50633 GRC_primary_assembly XREF 0 GRC primary assembly MISC \N \N Primary assembly of this species genome from the GRC
+50634 Ens_Ga_gene XREF 5 Ensembl Stickleback Gene MISC \N \N \N
+50635 Ens_Ga_transcript XREF 170 Ensembl Stickleback Transcript MISC \N \N \N
+50637 CSAC KNOWN 5 Chimpanzee Sequencing and Analysis Consortium MISC \N \N \N
50640 PomBase_Interaction_GENETIC 1 KNOWNXREF 5 PomBase Interaction Genetic MISC \N \N \N
-50641 PomBase_Interaction_PHYSICAL 1 KNOWNXREF 5 PomBase Interaction Physical MISC \N \N \N
+50641 PomBase_Interaction_PHYSICA 1 KNOWNXREF 5 PomBase Interaction Physical MISC \N \N \N
50642 PomBase_Gene_Name 1 KNOWNXREF 5 PomBase Gene Name MISC \N \N \N
50643 PomBase_Systematic_ID 1 KNOWNXREF 5 PomBase Systematic ID MISC \N \N \N
50644 PomBase_Ortholog 1 KNOWNXREF 5 Orthologous Gene MISC \N \N \N
-50645 Ens_Ss_translation \N XREF 5 Ensembl Pig Translation MISC \N \N \N
-50646 Psinensis_sequencing_consortium \N KNOWN 5 Pelodiscus sinensis sequencing consortium MISC \N \N \N
+50645 Ens_Ss_translation XREF 5 Ensembl Pig Translation MISC \N \N \N
+50646 Psinensis_sequencing_consor KNOWN 5 Pelodiscus sinensis sequencing consortium MISC \N \N \N
50647 BROAD_Magnaporthe_DB 1 KNOWNXREF 0 Magnaporthe comparative DB MISC \N \N Broad Institute Magnaporthe comparative Database
50648 BROAD_Magnaporthe_DB_GENE 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
-50649 BROAD_Magnaporthe_DB_TRANSCRIPT 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
-50650 BGI Shenzhen \N KNOWN 5 Beijing Genomics Institute, Shenzhen MISC \N \N \N
-50651 ICGSC \N KNOWN 5 International Cat Genome Sequencing Consortium MISC \N \N \N
+50649 BROAD_Magnaporthe_DB_TRANSC 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
+50650 BGI Shenzhen KNOWN 5 Beijing Genomics Institute, Shenzhen MISC \N \N \N
+50651 ICGSC KNOWN 5 International Cat Genome Sequencing Consortium MISC \N \N \N
50652 SGD_TRANSLATION 1 KNOWNXREF 0 SGD MISC \N \N SGD Mapping attached to S.cerevisiae translations objects so we can attach GO dependant annotations at the translation level as well.
-50653 WashingtonUniversity \N KNOWN 5 The Genome Institute, Washington University School of Medicine MISC \N \N \N
+50653 WashingtonUniversity KNOWN 5 The Genome Institute, Washington University School of Medicine MISC \N \N \N
50654 BDGP_cDNA 1 KNOWN 50 Fly cDNA MISC \N \N cDNA from the Berkeley Drosophila Genome Project
50655 BDGP_cDNA_Gold_Collection 1 KNOWN 50 Fly gold cDNA MISC \N \N Gold Collection cDNA from the Berkeley Drosophila Genome Project
-50656 Ens_Tg_translation \N KNOWN 5 Ensembl Zebrafinch Translation MISC \N \N \N
-50657 BudgerigarGenomeProject \N KNOWN 0 Budgerigar Genome Project MISC \N \N Melopsittacus undulatus sequenced by Washington University School of Medicine
+50656 Ens_Tg_translation KNOWN 5 Ensembl Zebrafinch Translation MISC \N \N \N
+50657 BudgerigarGenomeProject KNOWN 0 Budgerigar Genome Project MISC \N \N Melopsittacus undulatus sequenced by Washington University School of Medicine
50658 ToxoDB 1 KNOWNXREF 1 ToxoDB PRIMARY_DB_SYNONYM \N \N Toxoplasma Genomic Resource Database.
-50659 Orphanet \N XREF 50 Orphanet MISC \N \N Database of rare diseases and orphan drugs
+50659 Orphanet XREF 50 Orphanet MISC \N \N Database of rare diseases and orphan drugs
50660 SO 1 KNOWNXREF 0 Sequence Ontology MISC \N \N Sequence Ontology
50661 BRAD_GENE 1 XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
50662 BRAD_TRANSCRIPT 1 XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
-50663 Quick_Go \N KNOWN 1 GOA MISC \N \N Resource to show GOA records for Uniprot Accessions
-50664 Quick_Go_Evidence \N KNOWN 1 Quick Go MISC \N \N Resource to show GOA view of original annotation sources
+50663 Quick_Go KNOWN 1 GOA MISC \N \N Resource to show GOA records for Uniprot Accessions
+50664 Quick_Go_Evidence KNOWN 1 Quick Go MISC \N \N Resource to show GOA view of original annotation sources
50665 Painted_Turtle_Consortium 3.0.1 KNOWN 5 International Painted Turtle Genome Sequencing Consortium MISC \N \N http://www.ncbi.nlm.nih.gov/genome/assembly/326468/
50666 IGDBCAS-v1.4_GENE 1.4 KNOWN 1 IGDBCAS v1.4 Gene MISC \N \N \N
50667 IGDBCAS-v1.4_TRANSCRIPT 1.4 KNOWN 1 IGDBCAS v1.4 Transcript MISC \N \N \N
@@ -484,41 +484,41 @@
50671 ITAG_TRANSCRIPT ITAG_pre2.3 KNOWNXREF 1 ITAG pre2.3 Transcript MISC \N \N \N
50672 IRGSPv1_GENE 1 KNOWNXREF 1 IRGSP v1 Gene MISC \N \N \N
50673 IRGSPv1_TRANSCRIPT 1 KNOWNXREF 1 IRGSP v1 Transcript MISC \N \N \N
-50674 Ens_Lc_gene \N XREF 5 Ensembl Coelacanth Gene MISC \N \N \N
-50675 Ens_Lc_transcript \N XREF 170 Ensembl Coelacanth Transcript MISC \N \N \N
-50676 Ens_Lc_translation \N XREF 5 Ensembl Coelacanth Translation MISC \N \N \N
-50677 RGSC \N KNOWNXREF 0 Rat Genome Sequencing Consortium MISC \N \N Rat Genome Sequencing Consortium
-50678 BROAD_coelacanth_transcriptome \N XREF 0 BROAD Institute coelacanth transcriptome MISC \N \N \N
-50679 Ens_Ac_translation \N XREF 40 Ensembl Anole Lizard Translation MISC \N \N \N
-50680 Ens_Ac_gene \N XREF 40 Ensembl Anole Lizard Gene MISC \N \N \N
-50681 Ens_Ac_transcript \N XREF 40 Ensembl Anole Lizard Transcript MISC \N \N \N
+50674 Ens_Lc_gene XREF 5 Ensembl Coelacanth Gene MISC \N \N \N
+50675 Ens_Lc_transcript XREF 170 Ensembl Coelacanth Transcript MISC \N \N \N
+50676 Ens_Lc_translation XREF 5 Ensembl Coelacanth Translation MISC \N \N \N
+50677 RGSC KNOWNXREF 0 Rat Genome Sequencing Consortium MISC \N \N Rat Genome Sequencing Consortium
+50678 BROAD_coelacanth_transcript XREF 0 BROAD Institute coelacanth transcriptome MISC \N \N \N
+50679 Ens_Ac_translation XREF 40 Ensembl Anole Lizard Translation MISC \N \N \N
+50680 Ens_Ac_gene XREF 40 Ensembl Anole Lizard Gene MISC \N \N \N
+50681 Ens_Ac_transcript XREF 40 Ensembl Anole Lizard Transcript MISC \N \N \N
50682 BGI_Gene 1 XREF 50 BGI_2005_indica_Gene MISC \N \N BGI gene identifier
50683 GeneIndex 1 XREF 50 GeneIndex MISC \N \N \N
50684 EO 1 XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms. More information in there: http://www.gramene.org/plant_ontology/ontology_browse.html#eo
-50685 Ens_Rn_transcript \N XREF 5 Ensembl Rat Transcript MISC \N \N \N
-50686 Ens_Rn_translation \N XREF 5 Ensembl Rat Translation MISC \N \N \N
-50687 Uppsala University \N KNOWN 5 Uppsala University MISC \N \N \N
+50685 Ens_Rn_transcript XREF 5 Ensembl Rat Transcript MISC \N \N \N
+50686 Ens_Rn_translation XREF 5 Ensembl Rat Translation MISC \N \N \N
+50687 Uppsala University KNOWN 5 Uppsala University MISC \N \N \N
50688 GenBank 1 XREF 1 GenBank MISC \N \N GenBank identifier
50689 MaizeGDB_GenBank 1 XREF 1 MaizeGDB_GenBank MISC \N \N GenBank identifiers for Maize Genome DB entries.
-50690 RefSeq_gene_name \N KNOWN 200 RefSeq gene name MISC \N \N This is read out of the *.gff files provided to us by the NCBI when we do a RefSeq import or a CCDS comparison. It has the key "gene_id" and is found at the start of the 9th field.
+50690 RefSeq_gene_name KNOWN 200 RefSeq gene name MISC \N \N This is read out of the *.gff files provided to us by the NCBI when we do a RefSeq import or a CCDS comparison. It has the key "gene_id" and is found at the start of the 9th field.
50691 SGN 1 KNOWNXREF 1 Sol Genomics Network MISC \N \N \N
-50692 GRC_alignment_import \N XREF 0 GRC alignment import MISC \N \N Imported alignments from the Genome Reference Consortium.
-50693 BROAD_monodelphis_transcriptome \N XREF 0 Broad Institute transcriptome data for monodelphis MISC \N \N \N
-50694 SIB_mondelphis_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for monodelphis MISC \N \N \N
-50695 SIB_platypus_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for platypus MISC \N \N \N
-50696 SIB_orangutan_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for orangutan MISC \N \N \N
+50692 GRC_alignment_import XREF 0 GRC alignment import MISC \N \N Imported alignments from the Genome Reference Consortium.
+50693 BROAD_monodelphis_transcrip XREF 0 Broad Institute transcriptome data for monodelphis MISC \N \N \N
+50694 SIB_mondelphis_transcriptom XREF 0 Swiss Institute of Bioinformatics transcriptome data for monodelphis MISC \N \N \N
+50695 SIB_platypus_transcriptome XREF 0 Swiss Institute of Bioinformatics transcriptome data for platypus MISC \N \N \N
+50696 SIB_orangutan_transcriptome XREF 0 Swiss Institute of Bioinformatics transcriptome data for orangutan MISC \N \N \N
50697 NCBI_TAXONOMY 1 KNOWNXREF 1 NCBI species MISC \N \N Organism listed in NCBI
50698 PHI 1 KNOWNXREF 1 PHI-base accession MISC \N \N Parasite-host interaction identifiers from PHI-base
50700 AnoXcel 2 KNOWN 50 AnoXcel MISC \N \N VectorBase xref.
50701 PGSC_GENE 1 XREF 1 PGSC MISC \N \N Potato Genome Sequencing Consortium database
50702 PHYTOZOME_GMAX_GENE 1.1 XREF 1 Phytozome MISC \N \N Phytozome Gmax
-50703 Uniprot_gn_trans_name \N KNOWNXREF 5 UniProt transcript name MISC \N \N transcript name projected from UniProt gene name
-50705 Uniprot_gn_gene_name \N KNOWNXREF 5 UniProt gene name MISC \N \N gene name from UniProt
-50707 Ensembl_Bam2Genes_intron \N PRED 5 Intron identified by Ensembl RNASeq pipeline MISC \N \N Ensembl_Bam2Genes_intron are the introns indentified at the bam2genes stage in the Ensembl RNAseq pipeline. They are stored as Clusters in the dna_align_feature table.
+50703 Uniprot_gn_trans_name KNOWNXREF 5 UniProt transcript name MISC \N \N transcript name projected from UniProt gene name
+50705 Uniprot_gn_gene_name KNOWNXREF 5 UniProt gene name MISC \N \N gene name from UniProt
+50707 Ensembl_Bam2Genes_intron PRED 5 Intron identified by Ensembl RNASeq pipeline MISC \N \N Ensembl_Bam2Genes_intron are the introns indentified at the bam2genes stage in the Ensembl RNAseq pipeline. They are stored as Clusters in the dna_align_feature table.
50708 GMGC_GENE 1 KNOWNXREF 1 GMGC PRIMARY_DB_SYNONYM \N \N Global Musa Genomics Consortium gene cross-references
-50709 tamu_vibs \N KNOWN 0 TAMU VIBS MISC \N \N The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences.
+50709 tamu_vibs KNOWN 0 TAMU VIBS MISC \N \N The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences.
50710 INSDC 0 KNOWNXREF 5 International Nucleotide Sequence Database Collaboration MISC INSDC \N This external_db_id was initially made for use in the seq_region_synonym table. For species such as human, cow, dog we store chromosome names (1-22, X,Y) in the name column of the seq_region table. The INSDC accession is stored as a synonym.
-50711 ISGC \N KNOWNXREF 0 International Sheep Genome Consortium MISC \N \N International Sheep Genome Consortium
+50711 ISGC KNOWNXREF 0 International Sheep Genome Consortium MISC \N \N International Sheep Genome Consortium
50712 PO_to_transcript 1 KNOWNXREF 1 PO MISC \N \N Plants Ontology terms attached to transcripts
50713 TAIR_SYMBOL 10 KNOWN 60 TAIR Gene Name PRIMARY_DB_SYNONYM \N \N TAIR gene names
50714 GO_to_transcript 1 KNOWNXREF 1 GO MISC \N \N GO Terms attached to transcripts
@@ -528,27 +528,27 @@
50718 ENA_GENE 1 KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source gene model when importing from ENA.
50719 ENA_TRANSCRIPT 1 KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source transcript model when importing from ENA.
50720 LGBPratt_EST_Cluster 1 KNOWNXREF 1 LGBPratt_EST_Cluster MISC \N \N \N
-50721 BaylorCollege \N KNOWN 5 Baylor College of Medicine, Texas Medical Center MISC \N \N \N
+50721 BaylorCollege KNOWN 5 Baylor College of Medicine, Texas Medical Center MISC \N \N \N
50722 Rhea 1 KNOWNXREF 1 Rhea MISC \N \N Cross-references to Rhea attached to translation objects
-50723 Ens_Bt_translation \N XREF 5 Ensembl Cow Translation MISC \N \N \N
+50723 Ens_Bt_translation XREF 5 Ensembl Cow Translation MISC \N \N \N
50724 RegulonDB_GENE 1 KNOWNXREF 1 RegulonDB MISC \N \N cross-references to RegulonDb attached to gene objects
50725 RegulonDB_OPERON 1 KNOWNXREF 1 RegulonDB MISC \N \N cross-references to RegulonDb attached to operon objects
50726 ENA_FEATURE_GENE 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the gene has been inferred, when loading a genome from ENA records.
50727 ENA_FEATURE_TRANSCRIPT 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the transcript has been inferred, when loading a genome from ENA records.
50728 ENA_FEATURE_PROTEIN 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the translation has been inferred, when loading a genome from ENA records.
-50729 RefSeq_import \N KNOWN 240 RefSeq_import MISC \N \N \N
-50730 AGP \N KNOWN 5 Anolis Genome Project MISC \N \N \N
-50731 Turkey Genome Consortium \N KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
-50732 Yutaka_Satou_Kyoto_University \N KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
-50733 Chicken_Genome_Consortium \N KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
+50729 RefSeq_import KNOWN 240 RefSeq_import MISC \N \N \N
+50730 AGP KNOWN 5 Anolis Genome Project MISC \N \N \N
+50731 Turkey Genome Consortium KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
+50732 Yutaka_Satou_Kyoto_Universi KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
+50733 Chicken_Genome_Consortium KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
50734 TAIR_TRANSLATION 1 XREF 1 TAIR Translation identifiers MISC \N \N TAIR identifiers to link to Ensembl Translation identifiers. The main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translations.
50735 AGI_GENE 1 XREF 1 AGI Gene MISC \N \N annotation provided by Arizona Genome Institute
50736 AGI_TRANSCRIPT 1 XREF 1 AGI Transcript MISC \N \N annotation provided by Arizona Genome Institute
-50737 CGNC \N KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
+50737 CGNC KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
50738 MetaCyc 1 KNOWNXREF 1 MetaCyc MISC \N \N MetaCyc database of metabolic pathways
50739 PHIP 1 KNOWNXREF 1 PHI-base phenotype ontology MISC \N \N PHI-base phenotype ontology for genes proven to affect the outcome of pathogen-host interactions
50740 PHIE 1 KNOWNXREF 1 PHI-base condition ontology MISC \N \N PHI-base experimental evidence ontology for genes proven to affect the outcome of pathogen-host interactions
-50741 dbSNP \N XREF 0 dbSNP MISC \N \N dbSNP variant corresponding to Vega 1kG LOF Variant.
-50742 PubMedCentral \N KNOWN 5 PubMedCentral LIT \N \N PMC identifier for use with PubMedCentral (http://www.ncbi.nlm.nih.gov/pmc and http://europepmc.org/)
+50741 dbSNP XREF 0 dbSNP MISC \N \N dbSNP variant corresponding to Vega 1kG LOF Variant.
+50742 PubMedCentral KNOWN 5 PubMedCentral LIT \N \N PMC identifier for use with PubMedCentral (http://www.ncbi.nlm.nih.gov/pmc and http://europepmc.org/)
50743 PFAM 27 XREF 0 PFAM MISC \N \N Pfam release 27, from Vega
-50744 EntrezGene_trans_name \N KNOWNXREF 250 EntrezGene transcript name MISC \N \N transcript name projected from EntrezGene gene name
+50744 EntrezGene_trans_name KNOWNXREF 250 EntrezGene transcript name MISC \N \N transcript name projected from EntrezGene gene name
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 6839dceaea3e8292ab50f438bbd074065b5429ee..34314266193b5e5b3be9998762cec2ddc516c8c4 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -134,3 +134,4 @@
134 \N patch patch_97_98_a.sql|schema_version
135 \N patch patch_98_99_a.sql|schema_version
136 \N patch patch_99_100_a.sql|schema_version
+137 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index 424e1180b6bc877ce22d2b2ce26153bcedb1e995..8866da31b74bf161e881417902a3fe4ea3205ee4 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=137 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=138 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
index 51aab7d2e5b0494b457c8fdc1222929eeb21d0be..f05436619d99feec471cc21e63340cd49983887f 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:27 2019
+-- Created on Fri Nov 1 15:18:46 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt b/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt
index 4e0f02238490a68bc753f440fc22941d2242dfcd..ee531e4b474725eaef4726cee62b046b04207eb8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt
@@ -108,4 +108,4 @@
4000 MEDLINE 1 KNOWN 5 MEDLINE LIT \N \N \N
4100 UniGene 1 KNOWN 5 UniGene MISC \N \N \N
4200 RFAM 1 XREF 5 RFAM MISC \N \N \N
-11000 UCSC \N KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
+11000 UCSC KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 443716fad1b5630617c71d993d4b6586137901f1..b538bbe41f8e77402329fcd15c313ef08dfaaffa 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -113,3 +113,4 @@
180 \N patch patch_97_98_a.sql|schema_version
188 \N patch patch_98_99_a.sql|schema_version
189 \N patch patch_99_100_a.sql|schema_version
+190 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 2129ad037ad54dcbc5082ebc6b5a74137879d960..60863488cb37a5d686d506684c5bb29f7f5ad6ff 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=8415 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=394 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM AUTO_INCREMENT=3278361 DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM AUTO_INCREMENT=4828765 DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=162071 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM AUTO_INCREMENT=103 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=190 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=191 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM AUTO_INCREMENT=12 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=1000011 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=965915 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=21765 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=21757 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
index 5ab49ab63c146d9ab8e151d248f7585c768c42f9..505f48fc76b861e2f8391ee3bc6fadf02286e363 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:32 2019
+-- Created on Fri Nov 1 15:19:08 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 01e4f6e43cb2ce9fe88772656382c9fb2a2e5609..bae2072de4f0626e292d46c4537f7dde2c4e28c2 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -113,3 +113,4 @@
162 \N patch patch_97_98_a.sql|schema_version
163 \N patch patch_98_99_a.sql|schema_version
164 \N patch patch_99_100_a.sql|schema_version
+165 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index cdf189845fde23057962ac704229066a998fafc8..06e83c39a10d9d3000c9b3e7662fa074d8d2b359 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=6903 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=165 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=166 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=6889 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
index e5129bc69fee045c623bd3e082f6dcaf03cbd5d7..8b678770af45baf7dc98502974368cfa0d50cc2a 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:37 2019
+-- Created on Fri Nov 1 15:19:31 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/external_db.txt b/modules/t/test-genome-DBs/homo_sapiens/patch/external_db.txt
index 197580f14341585f5f0ca95d872522d5d36b74f4..25d3497a098ed400b8a877907e3c143a1c0a1c6b 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/external_db.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/external_db.txt
@@ -1,310 +1,310 @@
-210 Anopheles_symbol \N KNOWN 50 Anopheles symbol MISC \N \N \N
-211 VB_Community_Symbol \N KNOWN 50 VB Community Symbol MISC \N \N \N
+210 Anopheles_symbol KNOWN 50 Anopheles symbol MISC \N \N \N
+211 VB_Community_Symbol KNOWN 50 VB Community Symbol MISC \N \N \N
212 VB_External_Description 1 PRED 50 VB External Description MISC \N \N \N
213 VB_RNA_Description 1 PRED 50 VB RNA Description MISC \N \N \N
-230 Ribosomal_Protein_Gene_Database Dec.2010 XREF 50 Ribosomal Protein Gene DB MISC \N \N \N
+230 Ribosomal_Protein_Gene_Data Dec.2010 XREF 50 Ribosomal Protein Gene DB MISC \N \N \N
250 ImmunoDB 1 KNOWN 50 ImmunoDB MISC \N \N \N
-300 BRIGGSAE_HYBRID \N KNOWNXREF 5 Briggsae Hybrid MISC \N \N \N
-400 Celera_Gene \N PRED 5 Celera gene MISC \N \N \N
-410 Celera_Pep \N PRED 5 Celera peptide MISC \N \N \N
-420 Celera_Trans \N PRED 5 Celera transcript MISC \N \N \N
-600 DROS_ORTH \N ORTH 5 DROS ORTH MISC \N \N \N
-700 EMBL \N KNOWNXREF 5 European Nucleotide Archive MISC \N \N \N
-701 EMBL_predicted \N PRED 119 Predicted European Nucleotide Archive MISC \N \N \N
-800 flybase_gene_id \N KNOWNXREF 5 Flybase Gene MISC \N \N \N
-801 flybase_translation_id \N KNOWNXREF 5 Flybase translation ID MISC \N \N \N
-802 flybase_gff \N KNOWNXREF 5 Flybase GFF MISC \N \N \N
-803 flybase_polypeptide_id \N KNOWNXREF 5 Flybase Polypeptide ID MISC \N \N \N
-804 flybase_annotation_id \N KNOWNXREF 5 Flybase Annotation ID MISC \N \N \N
-805 flybase_symbol \N KNOWNXREF 50 Flybase Symbol MISC \N \N \N
-806 flybase_synonym \N KNOWNXREF 5 Flybase Synonym MISC \N \N \N
-807 flybase_name \N KNOWNXREF 5 Flybase Name MISC \N \N \N
-808 flybase_transcript_id \N KNOWNXREF 299 Flybase transcript ID MISC \N \N \N
-810 gadfly_gene_cgid \N XREF 10 Gadfly gene CGID MISC \N \N \N
-811 gadfly_transcript_cgid \N XREF 10 Gadfly transcript CGID MISC \N \N \N
-812 gadfly_translation_cgid \N XREF 10 Gadfly translation CGID MISC \N \N \N
-821 FlyBaseName_gene \N KNOWN 5 FlyBase gene name MISC \N \N \N
-824 FlyBaseName_translation \N KNOWN 5 FlyBase translation name MISC \N \N \N
-825 FlyBaseName_transcript \N XREF 50 FlyBase transcript name MISC \N \N \N
-826 FlyBaseCGID_gene \N XREF 5 FlyBase gene CGID MISC \N \N \N
-827 FlyBaseCGID_transcript \N XREF 50 FlyBase transcript CGID MISC \N \N \N
-828 FlyBaseCGID_translation \N XREF 50 FlyBase translation CGID MISC \N \N \N
-829 BioGRID \N KNOWNXREF 5 BioGRID Interaction data, The General Repository for Interaction Datasets MISC \N \N \N
-830 FlyExpress \N KNOWNXREF 5 FlyExpress, expression patterns of developmentally relevant genes in Drosophila embryogenesis MISC \N \N \N
-831 GenomeRNAi \N KNOWNXREF 5 GenomeRNAi, a database for cell-based RNAi phenotypes MISC \N \N \N
-832 InteractiveFly \N KNOWNXREF 5 The Interactive Fly MISC \N \N \N
-833 MitoDrome \N KNOWNXREF 5 Nuclear genes encoding proteins targeted to the mitochondrion MISC \N \N \N
-880 BDGP_insitu_expr \N KNOWNXREF 5 Berkeley Drosophila Genome Project in situ Gene Expression Database (embryogenesis) MISC \N \N \N
-882 FlyGrid \N KNOWNXREF 5 FlyGRID Interaction Data, The General Repository for Interaction Datasets MISC \N \N \N
-883 FlyReactome \N KNOWNXREF 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC \N \N \N
-890 DEDb \N KNOWNXREF 5 Drosophila melanogaster Exon Database MISC \N \N \N
-900 GKB \N XREF 5 GKB MISC \N \N \N
-1000 GO GOA Human (version 123), released on 26 June, 2013 and assembled using the publicly released data available in the source databases on 22 June, 2013. XREF 5 GO MISC \N \N \N
-1001 GO_REF \N KNOWN 5 GO Reference Collection LIT \N \N \N
-1100 HGNC \N KNOWNXREF 100 HGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
-1200 Interpro \N XREF 5 InterPro MISC \N \N \N
-1300 EntrezGene \N KNOWNXREF 250 EntrezGene MISC \N \N \N
-1400 MGI \N KNOWNXREF 270 MGI Symbol MISC \N \N \N
-1500 MIM \N KNOWNXREF 5 MIM MISC \N \N \N
-1510 MIM_GENE \N KNOWNXREF 5 MIM gene MISC \N \N \N
-1520 MIM_MORBID \N KNOWNXREF 150 MIM disease MISC \N \N \N
-1600 PDB \N KNOWNXREF 5 PDB MISC \N \N \N
-1700 protein_id \N KNOWNXREF 5 INSDC protein ID MISC \N \N \N
-1701 protein_id_predicted \N PRED 4 Predicted INSDC Protein ID MISC \N \N \N
-1800 RefSeq_dna \N KNOWN 200 RefSeq DNA MISC \N \N \N
-1801 RefSeq_mRNA NCBI Reference Sequence (RefSeq) Database Release 60, July 19, 2013 KNOWN 200 RefSeq mRNA MISC \N \N \N
-1803 RefSeq_ncRNA NCBI Reference Sequence (RefSeq) Database Release 58, March 11, 2013 KNOWN 200 RefSeq ncRNA MISC \N \N \N
-1805 RefSeq_dna_predicted \N PRED 199 RefSeq DNA predicted MISC \N \N \N
-1806 RefSeq_mRNA_predicted NCBI Reference Sequence (RefSeq) Database Release 58, March 11, 2013 PRED 199 RefSeq mRNA predicted MISC \N \N \N
-1808 RefSeq_ncRNA_predicted NCBI Reference Sequence (RefSeq) Database Release 58, March 11, 2013 PRED 199 RefSeq ncRNA predicted MISC \N \N \N
-1810 RefSeq_peptide NCBI Reference Sequence (RefSeq) Database Release 60, July 19, 2013 KNOWN 210 RefSeq peptide MISC \N \N \N
-1815 RefSeq_peptide_predicted NCBI Reference Sequence (RefSeq) Database Release 58, March 11, 2013 PRED 197 RefSeq peptide predicted MISC \N \N \N
-1820 RefSeq_rna \N KNOWN 230 RefSeq RNA MISC \N \N \N
-1825 RefSeq_rna_predicted \N PRED 195 RefSeq RNA predicted MISC \N \N \N
-1830 RefSeq_genomic \N KNOWN 193 RefSeq Genomic MISC \N \N \N
-1900 Sanger_Hver1_2_1 \N XREF 5 Sanger Hver 121 MISC \N \N \N
-1901 Sanger_Hver1_3_1 \N XREF 5 Sanger Hver 131 MISC \N \N \N
-1902 SNGR_Hver \N XREF 5 Sanger Hver MISC \N \N \N
-1910 Sanger_Mver1_1_1 \N XREF 5 Sanger Hver 111 MISC \N \N \N
-2000 Uniprot/SPTREMBL UniProtKB/TrEMBL Release 2013_07 of 26-Jun-2013 KNOWN 119 UniProtKB/TrEMBL MISC \N \N \N
-2001 Uniprot/SPTREMBL_predicted \N PRED 117 Predicted UniProtKB/TrEMBL MISC \N \N \N
-2010 prediction_SPTREMBL \N XREF 10 Prediction UniProtKB/TrEMBL MISC \N \N \N
-2100 Superfamily \N KNOWNXREF 5 Superfamily MISC \N \N \N
-2200 Uniprot/SWISSPROT UniProtKB/Swiss-Prot Release 2013_07 of 26-Jun-2013 KNOWN 220 UniProtKB/Swiss-Prot MISC \N \N \N
-2201 Uniprot/SWISSPROT_predicted \N PRED 15 Predicted UniProtKB/Swiss-Prot MISC \N \N \N
-2202 Uniprot/Varsplic \N KNOWN 15 UniProtKB/SpliceVariant MISC \N \N \N
-2250 UniProtKB_all \N XREF 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC \N \N \N
-2300 Vega_gene \N KNOWNXREF 5 Vega gene MISC \N \N \N
-2305 Vega_gene_like \N XREF 5 Vega gene like MISC \N \N \N
-2310 Vega_transcript \N KNOWNXREF 160 Vega transcript MISC \N \N \N
-2315 Vega_transcript_like \N XREF 5 Vega transcript like MISC \N \N \N
-2320 Vega_translation \N KNOWNXREF 5 Vega translation MISC \N \N \N
-2400 wormbase_gene \N KNOWN 5 WormBase Gene MISC \N \N \N
-2410 wormbase_transcript \N KNOWN 5 WormBase Transcript MISC \N \N \N
-2420 wormpep_id \N KNOWN 5 Wormpep ID MISC \N \N \N
-2430 wormbase_pseudogene \N PSEUDO 5 WormBase Pseudogene MISC \N \N \N
-2440 wormbase_locus \N KNOWN 5 WormBase Locus MISC \N \N \N
-2510 ZFIN_ID \N KNOWNXREF 260 ZFIN PRIMARY_DB_SYNONYM \N \N \N
-2530 ZFIN_xpat \N KNOWNXREF 4 ZFIN expression patterns MISC \N \N \N
-2600 GeneDB \N KNOWN 5 GeneDB MISC \N \N \N
-2601 cint_jgi_v1 \N KNOWN 10 JGI Gene ID (JGI 1.0) MISC \N \N \N
-2602 cint_jgi_v2 \N KNOWN 5 JGI Gene ID (JGI 2.0) MISC \N \N \N
-2610 cint_aniseed_v1 \N KNOWN 5 ANISEED (JGI 1.0) MISC \N \N \N
-2611 cint_aniseed_v2 \N KNOWN 5 ANISEED (JGI 2.0) MISC \N \N \N
-2700 Ens_Hs_gene \N XREF 5 Ensembl Human Gene MISC \N \N \N
-2710 Ens_Hs_transcript \N XREF 170 Ensembl Human Transcript MISC \N \N \N
-2720 Ens_Hs_translation \N XREF 5 Ensembl Human Translation MISC \N \N \N
-2800 RGD \N KNOWNXREF 50 RGD Symbol MISC \N \N \N
-2900 Genoscope_pred_gene \N XREF 38 Genoscope pred gene MISC \N \N \N
-2910 Genoscope_pred_transcript \N XREF 39 Genoscope pred transcript MISC \N \N \N
-2920 Genoscope_annotated_gene \N KNOWN 40 Genoscope annotated gene MISC \N \N \N
-2930 Genoscope_pred_translation \N XREF 40 Genoscope pred translation MISC \N \N \N
-2940 Genoscope_ann_transcript \N KNOWN 40 Genoscope annotated transcript MISC \N \N \N
-2950 Genoscope_ann_translation \N KNOWN 40 Genoscope annotated translation MISC \N \N \N
-3300 miRBase \N KNOWNXREF 180 miRBase MISC \N \N \N
-3310 miRBase_predicted \N XREF 1 miRBase predicted MISC \N \N \N
-3400 SGD \N KNOWN 50 SGD MISC \N \N \N
-3500 IPI \N KNOWN 5 IPI MISC \N \N \N
-3800 CCDS \N KNOWN 240 CCDS MISC \N \N \N
-3900 PUBMED \N KNOWN 5 Sequence Publications LIT \N \N \N
-4000 MEDLINE \N KNOWN 5 MEDLINE LIT \N \N \N
-4100 UniGene 25 Apr 2013 \\t, UniGene Build #236 Homo sapiens KNOWN 5 UniGene MISC \N \N \N
-4200 RFAM \N XREF 190 RFAM MISC \N \N \N
-4400 Xenopus_Jamboree \N KNOWN 1 Jamboree MISC \N \N \N
-4500 Tiffin \N XREF 1 Tiffin DNA motifs MISC \N \N \N
-4600 OTTG \N XREF 1 Havana gene ALT_GENE \N \N \N
-4610 OTTT \N XREF 1 Havana transcript ALT_TRANS \N \N \N
-4620 OTTP \N XREF 1 Havana translation MISC \N \N \N
-4650 shares_CDS_with \N XREF 1 transcript having same CDS ALT_TRANS \N \N \N
-4670 shares_CDS_with_OTTT \N XREF 1 Havana transcript having same CDS ALT_TRANS \N \N \N
-4680 shares_CDS_and_UTR_with_OTTT \N XREF 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS \N \N \N
-4690 ENSG \N XREF 1 Ensembl gene ALT_GENE \N \N \N
-4700 Medaka \N XREF 1 Medaka Genome Project MISC \N \N \N
-4800 ENST \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
-4810 ENST_ident \N XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
-4820 ENST_CDS \N XREF 1 Ensembl transcript sharing CDS with Havana ALT_TRANS \N \N \N
-4900 TCAG \N KNOWN 75 TCAG Chr 7 Annotation MISC \N \N \N
-5000 Ens_Mm_gene \N XREF 40 Ensembl Mouse Gene MISC \N \N \N
-5010 Ens_Mm_transcript \N XREF 40 Ensembl Mouse Transcript MISC \N \N \N
-5020 Ens_Mm_translation \N XREF 40 Ensembl Mouse Translation MISC \N \N \N
-5100 IMGT_HLA \N KNOWN 7 IMGT/HLA MISC \N \N \N
-5200 Oxford_FGU_Md_gene \N PRED 1 Oxford Ponting Group Monodelphis predictions gene id MISC \N \N \N
-5300 Oxford_FGU_Md_tscript \N PRED 1 Oxford Ponting Group Monodelphis predictions transcript id MISC \N \N Updated from alt_gene to misc due to user query
-5400 Oxford_FGU_Oa_gene \N PRED 1 Oxford Ponting Group Platypus predictions gene id MISC \N \N Updated from alt_gene to misc due to user query
-5500 Oxford_FGU_Oa_tscript \N PRED 1 Oxford Ponting Group Platypus predictions transcript id MISC \N \N \N
-5700 Ens_Cf_gene \N XREF 5 Ensembl Dog Gene MISC \N \N \N
-5710 Ens_Cf_transcript \N XREF 5 Ensembl Dog Transcript MISC \N \N \N
-5720 Ens_Cf_translation \N XREF 5 Ensembl Dog Translation MISC \N \N \N
-5800 Ens_Dr_gene \N XREF 5 Ensembl Zebrafish Gene MISC \N \N \N
-5810 Ens_Dr_transcript \N XREF 5 Ensembl Zebrafish Transcript MISC \N \N \N
-5820 Ens_Dr_translation \N XREF 5 Ensembl Zebrafish Translation MISC \N \N \N
-5900 Ens_Md_gene \N XREF 5 Ensembl Monodelphis Gene MISC \N \N \N
-5901 Ens_Md_transcript \N XREF 5 Ensembl Monodelphis Transcript MISC \N \N \N
-6100 Havana_gene \N XREF 100 Havana gene ID MISC \N \N \N
-6200 Ens_Rn_gene \N XREF 5 Ensembl Rat Gene MISC \N \N \N
-6300 Ens_Ol_gene \N XREF 5 Ensembl Medaka Gene MISC \N \N \N
-6400 Ens_Gg_gene \N XREF 40 Ensembl Chicken Gene MISC \N \N \N
-6410 Ens_Gg_transcript \N XREF 40 Ensembl Chicken Transcript MISC \N \N \N
-6420 Ens_Gg_translation \N XREF 40 Ensembl Chicken Translation MISC \N \N \N
-6500 IMCB_Tr_gene \N XREF 40 IMCB Fugu Gene MISC \N \N \N
-6600 Ens_Ag_gene \N XREF 5 Ensembl Mosquito Gene MISC \N \N \N
-6630 Ens_Am_gene \N XREF 5 Ensembl Bee Gene MISC \N \N \N
-6660 Ens_Ce_gene \N XREF 5 Ensembl Worm Gene MISC \N \N \N
-6690 Ens_Dm_gene \N XREF 5 Ensembl FruitFly Gene MISC \N \N \N
-6720 Ens_Fr_gene \N XREF 5 Ensembl Fugu Gene MISC \N \N \N
-6750 Ens_Pt_gene \N XREF 5 Ensembl Chimpanzee Gene MISC \N \N \N
-6810 Ens_Tn_gene \N XREF 5 Ensembl PufferFish Gene MISC \N \N \N
-6820 Ens_Tr_transcript \N XREF 40 Ensembl Fugu Transcript MISC \N \N \N
-6900 Ens_Ga_translation \N XREF 5 Ensembl Stickleback Translation MISC \N \N \N
-7120 Ens_Aa_translation \N XREF 40 Ensembl Aedes Translation MISC \N \N \N
-7159 AedesGenBank \N PRED 30 Aedes GenBank MISC \N \N \N
-7160 Aedes_ManualAnnotation \N PRED 30 Aedes ManualAnnotation MISC \N \N \N
-7170 Ixodes_ManualAnnotation \N PRED 30 Ixodes ManualAnnotation MISC \N \N \N
+300 BRIGGSAE_HYBRID KNOWNXREF 5 Briggsae Hybrid MISC \N \N \N
+400 Celera_Gene PRED 5 Celera gene MISC \N \N \N
+410 Celera_Pep PRED 5 Celera peptide MISC \N \N \N
+420 Celera_Trans PRED 5 Celera transcript MISC \N \N \N
+600 DROS_ORTH ORTH 5 DROS ORTH MISC \N \N \N
+700 EMBL KNOWNXREF 5 European Nucleotide Archive MISC \N \N \N
+701 EMBL_predicted PRED 119 Predicted European Nucleotide Archive MISC \N \N \N
+800 flybase_gene_id KNOWNXREF 5 Flybase Gene MISC \N \N \N
+801 flybase_translation_id KNOWNXREF 5 Flybase translation ID MISC \N \N \N
+802 flybase_gff KNOWNXREF 5 Flybase GFF MISC \N \N \N
+803 flybase_polypeptide_id KNOWNXREF 5 Flybase Polypeptide ID MISC \N \N \N
+804 flybase_annotation_id KNOWNXREF 5 Flybase Annotation ID MISC \N \N \N
+805 flybase_symbol KNOWNXREF 50 Flybase Symbol MISC \N \N \N
+806 flybase_synonym KNOWNXREF 5 Flybase Synonym MISC \N \N \N
+807 flybase_name KNOWNXREF 5 Flybase Name MISC \N \N \N
+808 flybase_transcript_id KNOWNXREF 299 Flybase transcript ID MISC \N \N \N
+810 gadfly_gene_cgid XREF 10 Gadfly gene CGID MISC \N \N \N
+811 gadfly_transcript_cgid XREF 10 Gadfly transcript CGID MISC \N \N \N
+812 gadfly_translation_cgid XREF 10 Gadfly translation CGID MISC \N \N \N
+821 FlyBaseName_gene KNOWN 5 FlyBase gene name MISC \N \N \N
+824 FlyBaseName_translation KNOWN 5 FlyBase translation name MISC \N \N \N
+825 FlyBaseName_transcript XREF 50 FlyBase transcript name MISC \N \N \N
+826 FlyBaseCGID_gene XREF 5 FlyBase gene CGID MISC \N \N \N
+827 FlyBaseCGID_transcript XREF 50 FlyBase transcript CGID MISC \N \N \N
+828 FlyBaseCGID_translation XREF 50 FlyBase translation CGID MISC \N \N \N
+829 BioGRID KNOWNXREF 5 BioGRID Interaction data, The General Repository for Interaction Datasets MISC \N \N \N
+830 FlyExpress KNOWNXREF 5 FlyExpress, expression patterns of developmentally relevant genes in Drosophila embryogenesis MISC \N \N \N
+831 GenomeRNAi KNOWNXREF 5 GenomeRNAi, a database for cell-based RNAi phenotypes MISC \N \N \N
+832 InteractiveFly KNOWNXREF 5 The Interactive Fly MISC \N \N \N
+833 MitoDrome KNOWNXREF 5 Nuclear genes encoding proteins targeted to the mitochondrion MISC \N \N \N
+880 BDGP_insitu_expr KNOWNXREF 5 Berkeley Drosophila Genome Project in situ Gene Expression Database (embryogenesis) MISC \N \N \N
+882 FlyGrid KNOWNXREF 5 FlyGRID Interaction Data, The General Repository for Interaction Datasets MISC \N \N \N
+883 FlyReactome KNOWNXREF 5 FlyReactome, a Curated Knowledgebase of Drosophila Melanogaster Pathways MISC \N \N \N
+890 DEDb KNOWNXREF 5 Drosophila melanogaster Exon Database MISC \N \N \N
+900 GKB XREF 5 GKB MISC \N \N \N
+1000 GO GOA Human (version 123), released on 26 XREF 5 GO MISC \N \N \N
+1001 GO_REF KNOWN 5 GO Reference Collection LIT \N \N \N
+1100 HGNC KNOWNXREF 100 HGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
+1200 Interpro XREF 5 InterPro MISC \N \N \N
+1300 EntrezGene KNOWNXREF 250 EntrezGene MISC \N \N \N
+1400 MGI KNOWNXREF 270 MGI Symbol MISC \N \N \N
+1500 MIM KNOWNXREF 5 MIM MISC \N \N \N
+1510 MIM_GENE KNOWNXREF 5 MIM gene MISC \N \N \N
+1520 MIM_MORBID KNOWNXREF 150 MIM disease MISC \N \N \N
+1600 PDB KNOWNXREF 5 PDB MISC \N \N \N
+1700 protein_id KNOWNXREF 5 INSDC protein ID MISC \N \N \N
+1701 protein_id_predicted PRED 4 Predicted INSDC Protein ID MISC \N \N \N
+1800 RefSeq_dna KNOWN 200 RefSeq DNA MISC \N \N \N
+1801 RefSeq_mRNA NCBI Reference Sequence (RefSeq) Databas KNOWN 200 RefSeq mRNA MISC \N \N \N
+1803 RefSeq_ncRNA NCBI Reference Sequence (RefSeq) Databas KNOWN 200 RefSeq ncRNA MISC \N \N \N
+1805 RefSeq_dna_predicted PRED 199 RefSeq DNA predicted MISC \N \N \N
+1806 RefSeq_mRNA_predicted NCBI Reference Sequence (RefSeq) Databas PRED 199 RefSeq mRNA predicted MISC \N \N \N
+1808 RefSeq_ncRNA_predicted NCBI Reference Sequence (RefSeq) Databas PRED 199 RefSeq ncRNA predicted MISC \N \N \N
+1810 RefSeq_peptide NCBI Reference Sequence (RefSeq) Databas KNOWN 210 RefSeq peptide MISC \N \N \N
+1815 RefSeq_peptide_predicted NCBI Reference Sequence (RefSeq) Databas PRED 197 RefSeq peptide predicted MISC \N \N \N
+1820 RefSeq_rna KNOWN 230 RefSeq RNA MISC \N \N \N
+1825 RefSeq_rna_predicted PRED 195 RefSeq RNA predicted MISC \N \N \N
+1830 RefSeq_genomic KNOWN 193 RefSeq Genomic MISC \N \N \N
+1900 Sanger_Hver1_2_1 XREF 5 Sanger Hver 121 MISC \N \N \N
+1901 Sanger_Hver1_3_1 XREF 5 Sanger Hver 131 MISC \N \N \N
+1902 SNGR_Hver XREF 5 Sanger Hver MISC \N \N \N
+1910 Sanger_Mver1_1_1 XREF 5 Sanger Hver 111 MISC \N \N \N
+2000 Uniprot/SPTREMBL UniProtKB/TrEMBL Release 2013_07 of 26-J KNOWN 119 UniProtKB/TrEMBL MISC \N \N \N
+2001 Uniprot/SPTREMBL_predicted PRED 117 Predicted UniProtKB/TrEMBL MISC \N \N \N
+2010 prediction_SPTREMBL XREF 10 Prediction UniProtKB/TrEMBL MISC \N \N \N
+2100 Superfamily KNOWNXREF 5 Superfamily MISC \N \N \N
+2200 Uniprot/SWISSPROT UniProtKB/Swiss-Prot Release 2013_07 of KNOWN 220 UniProtKB/Swiss-Prot MISC \N \N \N
+2201 Uniprot/SWISSPROT_predicted PRED 15 Predicted UniProtKB/Swiss-Prot MISC \N \N \N
+2202 Uniprot/Varsplic KNOWN 15 UniProtKB/SpliceVariant MISC \N \N \N
+2250 UniProtKB_all XREF 40 UniProtKB generic accession number (TrEMBL or SwissProt not differentiated) MISC \N \N \N
+2300 Vega_gene KNOWNXREF 5 Vega gene MISC \N \N \N
+2305 Vega_gene_like XREF 5 Vega gene like MISC \N \N \N
+2310 Vega_transcript KNOWNXREF 160 Vega transcript MISC \N \N \N
+2315 Vega_transcript_like XREF 5 Vega transcript like MISC \N \N \N
+2320 Vega_translation KNOWNXREF 5 Vega translation MISC \N \N \N
+2400 wormbase_gene KNOWN 5 WormBase Gene MISC \N \N \N
+2410 wormbase_transcript KNOWN 5 WormBase Transcript MISC \N \N \N
+2420 wormpep_id KNOWN 5 Wormpep ID MISC \N \N \N
+2430 wormbase_pseudogene PSEUDO 5 WormBase Pseudogene MISC \N \N \N
+2440 wormbase_locus KNOWN 5 WormBase Locus MISC \N \N \N
+2510 ZFIN_ID KNOWNXREF 260 ZFIN PRIMARY_DB_SYNONYM \N \N \N
+2530 ZFIN_xpat KNOWNXREF 4 ZFIN expression patterns MISC \N \N \N
+2600 GeneDB KNOWN 5 GeneDB MISC \N \N \N
+2601 cint_jgi_v1 KNOWN 10 JGI Gene ID (JGI 1.0) MISC \N \N \N
+2602 cint_jgi_v2 KNOWN 5 JGI Gene ID (JGI 2.0) MISC \N \N \N
+2610 cint_aniseed_v1 KNOWN 5 ANISEED (JGI 1.0) MISC \N \N \N
+2611 cint_aniseed_v2 KNOWN 5 ANISEED (JGI 2.0) MISC \N \N \N
+2700 Ens_Hs_gene XREF 5 Ensembl Human Gene MISC \N \N \N
+2710 Ens_Hs_transcript XREF 170 Ensembl Human Transcript MISC \N \N \N
+2720 Ens_Hs_translation XREF 5 Ensembl Human Translation MISC \N \N \N
+2800 RGD KNOWNXREF 50 RGD Symbol MISC \N \N \N
+2900 Genoscope_pred_gene XREF 38 Genoscope pred gene MISC \N \N \N
+2910 Genoscope_pred_transcript XREF 39 Genoscope pred transcript MISC \N \N \N
+2920 Genoscope_annotated_gene KNOWN 40 Genoscope annotated gene MISC \N \N \N
+2930 Genoscope_pred_translation XREF 40 Genoscope pred translation MISC \N \N \N
+2940 Genoscope_ann_transcript KNOWN 40 Genoscope annotated transcript MISC \N \N \N
+2950 Genoscope_ann_translation KNOWN 40 Genoscope annotated translation MISC \N \N \N
+3300 miRBase KNOWNXREF 180 miRBase MISC \N \N \N
+3310 miRBase_predicted XREF 1 miRBase predicted MISC \N \N \N
+3400 SGD KNOWN 50 SGD MISC \N \N \N
+3500 IPI KNOWN 5 IPI MISC \N \N \N
+3800 CCDS KNOWN 240 CCDS MISC \N \N \N
+3900 PUBMED KNOWN 5 Sequence Publications LIT \N \N \N
+4000 MEDLINE KNOWN 5 MEDLINE LIT \N \N \N
+4100 UniGene 25 Apr 2013 \t, UniGene Build #236 Homo KNOWN 5 UniGene MISC \N \N \N
+4200 RFAM XREF 190 RFAM MISC \N \N \N
+4400 Xenopus_Jamboree KNOWN 1 Jamboree MISC \N \N \N
+4500 Tiffin XREF 1 Tiffin DNA motifs MISC \N \N \N
+4600 OTTG XREF 1 Havana gene ALT_GENE \N \N \N
+4610 OTTT XREF 1 Havana transcript ALT_TRANS \N \N \N
+4620 OTTP XREF 1 Havana translation MISC \N \N \N
+4650 shares_CDS_with XREF 1 transcript having same CDS ALT_TRANS \N \N \N
+4670 shares_CDS_with_OTTT XREF 1 Havana transcript having same CDS ALT_TRANS \N \N \N
+4680 shares_CDS_and_UTR_with_OTT XREF 1 Transcript having exact match between ENSEMBL and HAVANA ALT_TRANS \N \N \N
+4690 ENSG XREF 1 Ensembl gene ALT_GENE \N \N \N
+4700 Medaka XREF 1 Medaka Genome Project MISC \N \N \N
+4800 ENST XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
+4810 ENST_ident XREF 1 Ensembl transcript having exact match with Havana ALT_TRANS \N \N \N
+4820 ENST_CDS XREF 1 Ensembl transcript sharing CDS with Havana ALT_TRANS \N \N \N
+4900 TCAG KNOWN 75 TCAG Chr 7 Annotation MISC \N \N \N
+5000 Ens_Mm_gene XREF 40 Ensembl Mouse Gene MISC \N \N \N
+5010 Ens_Mm_transcript XREF 40 Ensembl Mouse Transcript MISC \N \N \N
+5020 Ens_Mm_translation XREF 40 Ensembl Mouse Translation MISC \N \N \N
+5100 IMGT_HLA KNOWN 7 IMGT/HLA MISC \N \N \N
+5200 Oxford_FGU_Md_gene PRED 1 Oxford Ponting Group Monodelphis predictions gene id MISC \N \N \N
+5300 Oxford_FGU_Md_tscript PRED 1 Oxford Ponting Group Monodelphis predictions transcript id MISC \N \N Updated from alt_gene to misc due to user query
+5400 Oxford_FGU_Oa_gene PRED 1 Oxford Ponting Group Platypus predictions gene id MISC \N \N Updated from alt_gene to misc due to user query
+5500 Oxford_FGU_Oa_tscript PRED 1 Oxford Ponting Group Platypus predictions transcript id MISC \N \N \N
+5700 Ens_Cf_gene XREF 5 Ensembl Dog Gene MISC \N \N \N
+5710 Ens_Cf_transcript XREF 5 Ensembl Dog Transcript MISC \N \N \N
+5720 Ens_Cf_translation XREF 5 Ensembl Dog Translation MISC \N \N \N
+5800 Ens_Dr_gene XREF 5 Ensembl Zebrafish Gene MISC \N \N \N
+5810 Ens_Dr_transcript XREF 5 Ensembl Zebrafish Transcript MISC \N \N \N
+5820 Ens_Dr_translation XREF 5 Ensembl Zebrafish Translation MISC \N \N \N
+5900 Ens_Md_gene XREF 5 Ensembl Monodelphis Gene MISC \N \N \N
+5901 Ens_Md_transcript XREF 5 Ensembl Monodelphis Transcript MISC \N \N \N
+6100 Havana_gene XREF 100 Havana gene ID MISC \N \N \N
+6200 Ens_Rn_gene XREF 5 Ensembl Rat Gene MISC \N \N \N
+6300 Ens_Ol_gene XREF 5 Ensembl Medaka Gene MISC \N \N \N
+6400 Ens_Gg_gene XREF 40 Ensembl Chicken Gene MISC \N \N \N
+6410 Ens_Gg_transcript XREF 40 Ensembl Chicken Transcript MISC \N \N \N
+6420 Ens_Gg_translation XREF 40 Ensembl Chicken Translation MISC \N \N \N
+6500 IMCB_Tr_gene XREF 40 IMCB Fugu Gene MISC \N \N \N
+6600 Ens_Ag_gene XREF 5 Ensembl Mosquito Gene MISC \N \N \N
+6630 Ens_Am_gene XREF 5 Ensembl Bee Gene MISC \N \N \N
+6660 Ens_Ce_gene XREF 5 Ensembl Worm Gene MISC \N \N \N
+6690 Ens_Dm_gene XREF 5 Ensembl FruitFly Gene MISC \N \N \N
+6720 Ens_Fr_gene XREF 5 Ensembl Fugu Gene MISC \N \N \N
+6750 Ens_Pt_gene XREF 5 Ensembl Chimpanzee Gene MISC \N \N \N
+6810 Ens_Tn_gene XREF 5 Ensembl PufferFish Gene MISC \N \N \N
+6820 Ens_Tr_transcript XREF 40 Ensembl Fugu Transcript MISC \N \N \N
+6900 Ens_Ga_translation XREF 5 Ensembl Stickleback Translation MISC \N \N \N
+7120 Ens_Aa_translation XREF 40 Ensembl Aedes Translation MISC \N \N \N
+7159 AedesGenBank PRED 30 Aedes GenBank MISC \N \N \N
+7160 Aedes_ManualAnnotation PRED 30 Aedes ManualAnnotation MISC \N \N \N
+7170 Ixodes_ManualAnnotation PRED 30 Ixodes ManualAnnotation MISC \N \N \N
7180 VB_Community_Annotation 1 KNOWN 50 VB Community Annotation MISC \N \N \N
-7200 IMGT/LIGM_DB \N XREF 10 IMGT/LIGM-DB MISC \N \N \N
-7201 IMGT/GENE_DB \N KNOWN 40 IMGT/GENE-DB MISC \N \N \N
-7300 Ens_Mg_transcript \N XREF 40 Ensembl Turkey Transcript MISC \N \N \N
-7400 Ens_Tg_transcript \N XREF 40 Ensembl Zebrafinch Transcript MISC \N \N \N
-7500 Ens_St_transcript \N XREF 40 Ensembl Squirrel Transcript MISC \N \N \N
-7600 Ens_Fc_transcript \N XREF 40 Ensembl Cat Transcript MISC \N \N \N
-7620 Ens_Fc_translation \N XREF 40 Ensembl Cat Translation MISC \N \N \N
-8000 Vega_mouse_transcript \N XREF 5 Vega mouse transcript MISC \N \N \N
-8100 Platypus_olfactory_receptor \N XREF 40 Platypus olfactory receptor gene MISC \N \N \N
-8200 PRF \N XREF 5 PRF MISC \N \N \N
-8300 PIR \N XREF 5 PIR MISC \N \N \N
-8400 TetNig_cdna \N XREF 40 Genoscope tetraodon cDNA MISC \N \N \N
-8500 GasAcu_cdna \N XREF 40 Stickleback cDNA MISC \N \N \N
-8600 OrnAna_454_cdna \N XREF 40 Platypus 454 cDNA MISC \N \N \N
-8700 TakRub_cdna \N XREF 40 Takifugu cDNA MISC \N \N \N
-8800 CioInt_est \N XREF 40 Ciona intestinalis EST MISC \N \N \N
-8900 CioInt_cdna \N XREF 40 Ciona intestinalis cDNA MISC \N \N \N
-9000 CaeEle_est \N XREF 40 C Elegans EST MISC \N \N \N
-9100 XenTro_Gurdon_EST \N XREF 40 Xenopus Gurdon EST Clusters MISC \N \N \N
-9110 XenTro_cdna \N XREF 40 Xenopus Tropicalis cDNA MISC \N \N \N
-9120 XenLae_cdna \N XREF 40 Xenopus Laevis cDNA MISC \N \N \N
-9200 TakRub_est \N XREF 40 Takifugu EST MISC \N \N \N
-9210 TakRub_annotation \N XREF 40 Takifugu gene annotation MISC \N \N \N
-9220 TakRub_seleno_annotation \N XREF 40 Takifugu selenoprotein annotation MISC \N \N \N
-9400 TetNig_mouse_econtig \N XREF 40 Genoscope mouse exofish econtig MISC \N \N \N
-9410 TetNig_fugu_econtig \N XREF 40 Genoscope fugu exofish econtig MISC \N \N \N
-9420 TetNig_human_econtig \N XREF 40 Genoscope human exofish econtig MISC \N \N \N
-9430 TetNig_human_IPI_econtig \N XREF 40 Genoscope human IPI exofish econtig MISC \N \N \N
-9440 TetNig_mouse_IPI_econtig \N XREF 40 Genoscope mouse IPI exofish econtig MISC \N \N \N
-9450 TetNig_rat_econtig \N XREF 40 Genoscope rat exofish econtig MISC \N \N \N
-9460 TetNig_chick_econtig \N XREF 40 Genoscope chicken exofish econtig MISC \N \N \N
-9500 OryLat_est \N XREF 40 Medaka EST MISC \N \N \N
-9600 Trace_archive \N XREF 40 Trace Archive id MISC \N \N \N
-9700 CioSav_est \N XREF 40 Ciona savignyi EST MISC \N \N \N
-9800 kyotograil_2004 \N PRED 30 Ciona intestinalis Kyotograil 2004 predictions MISC \N \N \N
-9900 kyotograil_2005 \N PRED 30 Ciona intestinalis Kyotograil 2005 predictions MISC \N \N \N
-9950 Kyoto_University \N KNOWN 5 Kyoto University MISC \N \N \N
-10000 wormbase_id \N XREF 30 Generic exdb for WormBase id of any type for feature table MISC \N \N \N
-10100 EPD \N KNOWNXREF 5 Eukaryotic Promoter Database (Bucher) MISC \N \N \N
-10200 GPCR \N KNOWNXREF 5 The G protein-coupled receptor database MISC \N \N \N
-10300 MEROPS \N KNOWNXREF 5 MEROPS - the Peptidase Database MISC \N \N \N
-10500 TransFac \N KNOWNXREF 5 TransFac, database of transcription factors and their binding sites MISC \N \N \N
-10600 modCB_gene \N KNOWNXREF 5 Caenorhabditis briggsae, InParanoid model organism database MISC \N \N \N
-10700 modCE_gene \N KNOWNXREF 5 Caenorhabditis elegans, InParanoid model organism database MISC \N \N \N
-10800 modDD_gene \N KNOWNXREF 5 Dictyostelium discoideum, InParanoid model organism database MISC \N \N \N
-10900 GI \N XREF 5 GenInfo Identifier, a sequence identification number for a nucleotide sequence MISC \N \N \N
-11000 UCSC \N KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
-11100 Culex_ncRNA \N XREF 70 Culex ncRNAs MISC \N \N \N
-12300 HGNC_curated_gene \N KNOWNXREF 5 HGNC (curated) MISC \N \N \N
-12305 HGNC_automatic_gene \N KNOWNXREF 5 HGNC (automatic) MISC \N \N \N
-12310 Clone_based_vega_gene \N KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
-12315 Clone_based_ensembl_gene \N XREF 5 Clone-based (Ensembl) MISC \N \N \N
-12400 HGNC_curated_transcript \N KNOWNXREF 300 HGNC (curated) MISC \N \N \N
-12405 HGNC_automatic_transcript \N KNOWNXREF 290 HGNC (automatic) MISC \N \N \N
-12410 Clone_based_vega_transcript \N KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
-12415 Clone_based_ensembl_transcript \N XREF 5 Clone-based (Ensembl) MISC \N \N \N
-12500 DBASS3 \N XREF 50 DataBase of Aberrant 3' Splice Sites MISC \N \N \N
-12505 DBASS5 \N XREF 50 DataBase of Aberrant 5' Splice Sites MISC \N \N \N
-12510 HPA \N XREF 50 Human Protein Atlas MISC \N \N \N
-12550 MGI_curated_gene \N KNOWNXREF 5 MGI (curated) MISC \N \N \N
-12555 MGI_automatic_gene \N KNOWNXREF 5 MGI (automatic) MISC \N \N \N
-12560 MGI_curated_transcript \N KNOWNXREF 140 MGI (curated) MISC \N \N \N
-12565 MGI_automatic_transcript \N KNOWNXREF 279 MGI (automatic) MISC \N \N \N
-12600 WikiGene \N XREF 50 WikiGene MISC \N \N \N
-12601 Tgut_symbol \N KNOWNXREF 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM \N \N \N
-12610 Fantom \N XREF 50 Fantom MISC \N \N \N
-12620 Duck_consortium \N XREF 0 Duck consortium MISC \N \N \N
-12630 BGI_duck_transcriptome \N XREF 0 Beijing Genomics Institute (BGI) duck transcriptome MISC \N \N \N
-12700 goslim_goa \N XREF 5 GOSlim GOA MISC \N \N \N
-12701 goslim_generic \N XREF 5 GOSlim Generic MISC \N \N \N
-12710 WTSI_gorilla_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC \N \N \N
-12720 WTSI_zebrafish_transcriptome \N XREF 0 Wellcome Trust Sanger Institute (WTSI) zebrafish transcriptome MISC \N \N \N
-20005 UniParc \N KNOWNXREF 0 UniParc PRIMARY_DB_SYNONYM \N \N \N
-20008 BRENDA \N KNOWNXREF 0 BRENDA PRIMARY_DB_SYNONYM \N \N \N
-20009 BioCyc \N KNOWNXREF 0 BioCyc PRIMARY_DB_SYNONYM \N \N \N
-20010 BuruList \N KNOWNXREF 0 BuruList PRIMARY_DB_SYNONYM \N \N \N
-20013 EchoBASE \N KNOWNXREF 0 EchoBASE PRIMARY_DB_SYNONYM \N \N \N
-20014 EcoGene \N KNOWNXREF 0 EcoGene PRIMARY_DB_SYNONYM \N \N \N
-20017 GeneDB_Spombe \N KNOWNXREF 0 GeneDB_Spombe PRIMARY_DB_SYNONYM \N \N \N
-20025 Leproma \N KNOWNXREF 0 Leproma PRIMARY_DB_SYNONYM \N \N \N
-20031 2DBase_Ecoli \N KNOWNXREF 0 2DBase-Ecoli PRIMARY_DB_SYNONYM \N \N \N
-20038 SagaList \N KNOWNXREF 0 SagaList PRIMARY_DB_SYNONYM \N \N \N
-20040 SubtiList \N KNOWNXREF 0 SubtiList PRIMARY_DB_SYNONYM \N \N \N
-20042 TIGR \N KNOWNXREF 0 TIGR PRIMARY_DB_SYNONYM \N \N \N
-20043 TubercuList \N KNOWNXREF 0 TubercuList PRIMARY_DB_SYNONYM \N \N \N
-20046 ArrayExpress \N XREF 0 ArrayExpress MISC \N \N \N
-20050 GermOnline \N KNOWNXREF 0 GermOnline PRIMARY_DB_SYNONYM \N \N \N
-20059 DIP \N KNOWNXREF 0 DIP PRIMARY_DB_SYNONYM \N \N \N
-20061 DisProt \N KNOWNXREF 0 DisProt PRIMARY_DB_SYNONYM \N \N \N
-20062 DrugBank \N KNOWNXREF 0 DrugBank PRIMARY_DB_SYNONYM \N \N \N
-20065 GlycoSuiteDB \N KNOWNXREF 0 GlycoSuiteDB PRIMARY_DB_SYNONYM \N \N \N
-20066 HAMAP \N KNOWNXREF 0 HAMAP PRIMARY_DB_SYNONYM \N \N \N
-20067 HOGENOM \N KNOWNXREF 0 HOGENOM PRIMARY_DB_SYNONYM \N \N \N
-20071 HSSP \N KNOWNXREF 0 HSSP PRIMARY_DB_SYNONYM \N \N \N
-20072 IntAct \N KNOWNXREF 0 IntAct PRIMARY_DB_SYNONYM \N \N \N
-20074 KEGG \N KNOWNXREF 0 KEGG PRIMARY_DB_SYNONYM \N \N \N
-20078 PDBsum \N KNOWNXREF 0 PDBsum PRIMARY_DB_SYNONYM \N \N \N
-20082 PeroxiBase \N KNOWNXREF 0 PeroxiBase PRIMARY_DB_SYNONYM \N \N \N
-20083 PhosSite \N KNOWNXREF 0 PhosSite PRIMARY_DB_SYNONYM \N \N \N
-20084 PptaseDB \N KNOWNXREF 0 PptaseDB PRIMARY_DB_SYNONYM \N \N \N
-20085 REBASE \N KNOWNXREF 0 REBASE PRIMARY_DB_SYNONYM \N \N \N
-20088 Reactome \N KNOWNXREF 0 Reactome PRIMARY_DB_SYNONYM \N \N \N
-20090 SWISS_2DPAGE \N KNOWNXREF 0 SWISS-2DPAGE PRIMARY_DB_SYNONYM \N \N \N
-20097 RegulonDb_Transcript \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
-20099 RegulonDb_Gene \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
-20101 IntEnz \N KNOWNXREF 0 EnzymeCommission PRIMARY_DB_SYNONYM \N \N \N
-20102 ArrayExpressExperiment \N XREF 0 ArrayExpressExperiment MISC \N \N \N
-20200 EMBLBANK_GENE \N KNOWNXREF 117 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
-20201 GeneDB_SPombe_transcript \N KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
-20202 EBACTERIA_GENE \N KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
-20203 EBACTERIA_TRANSCRIPT \N KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
-20204 EPROTIST_GENE \N KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
-20205 EPROTIST_TRANSCRIPT \N KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
-20207 EFUNGI_GENE \N KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
-20208 EFUNGI_TRANSCRIPT \N KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
-20209 EMBLBANK_TRANSCRIPT \N KNOWNXREF 115 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
-20210 GeneDB_SPombe_gene \N KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
-20214 phatr_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20215 phatr_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20216 phatr_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20217 phatr_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20218 phatr_jgi_v2_bd_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20219 phatr_jgi_v2_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20220 thaps_jgi_v2_bd \N KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20221 thaps_jgi_v2 \N KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20222 thaps_jgi_v2_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20223 thaps_jgi_v2_bd_gene \N KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20225 thaps_jgi_v2_bd_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
-20226 thaps_jgi_v2_transcript \N KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
-20227 Diatom_EST_Cluster \N XREF 0 ENS EST Cluster (Diatom ESTDB) MISC \N \N \N
-20228 CADRE_Afum_A1163 \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20301 RNAMMER \N KNOWNXREF 0 RNAmmer MISC \N \N \N
-20302 TRNASCAN_SE \N KNOWNXREF 0 tRNAScan-SE MISC \N \N \N
-20303 dictyBase \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
-20304 dictyBase_gene \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
-20305 dictyBase_transcript \N KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
-20306 ASPGD \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
-20307 ASPGD_GENE \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
-20308 ASPGD_TRANSCRIPT \N KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
-20309 CADRE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20310 CADRE_GENE \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20311 CADRE_TRANSCRIPT \N KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
-20312 SGD_GENE \N KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
-20313 SGD_TRANSCRIPT \N KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
+7200 IMGT/LIGM_DB XREF 10 IMGT/LIGM-DB MISC \N \N \N
+7201 IMGT/GENE_DB KNOWN 40 IMGT/GENE-DB MISC \N \N \N
+7300 Ens_Mg_transcript XREF 40 Ensembl Turkey Transcript MISC \N \N \N
+7400 Ens_Tg_transcript XREF 40 Ensembl Zebrafinch Transcript MISC \N \N \N
+7500 Ens_St_transcript XREF 40 Ensembl Squirrel Transcript MISC \N \N \N
+7600 Ens_Fc_transcript XREF 40 Ensembl Cat Transcript MISC \N \N \N
+7620 Ens_Fc_translation XREF 40 Ensembl Cat Translation MISC \N \N \N
+8000 Vega_mouse_transcript XREF 5 Vega mouse transcript MISC \N \N \N
+8100 Platypus_olfactory_receptor XREF 40 Platypus olfactory receptor gene MISC \N \N \N
+8200 PRF XREF 5 PRF MISC \N \N \N
+8300 PIR XREF 5 PIR MISC \N \N \N
+8400 TetNig_cdna XREF 40 Genoscope tetraodon cDNA MISC \N \N \N
+8500 GasAcu_cdna XREF 40 Stickleback cDNA MISC \N \N \N
+8600 OrnAna_454_cdna XREF 40 Platypus 454 cDNA MISC \N \N \N
+8700 TakRub_cdna XREF 40 Takifugu cDNA MISC \N \N \N
+8800 CioInt_est XREF 40 Ciona intestinalis EST MISC \N \N \N
+8900 CioInt_cdna XREF 40 Ciona intestinalis cDNA MISC \N \N \N
+9000 CaeEle_est XREF 40 C Elegans EST MISC \N \N \N
+9100 XenTro_Gurdon_EST XREF 40 Xenopus Gurdon EST Clusters MISC \N \N \N
+9110 XenTro_cdna XREF 40 Xenopus Tropicalis cDNA MISC \N \N \N
+9120 XenLae_cdna XREF 40 Xenopus Laevis cDNA MISC \N \N \N
+9200 TakRub_est XREF 40 Takifugu EST MISC \N \N \N
+9210 TakRub_annotation XREF 40 Takifugu gene annotation MISC \N \N \N
+9220 TakRub_seleno_annotation XREF 40 Takifugu selenoprotein annotation MISC \N \N \N
+9400 TetNig_mouse_econtig XREF 40 Genoscope mouse exofish econtig MISC \N \N \N
+9410 TetNig_fugu_econtig XREF 40 Genoscope fugu exofish econtig MISC \N \N \N
+9420 TetNig_human_econtig XREF 40 Genoscope human exofish econtig MISC \N \N \N
+9430 TetNig_human_IPI_econtig XREF 40 Genoscope human IPI exofish econtig MISC \N \N \N
+9440 TetNig_mouse_IPI_econtig XREF 40 Genoscope mouse IPI exofish econtig MISC \N \N \N
+9450 TetNig_rat_econtig XREF 40 Genoscope rat exofish econtig MISC \N \N \N
+9460 TetNig_chick_econtig XREF 40 Genoscope chicken exofish econtig MISC \N \N \N
+9500 OryLat_est XREF 40 Medaka EST MISC \N \N \N
+9600 Trace_archive XREF 40 Trace Archive id MISC \N \N \N
+9700 CioSav_est XREF 40 Ciona savignyi EST MISC \N \N \N
+9800 kyotograil_2004 PRED 30 Ciona intestinalis Kyotograil 2004 predictions MISC \N \N \N
+9900 kyotograil_2005 PRED 30 Ciona intestinalis Kyotograil 2005 predictions MISC \N \N \N
+9950 Kyoto_University KNOWN 5 Kyoto University MISC \N \N \N
+10000 wormbase_id XREF 30 Generic exdb for WormBase id of any type for feature table MISC \N \N \N
+10100 EPD KNOWNXREF 5 Eukaryotic Promoter Database (Bucher) MISC \N \N \N
+10200 GPCR KNOWNXREF 5 The G protein-coupled receptor database MISC \N \N \N
+10300 MEROPS KNOWNXREF 5 MEROPS - the Peptidase Database MISC \N \N \N
+10500 TransFac KNOWNXREF 5 TransFac, database of transcription factors and their binding sites MISC \N \N \N
+10600 modCB_gene KNOWNXREF 5 Caenorhabditis briggsae, InParanoid model organism database MISC \N \N \N
+10700 modCE_gene KNOWNXREF 5 Caenorhabditis elegans, InParanoid model organism database MISC \N \N \N
+10800 modDD_gene KNOWNXREF 5 Dictyostelium discoideum, InParanoid model organism database MISC \N \N \N
+10900 GI XREF 5 GenInfo Identifier, a sequence identification number for a nucleotide sequence MISC \N \N \N
+11000 UCSC KNOWNXREF 100 UCSC Stable ID MISC \N \N \N
+11100 Culex_ncRNA XREF 70 Culex ncRNAs MISC \N \N \N
+12300 HGNC_curated_gene KNOWNXREF 5 HGNC (curated) MISC \N \N \N
+12305 HGNC_automatic_gene KNOWNXREF 5 HGNC (automatic) MISC \N \N \N
+12310 Clone_based_vega_gene KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
+12315 Clone_based_ensembl_gene XREF 5 Clone-based (Ensembl) MISC \N \N \N
+12400 HGNC_curated_transcript KNOWNXREF 300 HGNC (curated) MISC \N \N \N
+12405 HGNC_automatic_transcript KNOWNXREF 290 HGNC (automatic) MISC \N \N \N
+12410 Clone_based_vega_transcript KNOWNXREF 5 Clone-based (Vega) MISC \N \N \N
+12415 Clone_based_ensembl_transcr XREF 5 Clone-based (Ensembl) MISC \N \N \N
+12500 DBASS3 XREF 50 DataBase of Aberrant 3' Splice Sites MISC \N \N \N
+12505 DBASS5 XREF 50 DataBase of Aberrant 5' Splice Sites MISC \N \N \N
+12510 HPA XREF 50 Human Protein Atlas MISC \N \N \N
+12550 MGI_curated_gene KNOWNXREF 5 MGI (curated) MISC \N \N \N
+12555 MGI_automatic_gene KNOWNXREF 5 MGI (automatic) MISC \N \N \N
+12560 MGI_curated_transcript KNOWNXREF 140 MGI (curated) MISC \N \N \N
+12565 MGI_automatic_transcript KNOWNXREF 279 MGI (automatic) MISC \N \N \N
+12600 WikiGene XREF 50 WikiGene MISC \N \N \N
+12601 Tgut_symbol KNOWNXREF 100 Tgut symbol - Prof. David Burt, Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh University, UK PRIMARY_DB_SYNONYM \N \N \N
+12610 Fantom XREF 50 Fantom MISC \N \N \N
+12620 Duck_consortium XREF 0 Duck consortium MISC \N \N \N
+12630 BGI_duck_transcriptome XREF 0 Beijing Genomics Institute (BGI) duck transcriptome MISC \N \N \N
+12700 goslim_goa XREF 5 GOSlim GOA MISC \N \N \N
+12701 goslim_generic XREF 5 GOSlim Generic MISC \N \N \N
+12710 WTSI_gorilla_transcriptome XREF 0 Wellcome Trust Sanger Institute (WTSI) gorilla transcriptome MISC \N \N \N
+12720 WTSI_zebrafish_transcriptom XREF 0 Wellcome Trust Sanger Institute (WTSI) zebrafish transcriptome MISC \N \N \N
+20005 UniParc KNOWNXREF 0 UniParc PRIMARY_DB_SYNONYM \N \N \N
+20008 BRENDA KNOWNXREF 0 BRENDA PRIMARY_DB_SYNONYM \N \N \N
+20009 BioCyc KNOWNXREF 0 BioCyc PRIMARY_DB_SYNONYM \N \N \N
+20010 BuruList KNOWNXREF 0 BuruList PRIMARY_DB_SYNONYM \N \N \N
+20013 EchoBASE KNOWNXREF 0 EchoBASE PRIMARY_DB_SYNONYM \N \N \N
+20014 EcoGene KNOWNXREF 0 EcoGene PRIMARY_DB_SYNONYM \N \N \N
+20017 GeneDB_Spombe KNOWNXREF 0 GeneDB_Spombe PRIMARY_DB_SYNONYM \N \N \N
+20025 Leproma KNOWNXREF 0 Leproma PRIMARY_DB_SYNONYM \N \N \N
+20031 2DBase_Ecoli KNOWNXREF 0 2DBase-Ecoli PRIMARY_DB_SYNONYM \N \N \N
+20038 SagaList KNOWNXREF 0 SagaList PRIMARY_DB_SYNONYM \N \N \N
+20040 SubtiList KNOWNXREF 0 SubtiList PRIMARY_DB_SYNONYM \N \N \N
+20042 TIGR KNOWNXREF 0 TIGR PRIMARY_DB_SYNONYM \N \N \N
+20043 TubercuList KNOWNXREF 0 TubercuList PRIMARY_DB_SYNONYM \N \N \N
+20046 ArrayExpress XREF 0 ArrayExpress MISC \N \N \N
+20050 GermOnline KNOWNXREF 0 GermOnline PRIMARY_DB_SYNONYM \N \N \N
+20059 DIP KNOWNXREF 0 DIP PRIMARY_DB_SYNONYM \N \N \N
+20061 DisProt KNOWNXREF 0 DisProt PRIMARY_DB_SYNONYM \N \N \N
+20062 DrugBank KNOWNXREF 0 DrugBank PRIMARY_DB_SYNONYM \N \N \N
+20065 GlycoSuiteDB KNOWNXREF 0 GlycoSuiteDB PRIMARY_DB_SYNONYM \N \N \N
+20066 HAMAP KNOWNXREF 0 HAMAP PRIMARY_DB_SYNONYM \N \N \N
+20067 HOGENOM KNOWNXREF 0 HOGENOM PRIMARY_DB_SYNONYM \N \N \N
+20071 HSSP KNOWNXREF 0 HSSP PRIMARY_DB_SYNONYM \N \N \N
+20072 IntAct KNOWNXREF 0 IntAct PRIMARY_DB_SYNONYM \N \N \N
+20074 KEGG KNOWNXREF 0 KEGG PRIMARY_DB_SYNONYM \N \N \N
+20078 PDBsum KNOWNXREF 0 PDBsum PRIMARY_DB_SYNONYM \N \N \N
+20082 PeroxiBase KNOWNXREF 0 PeroxiBase PRIMARY_DB_SYNONYM \N \N \N
+20083 PhosSite KNOWNXREF 0 PhosSite PRIMARY_DB_SYNONYM \N \N \N
+20084 PptaseDB KNOWNXREF 0 PptaseDB PRIMARY_DB_SYNONYM \N \N \N
+20085 REBASE KNOWNXREF 0 REBASE PRIMARY_DB_SYNONYM \N \N \N
+20088 Reactome KNOWNXREF 0 Reactome PRIMARY_DB_SYNONYM \N \N \N
+20090 SWISS_2DPAGE KNOWNXREF 0 SWISS-2DPAGE PRIMARY_DB_SYNONYM \N \N \N
+20097 RegulonDb_Transcript KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20099 RegulonDb_Gene KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20101 IntEnz KNOWNXREF 0 EnzymeCommission PRIMARY_DB_SYNONYM \N \N \N
+20102 ArrayExpressExperiment XREF 0 ArrayExpressExperiment MISC \N \N \N
+20200 EMBLBANK_GENE KNOWNXREF 117 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
+20201 GeneDB_SPombe_transcript KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
+20202 EBACTERIA_GENE KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
+20203 EBACTERIA_TRANSCRIPT KNOWNXREF 0 e!Bacteria PRIMARY_DB_SYNONYM \N \N \N
+20204 EPROTIST_GENE KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
+20205 EPROTIST_TRANSCRIPT KNOWNXREF 0 e!Protists PRIMARY_DB_SYNONYM \N \N \N
+20207 EFUNGI_GENE KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
+20208 EFUNGI_TRANSCRIPT KNOWNXREF 0 e!Fungi PRIMARY_DB_SYNONYM \N \N \N
+20209 EMBLBANK_TRANSCRIPT KNOWNXREF 115 European Nucleotide Archive PRIMARY_DB_SYNONYM \N \N \N
+20210 GeneDB_SPombe_gene KNOWNXREF 0 GeneDB_SPombe PRIMARY_DB_SYNONYM \N \N \N
+20214 phatr_jgi_v2_bd KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20215 phatr_jgi_v2 KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20216 phatr_jgi_v2_bd_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20217 phatr_jgi_v2_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20218 phatr_jgi_v2_bd_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20219 phatr_jgi_v2_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20220 thaps_jgi_v2_bd KNOWNXREF 0 JGI ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20221 thaps_jgi_v2 KNOWNXREF 0 JGI ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20222 thaps_jgi_v2_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20223 thaps_jgi_v2_bd_gene KNOWNXREF 0 JGI Gene ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20225 thaps_jgi_v2_bd_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0 unmapped sequence) PRIMARY_DB_SYNONYM \N \N \N
+20226 thaps_jgi_v2_transcript KNOWNXREF 0 JGI transcript ID (JGI 2.0) PRIMARY_DB_SYNONYM \N \N \N
+20227 Diatom_EST_Cluster XREF 0 ENS EST Cluster (Diatom ESTDB) MISC \N \N \N
+20228 CADRE_Afum_A1163 KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20301 RNAMMER KNOWNXREF 0 RNAmmer MISC \N \N \N
+20302 TRNASCAN_SE KNOWNXREF 0 tRNAScan-SE MISC \N \N \N
+20303 dictyBase KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20304 dictyBase_gene KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20305 dictyBase_transcript KNOWNXREF 0 DictyBase PRIMARY_DB_SYNONYM \N \N \N
+20306 ASPGD KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20307 ASPGD_GENE KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20308 ASPGD_TRANSCRIPT KNOWNXREF 0 AspGD PRIMARY_DB_SYNONYM \N \N \N
+20309 CADRE KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20310 CADRE_GENE KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20311 CADRE_TRANSCRIPT KNOWNXREF 0 CADRE PRIMARY_DB_SYNONYM \N \N \N
+20312 SGD_GENE KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
+20313 SGD_TRANSCRIPT KNOWNXREF 0 SGD PRIMARY_DB_SYNONYM \N \N \N
20314 BROAD_PUCCINIA_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20315 BROAD_PUCCINIA_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20316 BROAD_PUCCINIA 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
@@ -315,7 +315,7 @@
20321 physo1_jgi_v1.1_gene 1.1 KNOWNXREF 0 JGI Gene ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
20322 physo1_jgi_v1.1_transcript 1.1 KNOWNXREF 0 JGI transcript ID (JGI 1.1) PRIMARY_DB_SYNONYM \N \N \N
20323 BROAD_P_infestans_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20324 BROAD_P_infestans_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20324 BROAD_P_infestans_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20325 BROAD_P_infestans 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20326 BROAD_M_oryzae_GENE 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20327 BROAD_M_oryzae_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
@@ -330,18 +330,18 @@
20336 SCHISTODB_TRANSCRIPT 1 KNOWNXREF 0 SchistoDB PRIMARY_DB_SYNONYM \N \N \N
20337 BROAD_F_oxysporum 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20338 BROAD_F_oxysporum_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20339 BROAD_F_oxysporum_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20339 BROAD_F_oxysporum_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20340 BROAD_G_zeae 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20341 BROAD_G_zeae_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20342 BROAD_G_zeae_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20343 BROAD_G_moniliformis 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20344 BROAD_G_moniliformis_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20345 BROAD_G_moniliformis_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20345 BROAD_G_moniliformis_TRANSC 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20346 GeneDB_TRANSLATION 1 KNOWNXREF 0 GeneDB Translation ID PRIMARY_DB_SYNONYM \N \N \N
20347 PGD 1 KNOWNXREF 0 Pythium genome database MISC \N \N \N
20348 PGD_GENE 1 KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
20349 PGD_TRANSCRIPT 1 KNOWNXREF 0 Pythium genome database PRIMARY_DB_SYNONYM \N \N \N
-20350 RegulonDb_Operon \N KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
+20350 RegulonDb_Operon KNOWNXREF 0 RegulonDb PRIMARY_DB_SYNONYM \N \N \N
20351 BROAD_N_crassa_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20352 BROAD_N_crassa_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20353 BROAD_N_crassa 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
@@ -350,7 +350,7 @@
20356 BROAD_U_maydis_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20357 BROAD_P_triticina 1 KNOWNXREF 0 Broad Institute MISC \N \N \N
20358 BROAD_P_triticina_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
-20359 BROAD_P_triticina_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
+20359 BROAD_P_triticina_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20360 SpBase 1 KNOWNXREF 0 SpBase MISC \N \N \N
20361 PHIbase 3.2 XREF 50 PHI-base MISC \N \N \N
20362 necha_jgi_v2.0_gene 2 KNOWNXREF 0 Nectria JGI gene PRIMARY_DB_SYNONYM \N \N \N
@@ -367,114 +367,114 @@
20373 BROAD_P_NODORUM_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N \N
20375 PomBase 1 KNOWN 0 PomBase MISC \N \N \N
20376 PomBase_GENE 1 KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
-20377 PomBase_TRANSCRIPT \N KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
+20377 PomBase_TRANSCRIPT KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
20378 PomBase_TRANSLATION 1 KNOWNXREF 0 PomBase PRIMARY_DB_SYNONYM \N \N \N
-20379 SPO \N KNOWNXREF 0 SPO ID MISC \N \N \N
-20380 CBS \N KNOWNXREF 0 CBS Server MISC \N \N \N
-20381 COG \N KNOWNXREF 0 Cluster of Orthologous Groups (NCBI) MISC \N \N \N
-20382 CGD \N KNOWN 0 Candida Genome Database MISC \N \N \N
-20383 ProSite \N XREF 0 ProSite ID MISC \N \N \N
-20385 SMART \N XREF 0 SMART ID MISC \N \N \N
-20386 SPD \N KNOWNXREF 0 SPD ID MISC \N \N \N
-20387 KOG \N KNOWNXREF 0 KOG ID MISC \N \N \N
-20388 PBO \N KNOWNXREF 0 PomBase Ontology ID MISC \N \N \N
-20389 FYPO \N KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
-20390 MOD \N KNOWNXREF 0 PSI-MOD, Post Translational Modification Ontology MISC \N \N \N
+20379 SPO KNOWNXREF 0 SPO ID MISC \N \N \N
+20380 CBS KNOWNXREF 0 CBS Server MISC \N \N \N
+20381 COG KNOWNXREF 0 Cluster of Orthologous Groups (NCBI) MISC \N \N \N
+20382 CGD KNOWN 0 Candida Genome Database MISC \N \N \N
+20383 ProSite XREF 0 ProSite ID MISC \N \N \N
+20385 SMART XREF 0 SMART ID MISC \N \N \N
+20386 SPD KNOWNXREF 0 SPD ID MISC \N \N \N
+20387 KOG KNOWNXREF 0 KOG ID MISC \N \N \N
+20388 PBO KNOWNXREF 0 PomBase Ontology ID MISC \N \N \N
+20389 FYPO KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
+20390 MOD KNOWNXREF 0 PSI-MOD, Post Translational Modification Ontology MISC \N \N \N
20391 AGD_GENE 1 KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
20392 AGD_TRANSCRIPT 1 KNOWNXREF 0 Ashbya Genome Database PRIMARY_DB_SYNONYM \N \N \N
20393 AGD 1 KNOWNXREF 0 Ashbya Genome Database MISC \N \N \N
20394 FYPO_GENE 1 KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
20395 FYPO_TRANSCRIPT 1 KNOWNXREF 0 Fission Yeast Phenotype Ontology MISC \N \N \N
-50000 BGI_EST_Cluster \N XREF 0 EST Cluster (BGI Indica) MISC \N \N \N
-50005 EC_NUMBER \N XREF 0 Enzyme EC Number MISC \N \N \N
-50010 FSTs \N XREF 0 Flanking Sequence Tag (FST) MISC \N \N \N
-50015 gene_name \N KNOWNXREF 0 Gene Name MISC \N \N \N
-50020 Gramene_Pathway \N XREF 0 Gramene Pathway MISC \N \N \N
-50030 Gramene_GenesDB \N KNOWNXREF 100 Gramene Curated Gene MISC \N \N \N
-50035 Gramene_MarkersDB \N XREF 0 Gramene MISC \N \N \N
-50040 Gramene_MarkersDB_mRNA \N XREF 0 GenBank mRNA (Gramene) MISC \N \N \N
-50050 Gramene_MarkersDB_EST \N XREF 0 GenBank EST (Gramene) MISC \N \N \N
-50060 IRGSP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
-50065 KOME \N KNOWNXREF 0 Full Length cDNA (KOME) MISC \N \N \N
-50070 miRNA_Accession \N XREF 0 miRNA miRBase accession MISC \N \N \N
-50080 miRNA_Registry \N XREF 1 miRNA Registry MISC \N \N \N
-50090 NASC_GENE_ID \N XREF 1 NASC Gene ID MISC \N \N \N
-50100 NASC_TRANSCRIPT_ID \N XREF 1 NASC Transcript ID MISC \N \N \N
-50110 PlantGDB_PUT \N XREF 1 PlantGDB Transcript MISC \N \N \N
-50120 RAP_Gene \N XREF 0 IRGSP/RAP Gene MISC \N \N \N
-50130 siRNA_Sunkar \N XREF 0 siRNA ID from Sunkar et. al. 2005 NAR 33(14):4443-54 MISC \N \N \N
-50140 TIGR_LOCUS \N XREF 1 MSU/TIGR Locus MISC \N \N \N
-50150 TIGR_LOCUS_MODEL \N XREF 0 MSU/TIGR Locus (Model) MISC \N \N \N
-50160 TAIR_LOCUS \N XREF 8 TAIR Locus MISC \N \N \N
-50170 TAIR_LOCUS_MODEL \N XREF 8 TAIR Locus (Model) MISC \N \N \N
-50180 TIGR_GeneIndex \N XREF 0 Gene Index MISC \N \N \N
-50185 TO \N XREF 0 Plant Trait Ontology MISC \N \N \N
-50190 PO \N XREF 0 Plant Structure Ontology MISC \N \N \N
-50195 PO_to_gene \N XREF 0 Plant Structure Ontology MISC \N \N \N
-50196 GO_to_gene \N XREF 0 Gene Ontology MISC \N \N \N
-50200 GRO \N XREF 0 Plant Growth Stage MISC \N \N \N
-50510 AFFY_RICE \N XREF 1 Affymx GeneChip Rice ARRAY \N \N \N
-50520 AFFY_ATH1 \N XREF 1 Affymx GeneChip ATH1 ARRAY \N \N \N
-50530 AFFY_Vitis_Vinifera \N XREF 1 Affymx GeneChip Vitis vinifera ARRAY \N \N \N
-50540 AFFY_Poplar \N XREF 1 Affymx GeneChip Poplar ARRAY \N \N \N
-50541 LRG \N KNOWN 10 Locus Reference Genomic MISC \N \N \N
-50542 ENS_LRG_gene \N KNOWN 10 LRG display in Ensembl MISC \N \N \N
-50543 ENS_LRG_transcript \N KNOWN 10 LRG display in Ensembl MISC \N \N \N
-50600 IKMCs_KOs \N XREF 10 International Knockout Mouse Consortium Knockouts MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (ES cells available) MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (Mice available) MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (No products available yet) MISC \N \N 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 \N XREF 10 International Knockout Mouse Consortium Knockouts (Vector available) MISC \N \N 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)
-50605 RFAM_gene_name \N KNOWNXREF 5 RFAM gene name MISC \N \N gene name from RFAM
-50606 miRBase_gene_name \N KNOWNXREF 5 miRBase gene name MISC \N \N gene name from miRBase
-50607 miRBase_trans_name \N KNOWNXREF 5 miRBase transcript name MISC \N \N transcript name from miRBase
-50608 RFAM_trans_name \N KNOWNXREF 5 RFAM transcript name MISC \N \N transcript name from RFAM
-50609 HGNC_trans_name \N KNOWNXREF 5 HGNC transcript name MISC \N \N transcript name from HGNC
-50610 MGI_trans_name \N KNOWNXREF 5 MGI transcript name MISC \N \N transcript name from MGI
-50611 ZFIN_ID_trans_name \N KNOWNXREF 5 ZFIN transcript name MISC \N \N transcript name from ZFIN
-50612 LampreyGenomeProject \N KNOWN 1 Lamprey Genome Project MISC \N \N \N
-50620 Illumina_Bodymap_transcriptome \N XREF 0 Illumina Bodymap transcriptome MISC \N \N \N
-50621 Uniprot_gn \N KNOWN 116 UniProtKB Gene Name MISC \N \N \N
-50622 GGSC \N KNOWNXREF 0 Gibbon Genome Sequencing Consortium MISC \N \N Gibbon Genome Sequencing Consortium
-50623 Broad Institute \N KNOWN 5 Broad Institute of MIT and Harvard MISC \N \N \N
-50624 PFAM \N XREF 0 PFAM MISC \N \N Pfam from Vega
-50625 SGSC \N KNOWN 5 Swine Genome Sequencing Consortium MISC \N \N \N
-50626 RIKEN \N KNOWN 5 Riken Institute MISC \N \N \N
-50627 SHSC \N KNOWNXREF 0 Tasmanian Devil Sequencing Consortium MISC \N \N Tasmanian Devil Genome Sequencing Consortium
+50000 BGI_EST_Cluster XREF 0 EST Cluster (BGI Indica) MISC \N \N \N
+50005 EC_NUMBER XREF 0 Enzyme EC Number MISC \N \N \N
+50010 FSTs XREF 0 Flanking Sequence Tag (FST) MISC \N \N \N
+50015 gene_name KNOWNXREF 0 Gene Name MISC \N \N \N
+50020 Gramene_Pathway XREF 0 Gramene Pathway MISC \N \N \N
+50030 Gramene_GenesDB KNOWNXREF 100 Gramene Curated Gene MISC \N \N \N
+50035 Gramene_MarkersDB XREF 0 Gramene MISC \N \N \N
+50040 Gramene_MarkersDB_mRNA XREF 0 GenBank mRNA (Gramene) MISC \N \N \N
+50050 Gramene_MarkersDB_EST XREF 0 GenBank EST (Gramene) MISC \N \N \N
+50060 IRGSP_Gene XREF 0 IRGSP/RAP Gene MISC \N \N \N
+50065 KOME KNOWNXREF 0 Full Length cDNA (KOME) MISC \N \N \N
+50070 miRNA_Accession XREF 0 miRNA miRBase accession MISC \N \N \N
+50080 miRNA_Registry XREF 1 miRNA Registry MISC \N \N \N
+50090 NASC_GENE_ID XREF 1 NASC Gene ID MISC \N \N \N
+50100 NASC_TRANSCRIPT_ID XREF 1 NASC Transcript ID MISC \N \N \N
+50110 PlantGDB_PUT XREF 1 PlantGDB Transcript MISC \N \N \N
+50120 RAP_Gene XREF 0 IRGSP/RAP Gene MISC \N \N \N
+50130 siRNA_Sunkar XREF 0 siRNA ID from Sunkar et. al. 2005 NAR 33(14):4443-54 MISC \N \N \N
+50140 TIGR_LOCUS XREF 1 MSU/TIGR Locus MISC \N \N \N
+50150 TIGR_LOCUS_MODEL XREF 0 MSU/TIGR Locus (Model) MISC \N \N \N
+50160 TAIR_LOCUS XREF 8 TAIR Locus MISC \N \N \N
+50170 TAIR_LOCUS_MODEL XREF 8 TAIR Locus (Model) MISC \N \N \N
+50180 TIGR_GeneIndex XREF 0 Gene Index MISC \N \N \N
+50185 TO XREF 0 Plant Trait Ontology MISC \N \N \N
+50190 PO XREF 0 Plant Structure Ontology MISC \N \N \N
+50195 PO_to_gene XREF 0 Plant Structure Ontology MISC \N \N \N
+50196 GO_to_gene XREF 0 Gene Ontology MISC \N \N \N
+50200 GRO XREF 0 Plant Growth Stage MISC \N \N \N
+50510 AFFY_RICE XREF 1 Affymx GeneChip Rice ARRAY \N \N \N
+50520 AFFY_ATH1 XREF 1 Affymx GeneChip ATH1 ARRAY \N \N \N
+50530 AFFY_Vitis_Vinifera XREF 1 Affymx GeneChip Vitis vinifera ARRAY \N \N \N
+50540 AFFY_Poplar XREF 1 Affymx GeneChip Poplar ARRAY \N \N \N
+50541 LRG KNOWN 10 Locus Reference Genomic MISC \N \N \N
+50542 ENS_LRG_gene KNOWN 10 LRG display in Ensembl MISC \N \N \N
+50543 ENS_LRG_transcript KNOWN 10 LRG display in Ensembl MISC \N \N \N
+50600 IKMCs_KOs XREF 10 International Knockout Mouse Consortium Knockouts MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (ES cells available) MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (Mice available) MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (No products available yet) MISC \N \N 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 XREF 10 International Knockout Mouse Consortium Knockouts (Vector available) MISC \N \N 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)
+50605 RFAM_gene_name KNOWNXREF 5 RFAM gene name MISC \N \N gene name from RFAM
+50606 miRBase_gene_name KNOWNXREF 5 miRBase gene name MISC \N \N gene name from miRBase
+50607 miRBase_trans_name KNOWNXREF 5 miRBase transcript name MISC \N \N transcript name from miRBase
+50608 RFAM_trans_name KNOWNXREF 5 RFAM transcript name MISC \N \N transcript name from RFAM
+50609 HGNC_trans_name KNOWNXREF 5 HGNC transcript name MISC \N \N transcript name from HGNC
+50610 MGI_trans_name KNOWNXREF 5 MGI transcript name MISC \N \N transcript name from MGI
+50611 ZFIN_ID_trans_name KNOWNXREF 5 ZFIN transcript name MISC \N \N transcript name from ZFIN
+50612 LampreyGenomeProject KNOWN 1 Lamprey Genome Project MISC \N \N \N
+50620 Illumina_Bodymap_transcript XREF 0 Illumina Bodymap transcriptome MISC \N \N \N
+50621 Uniprot_gn KNOWN 116 UniProtKB Gene Name MISC \N \N \N
+50622 GGSC KNOWNXREF 0 Gibbon Genome Sequencing Consortium MISC \N \N Gibbon Genome Sequencing Consortium
+50623 Broad Institute KNOWN 5 Broad Institute of MIT and Harvard MISC \N \N \N
+50624 PFAM XREF 0 PFAM MISC \N \N Pfam from Vega
+50625 SGSC KNOWN 5 Swine Genome Sequencing Consortium MISC \N \N \N
+50626 RIKEN KNOWN 5 Riken Institute MISC \N \N \N
+50627 SHSC KNOWNXREF 0 Tasmanian Devil Sequencing Consortium MISC \N \N Tasmanian Devil Genome Sequencing Consortium
50628 PFAM 22 XREF 0 PFAM MISC \N \N Pfam release 22, from Vega
50629 PFAM 23 XREF 0 PFAM MISC \N \N Pfam release 23, from Vega
50630 PFAM 24 XREF 0 PFAM MISC \N \N Pfam release 24, from Vega
50631 PFAM 25 XREF 0 PFAM MISC \N \N Pfam release 25, from Vega
50632 PFAM 26 XREF 0 PFAM MISC \N \N Pfam release 26, from Vega
-50633 GRC_primary_assembly \N XREF 0 GRC primary assembly MISC \N \N Primary assembly of this species genome from the GRC
-50634 Ens_Ga_gene \N XREF 5 Ensembl Stickleback Gene MISC \N \N \N
-50635 Ens_Ga_transcript \N XREF 170 Ensembl Stickleback Transcript MISC \N \N \N
-50637 CSAC \N KNOWN 5 Chimpanzee Sequencing and Analysis Consortium MISC \N \N \N
+50633 GRC_primary_assembly XREF 0 GRC primary assembly MISC \N \N Primary assembly of this species genome from the GRC
+50634 Ens_Ga_gene XREF 5 Ensembl Stickleback Gene MISC \N \N \N
+50635 Ens_Ga_transcript XREF 170 Ensembl Stickleback Transcript MISC \N \N \N
+50637 CSAC KNOWN 5 Chimpanzee Sequencing and Analysis Consortium MISC \N \N \N
50640 PomBase_Interaction_GENETIC 1 KNOWNXREF 5 PomBase Interaction Genetic MISC \N \N \N
-50641 PomBase_Interaction_PHYSICAL 1 KNOWNXREF 5 PomBase Interaction Physical MISC \N \N \N
+50641 PomBase_Interaction_PHYSICA 1 KNOWNXREF 5 PomBase Interaction Physical MISC \N \N \N
50642 PomBase_Gene_Name 1 KNOWNXREF 5 PomBase Gene Name MISC \N \N \N
50643 PomBase_Systematic_ID 1 KNOWNXREF 5 PomBase Systematic ID MISC \N \N \N
50644 PomBase_Ortholog 1 KNOWNXREF 5 Orthologous Gene MISC \N \N \N
-50645 Ens_Ss_translation \N XREF 5 Ensembl Pig Translation MISC \N \N \N
-50646 Psinensis_sequencing_consortium \N KNOWN 5 Pelodiscus sinensis sequencing consortium MISC \N \N \N
+50645 Ens_Ss_translation XREF 5 Ensembl Pig Translation MISC \N \N \N
+50646 Psinensis_sequencing_consor KNOWN 5 Pelodiscus sinensis sequencing consortium MISC \N \N \N
50647 BROAD_Magnaporthe_DB 1 KNOWNXREF 0 Magnaporthe comparative DB MISC \N \N Broad Institute Magnaporthe comparative Database
50648 BROAD_Magnaporthe_DB_GENE 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
-50649 BROAD_Magnaporthe_DB_TRANSCRIPT 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
-50650 BGI Shenzhen \N KNOWN 5 Beijing Genomics Institute, Shenzhen MISC \N \N \N
-50651 ICGSC \N KNOWN 5 International Cat Genome Sequencing Consortium MISC \N \N \N
+50649 BROAD_Magnaporthe_DB_TRANSC 1 KNOWNXREF 0 Magnaporthe comparative DB PRIMARY_DB_SYNONYM \N \N Broad Institute Magnaporthe comparative Database
+50650 BGI Shenzhen KNOWN 5 Beijing Genomics Institute, Shenzhen MISC \N \N \N
+50651 ICGSC KNOWN 5 International Cat Genome Sequencing Consortium MISC \N \N \N
50652 SGD_TRANSLATION 1 KNOWNXREF 0 SGD MISC \N \N SGD Mapping attached to S.cerevisiae translations objects so we can attach GO dependant annotations at the translation level as well.
-50653 WashingtonUniversity \N KNOWN 5 The Genome Institute, Washington University School of Medicine MISC \N \N \N
+50653 WashingtonUniversity KNOWN 5 The Genome Institute, Washington University School of Medicine MISC \N \N \N
50654 BDGP_cDNA 1 KNOWN 50 Fly cDNA MISC \N \N cDNA from the Berkeley Drosophila Genome Project
50655 BDGP_cDNA_Gold_Collection 1 KNOWN 50 Fly gold cDNA MISC \N \N Gold Collection cDNA from the Berkeley Drosophila Genome Project
-50656 Ens_Tg_translation \N KNOWN 5 Ensembl Zebrafinch Translation MISC \N \N \N
-50657 BudgerigarGenomeProject \N KNOWN 0 Budgerigar Genome Project MISC \N \N Melopsittacus undulatus sequenced by Washington University School of Medicine
+50656 Ens_Tg_translation KNOWN 5 Ensembl Zebrafinch Translation MISC \N \N \N
+50657 BudgerigarGenomeProject KNOWN 0 Budgerigar Genome Project MISC \N \N Melopsittacus undulatus sequenced by Washington University School of Medicine
50658 ToxoDB 1 KNOWNXREF 1 ToxoDB PRIMARY_DB_SYNONYM \N \N Toxoplasma Genomic Resource Database.
50659 Orphanet 1.0.20 [2012-12-14] XREF 50 Orphanet MISC \N \N Database of rare diseases and orphan drugs
50660 SO 1 KNOWNXREF 0 Sequence Ontology MISC \N \N Sequence Ontology
50661 BRAD_GENE 1 XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
50662 BRAD_TRANSCRIPT 1 XREF 5 BrassEnsembl MISC \N \N The Brassica Genome Database
-50663 Quick_Go \N KNOWN 1 GOA MISC \N \N Resource to show GOA records for Uniprot Accessions
-50664 Quick_Go_Evidence \N KNOWN 1 Quick Go MISC \N \N Resource to show GOA view of original annotation sources
+50663 Quick_Go KNOWN 1 GOA MISC \N \N Resource to show GOA records for Uniprot Accessions
+50664 Quick_Go_Evidence KNOWN 1 Quick Go MISC \N \N Resource to show GOA view of original annotation sources
50665 Painted_Turtle_Consortium 3.0.1 KNOWN 5 International Painted Turtle Genome Sequencing Consortium MISC \N \N http://www.ncbi.nlm.nih.gov/genome/assembly/326468/
50666 IGDBCAS-v1.4_GENE 1.4 KNOWN 1 IGDBCAS v1.4 Gene MISC \N \N \N
50667 IGDBCAS-v1.4_TRANSCRIPT 1.4 KNOWN 1 IGDBCAS v1.4 Transcript MISC \N \N \N
@@ -484,41 +484,43 @@
50671 ITAG_TRANSCRIPT ITAG_pre2.3 KNOWNXREF 1 ITAG pre2.3 Transcript MISC \N \N \N
50672 IRGSPv1_GENE 1 KNOWNXREF 1 IRGSP v1 Gene MISC \N \N \N
50673 IRGSPv1_TRANSCRIPT 1 KNOWNXREF 1 IRGSP v1 Transcript MISC \N \N \N
-50674 Ens_Lc_gene \N XREF 5 Ensembl Coelacanth Gene MISC \N \N \N
-50675 Ens_Lc_transcript \N XREF 170 Ensembl Coelacanth Transcript MISC \N \N \N
-50676 Ens_Lc_translation \N XREF 5 Ensembl Coelacanth Translation MISC \N \N \N
-50677 RGSC \N KNOWNXREF 0 Rat Genome Sequencing Consortium MISC \N \N Rat Genome Sequencing Consortium
-50678 BROAD_coelacanth_transcriptome \N XREF 0 BROAD Institute coelacanth transcriptome MISC \N \N \N
-50679 Ens_Ac_translation \N XREF 40 Ensembl Anole Lizard Translation MISC \N \N \N
-50680 Ens_Ac_gene \N XREF 40 Ensembl Anole Lizard Gene MISC \N \N \N
-50681 Ens_Ac_transcript \N XREF 40 Ensembl Anole Lizard Transcript MISC \N \N \N
+50674 Ens_Lc_gene XREF 5 Ensembl Coelacanth Gene MISC \N \N \N
+50675 Ens_Lc_transcript XREF 170 Ensembl Coelacanth Transcript MISC \N \N \N
+50676 Ens_Lc_translation XREF 5 Ensembl Coelacanth Translation MISC \N \N \N
+50677 RGSC KNOWNXREF 0 Rat Genome Sequencing Consortium MISC \N \N Rat Genome Sequencing Consortium
+50678 BROAD_coelacanth_transcript XREF 0 BROAD Institute coelacanth transcriptome MISC \N \N \N
+50679 Ens_Ac_translation XREF 40 Ensembl Anole Lizard Translation MISC \N \N \N
+50680 Ens_Ac_gene XREF 40 Ensembl Anole Lizard Gene MISC \N \N \N
+50681 Ens_Ac_transcript XREF 40 Ensembl Anole Lizard Transcript MISC \N \N \N
50682 BGI_Gene 1 XREF 50 BGI_2005_indica_Gene MISC \N \N BGI gene identifier
50683 GeneIndex 1 XREF 50 GeneIndex MISC \N \N \N
-50684 EO 1 XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms.\nMore information in there:\nhttp://www.gramene.org/plant_ontology/ontology_browse.html#eo
-50685 Ens_Rn_transcript \N XREF 5 Ensembl Rat Transcript MISC \N \N \N
-50686 Ens_Rn_translation \N XREF 5 Ensembl Rat Translation MISC \N \N \N
-50687 Uppsala University \N KNOWN 5 Uppsala University MISC \N \N \N
+50684 EO 1 XREF 0 Environment Ontology MISC \N \N Plant environmental conditions ontology terms.\
+More information in there:\
+http://www.gramene.org/plant_ontology/ontology_browse.html#eo
+50685 Ens_Rn_transcript XREF 5 Ensembl Rat Transcript MISC \N \N \N
+50686 Ens_Rn_translation XREF 5 Ensembl Rat Translation MISC \N \N \N
+50687 Uppsala University KNOWN 5 Uppsala University MISC \N \N \N
50688 GenBank 1 XREF 1 GenBank MISC \N \N GenBank identifier
50689 MaizeGDB_GenBank 1 XREF 1 MaizeGDB_GenBank MISC \N \N GenBank identifiers for Maize Genome DB entries.
-50690 RefSeq_gene_name \N KNOWN 200 RefSeq gene name MISC \N \N This is read out of the *.gff files provided to us by the NCBI when we do a RefSeq import or a CCDS comparison. It has the key "gene_id" and is found at the start of the 9th field.
+50690 RefSeq_gene_name KNOWN 200 RefSeq gene name MISC \N \N This is read out of the *.gff files provided to us by the NCBI when we do a RefSeq import or a CCDS comparison. It has the key "gene_id" and is found at the start of the 9th field.
50691 SGN 1 KNOWNXREF 1 Sol Genomics Network MISC \N \N \N
-50692 GRC_alignment_import \N XREF 0 GRC alignment import MISC \N \N Imported alignments from the Genome Reference Consortium.
-50693 BROAD_monodelphis_transcriptome \N XREF 0 Broad Institute transcriptome data for monodelphis MISC \N \N \N
-50694 SIB_mondelphis_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for monodelphis MISC \N \N \N
-50695 SIB_platypus_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for platypus MISC \N \N \N
-50696 SIB_orangutan_transcriptome \N XREF 0 Swiss Institute of Bioinformatics transcriptome data for orangutan MISC \N \N \N
+50692 GRC_alignment_import XREF 0 GRC alignment import MISC \N \N Imported alignments from the Genome Reference Consortium.
+50693 BROAD_monodelphis_transcrip XREF 0 Broad Institute transcriptome data for monodelphis MISC \N \N \N
+50694 SIB_mondelphis_transcriptom XREF 0 Swiss Institute of Bioinformatics transcriptome data for monodelphis MISC \N \N \N
+50695 SIB_platypus_transcriptome XREF 0 Swiss Institute of Bioinformatics transcriptome data for platypus MISC \N \N \N
+50696 SIB_orangutan_transcriptome XREF 0 Swiss Institute of Bioinformatics transcriptome data for orangutan MISC \N \N \N
50697 NCBI_TAXONOMY 1 KNOWNXREF 1 NCBI species MISC \N \N Organism listed in NCBI
50698 PHI 1 KNOWNXREF 1 PHI-base accession MISC \N \N Parasite-host interaction identifiers from PHI-base
50700 AnoXcel 2 KNOWN 50 AnoXcel MISC \N \N VectorBase xref.
50701 PGSC_GENE 1 XREF 1 PGSC MISC \N \N Potato Genome Sequencing Consortium database
50702 PHYTOZOME_GMAX_GENE 1.1 XREF 1 Phytozome MISC \N \N Phytozome Gmax
-50703 Uniprot_gn_trans_name \N KNOWNXREF 5 UniProt transcript name MISC \N \N transcript name projected from UniProt gene name
-50705 Uniprot_gn_gene_name \N KNOWNXREF 5 UniProt gene name MISC \N \N gene name from UniProt
-50707 Ensembl_Bam2Genes_intron \N PRED 5 Intron identified by Ensembl RNASeq pipeline MISC \N \N Ensembl_Bam2Genes_intron are the introns indentified at the bam2genes stage in the Ensembl RNAseq pipeline. They are stored as Clusters in the dna_align_feature table.
+50703 Uniprot_gn_trans_name KNOWNXREF 5 UniProt transcript name MISC \N \N transcript name projected from UniProt gene name
+50705 Uniprot_gn_gene_name KNOWNXREF 5 UniProt gene name MISC \N \N gene name from UniProt
+50707 Ensembl_Bam2Genes_intron PRED 5 Intron identified by Ensembl RNASeq pipeline MISC \N \N Ensembl_Bam2Genes_intron are the introns indentified at the bam2genes stage in the Ensembl RNAseq pipeline. They are stored as Clusters in the dna_align_feature table.
50708 GMGC_GENE 1 KNOWNXREF 1 GMGC PRIMARY_DB_SYNONYM \N \N Global Musa Genomics Consortium gene cross-references
-50709 tamu_vibs \N KNOWN 0 TAMU VIBS MISC \N \N The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences.
+50709 tamu_vibs KNOWN 0 TAMU VIBS MISC \N \N The Texas A&M College of Veterinary Medicine & Biomedical Sciences, Department of Veterinary Integrative Biosciences.
50710 INSDC 0 KNOWNXREF 5 International Nucleotide Sequence Database Collaboration MISC INSDC \N This external_db_id was initially made for use in the seq_region_synonym table. For species such as human, cow, dog we store chromosome names (1-22, X,Y) in the name column of the seq_region table. The INSDC accession is stored as a synonym.
-50711 ISGC \N KNOWNXREF 0 International Sheep Genome Consortium MISC \N \N International Sheep Genome Consortium
+50711 ISGC KNOWNXREF 0 International Sheep Genome Consortium MISC \N \N International Sheep Genome Consortium
50712 PO_to_transcript 1 KNOWNXREF 1 PO MISC \N \N Plants Ontology terms attached to transcripts
50713 TAIR_SYMBOL 10 KNOWN 60 TAIR Gene Name PRIMARY_DB_SYNONYM \N \N TAIR gene names
50714 GO_to_transcript 1 KNOWNXREF 1 GO MISC \N \N GO Terms attached to transcripts
@@ -528,30 +530,31 @@
50718 ENA_GENE 1 KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source gene model when importing from ENA.
50719 ENA_TRANSCRIPT 1 KNOWNXREF 1 European Nucleotide Archive MISC \N \N Cross-references to the source transcript model when importing from ENA.
50720 LGBPratt_EST_Cluster 1 KNOWNXREF 1 LGBPratt_EST_Cluster MISC \N \N \N
-50721 BaylorCollege \N KNOWN 5 Baylor College of Medicine, Texas Medical Center MISC \N \N \N
+50721 BaylorCollege KNOWN 5 Baylor College of Medicine, Texas Medical Center MISC \N \N \N
50722 Rhea 1 KNOWNXREF 1 Rhea MISC \N \N Cross-references to Rhea attached to translation objects
-50723 Ens_Bt_translation \N XREF 5 Ensembl Cow Translation MISC \N \N \N
+50723 Ens_Bt_translation XREF 5 Ensembl Cow Translation MISC \N \N \N
50724 RegulonDB_GENE 1 KNOWNXREF 1 RegulonDB MISC \N \N cross-references to RegulonDb attached to gene objects
50725 RegulonDB_OPERON 1 KNOWNXREF 1 RegulonDB MISC \N \N cross-references to RegulonDb attached to operon objects
50726 ENA_FEATURE_GENE 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the gene has been inferred, when loading a genome from ENA records.
50727 ENA_FEATURE_TRANSCRIPT 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the transcript has been inferred, when loading a genome from ENA records.
50728 ENA_FEATURE_PROTEIN 1 KNOWNXREF 1 ENA MISC \N \N Cross-reference to the ENA object from which the translation has been inferred, when loading a genome from ENA records.
-50729 RefSeq_import \N KNOWN 240 RefSeq_import MISC \N \N \N
-50730 AGP \N KNOWN 5 Anolis Genome Project MISC \N \N \N
-50731 Turkey Genome Consortium \N KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
-50732 Yutaka_Satou_Kyoto_University \N KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
-50733 Chicken_Genome_Consortium \N KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
-50734 TAIR_TRANSLATION 1 XREF 1 TAIR Translation identifiers MISC \N \N TAIR identifiers to link to Ensembl Translation identifiers.\nThe main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translations.
+50729 RefSeq_import KNOWN 240 RefSeq_import MISC \N \N \N
+50730 AGP KNOWN 5 Anolis Genome Project MISC \N \N \N
+50731 Turkey Genome Consortium KNOWN 5 Turkey Genome Consortium MISC \N \N Turkey Genome Consortium
+50732 Yutaka_Satou_Kyoto_Universi KNOWN 5 Yutaka Satou Kyoto University MISC \N \N Yutaka Satou Kyoto University
+50733 Chicken_Genome_Consortium KNOWN 5 International Chicken Genome Consortium MISC \N \N \N
+50734 TAIR_TRANSLATION 1 XREF 1 TAIR Translation identifiers MISC \N \N TAIR identifiers to link to Ensembl Translation identifiers.\
+The main requirement behind this entry, is to be able to link TAIR GO annotations to Ensembl Translations.
50735 AGI_GENE 1 XREF 1 AGI Gene MISC \N \N annotation provided by Arizona Genome Institute
50736 AGI_TRANSCRIPT 1 XREF 1 AGI Transcript MISC \N \N annotation provided by Arizona Genome Institute
-50737 CGNC \N KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
+50737 CGNC KNOWNXREF 100 CGNC Symbol PRIMARY_DB_SYNONYM \N \N \N
50738 MetaCyc 1 KNOWNXREF 1 MetaCyc MISC \N \N MetaCyc database of metabolic pathways
50739 PHIP 1 KNOWNXREF 1 PHI-base phenotype ontology MISC \N \N PHI-base phenotype ontology for genes proven to affect the outcome of pathogen-host interactions
50740 PHIE 1 KNOWNXREF 1 PHI-base condition ontology MISC \N \N PHI-base experimental evidence ontology for genes proven to affect the outcome of pathogen-host interactions
-50741 dbSNP \N XREF 0 dbSNP MISC \N \N dbSNP variant corresponding to Vega 1kG LOF Variant.
-50742 PubMedCentral \N KNOWN 5 PubMedCentral LIT \N \N PMC identifier for use with PubMedCentral (http://www.ncbi.nlm.nih.gov/pmc and http://europepmc.org/)
+50741 dbSNP XREF 0 dbSNP MISC \N \N dbSNP variant corresponding to Vega 1kG LOF Variant.
+50742 PubMedCentral KNOWN 5 PubMedCentral LIT \N \N PMC identifier for use with PubMedCentral (http://www.ncbi.nlm.nih.gov/pmc and http://europepmc.org/)
50743 PFAM 27 XREF 0 PFAM MISC \N \N Pfam release 27, from Vega
-50744 EntrezGene_trans_name \N KNOWNXREF 250 EntrezGene transcript name MISC \N \N transcript name projected from EntrezGene gene name
+50744 EntrezGene_trans_name KNOWNXREF 250 EntrezGene transcript name MISC \N \N transcript name projected from EntrezGene gene name
50745 BROAD_M_violaceum 1 KNOWNXREF 0 Broad Institute MISC \N \N Broad Institute Microbotryum violaceum Database
50746 BROAD_M_violaceum_GENE 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
-50747 BROAD_M_violaceum_TRANSCRIPT 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
+50747 BROAD_M_violaceum_TRANSCRIP 1 KNOWNXREF 0 Broad Institute PRIMARY_DB_SYNONYM \N \N Broad Institute Microbotryum violaceum Database
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
index 74993b1a234f40df1188607acb8d4ebe13a5fd14..185b545bc758dbc432bd96b1e6a95ba18ce125cc 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -118,3 +118,4 @@
2125 \N patch patch_97_98_a.sql|schema_version
2126 \N patch patch_98_99_a.sql|schema_version
2127 \N patch patch_99_100_a.sql|schema_version
+2128 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
index 71df0da717739f3271c95f151a9e1a20b80484cd..5ae6e282c7f73c2fb05c700f0737337da380ff8d 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=8453 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=410 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM AUTO_INCREMENT=1366612 DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM AUTO_INCREMENT=1221449 DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=7296966 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM AUTO_INCREMENT=27 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2128 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2129 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM AUTO_INCREMENT=93001 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=17375428 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=1001161224 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=2047756 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=1044748 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
index f831d70c942d4028d31700b6c5e592ccaf177ca4..3e03d2bcfde182c75fdb1cc13e43960956348ecc 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
@@ -1,5 +1,5 @@
1 \N schema_type variation
-2 \N schema_version 99
+2 \N schema_version 100
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
@@ -44,3 +44,8 @@
44 \N patch patch_96_97_c.sql|add an unique index on the name column
45 \N patch patch_97_98_a.sql|schema version
46 \N patch patch_98_99_a.sql|schema_version
+47 \N patch patch_98_99_b.sql|Add the column data_source_attrib in the table variation_citation
+48 \N patch patch_98_99_c.sql|Increase the size of the title and doi columns in the publication table
+49 \N patch patch_98_99_d.sql|add key data_source_attrib
+50 \N patch patch_98_99_e.sql|Fix attrib ids in table variation_citation
+51 \N patch patch_99_100_a.sql|schema version
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
index 043a9b70a34be4f2082c47dce883bd54c8f7613c..84e276006bc42b5875f6201d06b4c4fc105878fa 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` (
CREATE TABLE `attrib` (
`attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
PRIMARY KEY (`attrib_id`),
UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_set` (
- `attrib_set_id` int(11) unsigned NOT NULL DEFAULT 0,
- `attrib_id` int(11) unsigned NOT NULL DEFAULT 0,
+ `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
+ `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
KEY `attrib_idx` (`attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` (
`seq_region_start` int(11) NOT NULL,
`seq_region_end` int(11) NOT NULL,
`seq_region_strand` tinyint(4) NOT NULL,
- `genotypes` blob DEFAULT NULL,
+ `genotypes` blob,
KEY `pos_idx` (`seq_region_id`,`seq_region_start`),
KEY `sample_idx` (`sample_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` (
CREATE TABLE `compressed_genotype_var` (
`variation_id` int(11) unsigned NOT NULL,
`subsnp_id` int(11) unsigned DEFAULT NULL,
- `genotypes` blob DEFAULT NULL,
+ `genotypes` blob,
KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` (
CREATE TABLE `individual` (
`individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown',
`father_individual_id` int(10) unsigned DEFAULT NULL,
`mother_individual_id` int(10) unsigned DEFAULT NULL,
- `individual_type_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `individual_type_id` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`individual_id`),
KEY `father_individual_idx` (`father_individual_id`),
KEY `mother_individual_idx` (`mother_individual_id`)
@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` (
CREATE TABLE `individual_type` (
`individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) NOT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`individual_type_id`)
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=47 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=52 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` (
`variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL,
`motif_feature_id` int(11) unsigned NOT NULL,
- `allele_string` text DEFAULT NULL,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `allele_string` text,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`motif_start` int(11) unsigned DEFAULT NULL,
`motif_end` int(11) unsigned DEFAULT NULL,
`motif_score_delta` float DEFAULT NULL,
- `in_informative_position` tinyint(1) NOT NULL DEFAULT 0,
+ `in_informative_position` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`motif_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
@@ -233,7 +233,7 @@ CREATE TABLE `phenotype_feature` (
`study_id` int(11) unsigned DEFAULT NULL,
`type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') DEFAULT NULL,
`object_id` varchar(255) DEFAULT NULL,
- `is_significant` tinyint(1) unsigned DEFAULT 1,
+ `is_significant` tinyint(1) unsigned DEFAULT '1',
`seq_region_id` int(11) unsigned DEFAULT NULL,
`seq_region_start` int(11) unsigned DEFAULT NULL,
`seq_region_end` int(11) unsigned DEFAULT NULL,
@@ -267,8 +267,8 @@ CREATE TABLE `population` (
`population_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
`size` int(10) DEFAULT NULL,
- `description` text DEFAULT NULL,
- `collection` tinyint(1) DEFAULT 0,
+ `description` text,
+ `collection` tinyint(1) DEFAULT '0',
`freqs_from_gts` tinyint(1) DEFAULT NULL,
`display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
`display_group_id` tinyint(1) DEFAULT NULL,
@@ -310,7 +310,7 @@ CREATE TABLE `population_synonym` (
CREATE TABLE `protein_function_predictions` (
`translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL,
- `prediction_matrix` mediumblob DEFAULT NULL,
+ `prediction_matrix` mediumblob,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -318,18 +318,18 @@ CREATE TABLE `protein_function_predictions_attrib` (
`translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL,
`attrib_type_id` int(11) unsigned NOT NULL,
- `position_values` blob DEFAULT NULL,
+ `position_values` blob,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `publication` (
`publication_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `title` varchar(255) DEFAULT NULL,
+ `title` varchar(300) DEFAULT NULL,
`authors` varchar(255) CHARACTER SET latin2 DEFAULT NULL,
`pmid` int(10) DEFAULT NULL,
`pmcid` varchar(255) DEFAULT NULL,
`year` int(10) unsigned DEFAULT NULL,
- `doi` varchar(50) DEFAULT NULL,
+ `doi` varchar(80) DEFAULT NULL,
`ucsc_id` varchar(50) DEFAULT NULL,
PRIMARY KEY (`publication_id`),
KEY `pmid_idx` (`pmid`),
@@ -350,9 +350,9 @@ CREATE TABLE `regulatory_feature_variation` (
`regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL,
- `feature_type` text DEFAULT NULL,
- `allele_string` text DEFAULT NULL,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `feature_type` text,
+ `allele_string` text,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL,
PRIMARY KEY (`regulatory_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
@@ -365,10 +365,10 @@ CREATE TABLE `sample` (
`sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`individual_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`study_id` int(10) unsigned DEFAULT NULL,
`display` enum('REFERENCE','DEFAULT','DISPLAYABLE','UNDISPLAYABLE','LD','MARTDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
- `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT 0,
+ `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT '0',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') DEFAULT NULL,
PRIMARY KEY (`sample_id`),
KEY `individual_idx` (`individual_id`),
@@ -431,11 +431,11 @@ CREATE TABLE `structural_variation` (
`alias` varchar(255) DEFAULT NULL,
`source_id` int(10) unsigned NOT NULL,
`study_id` int(10) unsigned DEFAULT NULL,
- `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
- `is_evidence` tinyint(4) DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `is_evidence` tinyint(4) DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`copy_number` tinyint(2) DEFAULT NULL,
PRIMARY KEY (`structural_variation_id`),
UNIQUE KEY `variation_name` (`variation_name`),
@@ -466,10 +466,10 @@ CREATE TABLE `structural_variation_feature` (
`variation_name` varchar(255) DEFAULT NULL,
`source_id` int(10) unsigned NOT NULL,
`study_id` int(10) unsigned DEFAULT NULL,
- `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
- `allele_string` longtext DEFAULT NULL,
- `is_evidence` tinyint(1) NOT NULL DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `allele_string` longtext,
+ `is_evidence` tinyint(1) NOT NULL DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`breakpoint_order` tinyint(4) DEFAULT NULL,
`length` int(10) DEFAULT NULL,
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
@@ -496,7 +496,7 @@ CREATE TABLE `study` (
`study_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`url` varchar(255) DEFAULT NULL,
`external_reference` varchar(255) DEFAULT NULL,
`study_type` varchar(255) DEFAULT NULL,
@@ -539,8 +539,8 @@ CREATE TABLE `transcript_variation` (
`transcript_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL,
- `allele_string` text DEFAULT NULL,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `allele_string` text,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
`cds_start` int(11) unsigned DEFAULT NULL,
`cds_end` int(11) unsigned DEFAULT NULL,
@@ -549,16 +549,16 @@ CREATE TABLE `transcript_variation` (
`translation_start` int(11) unsigned DEFAULT NULL,
`translation_end` int(11) unsigned DEFAULT NULL,
`distance_to_transcript` int(11) unsigned DEFAULT NULL,
- `codon_allele_string` text DEFAULT NULL,
- `pep_allele_string` text DEFAULT NULL,
- `hgvs_genomic` text DEFAULT NULL,
- `hgvs_transcript` text DEFAULT NULL,
- `hgvs_protein` text DEFAULT NULL,
+ `codon_allele_string` text,
+ `pep_allele_string` text,
+ `hgvs_genomic` text,
+ `hgvs_transcript` text,
+ `hgvs_protein` text,
`polyphen_prediction` enum('unknown','benign','possibly damaging','probably damaging') DEFAULT NULL,
`polyphen_score` float DEFAULT NULL,
`sift_prediction` enum('tolerated','deleterious','tolerated - low confidence','deleterious - low confidence') DEFAULT NULL,
`sift_score` float DEFAULT NULL,
- `display` int(1) DEFAULT 1,
+ `display` int(1) DEFAULT '1',
PRIMARY KEY (`transcript_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
@@ -577,14 +577,14 @@ CREATE TABLE `variation` (
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
`flipped` tinyint(1) unsigned DEFAULT NULL,
- `class_attrib_id` int(10) unsigned DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`minor_allele` varchar(50) DEFAULT NULL,
`minor_allele_freq` float DEFAULT NULL,
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
- `display` int(1) DEFAULT 1,
+ `display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_id`),
UNIQUE KEY `name` (`name`),
KEY `source_idx` (`source_id`)
@@ -601,7 +601,9 @@ CREATE TABLE `variation_attrib` (
CREATE TABLE `variation_citation` (
`variation_id` int(10) unsigned NOT NULL,
`publication_id` int(10) unsigned NOT NULL,
- PRIMARY KEY (`variation_id`,`publication_id`)
+ `data_source_attrib` set('615','616','617') DEFAULT NULL,
+ PRIMARY KEY (`variation_id`,`publication_id`),
+ KEY `data_source_attrib_idx` (`data_source_attrib`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `variation_feature` (
@@ -619,15 +621,15 @@ CREATE TABLE `variation_feature` (
`source_id` int(10) unsigned NOT NULL,
`consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
- `class_attrib_id` int(10) unsigned DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`minor_allele` varchar(50) DEFAULT NULL,
`minor_allele_freq` float DEFAULT NULL,
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`alignment_quality` double DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
- `display` int(1) DEFAULT 1,
+ `display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_feature_id`),
KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
KEY `variation_idx` (`variation_id`),
@@ -651,7 +653,7 @@ CREATE TABLE `variation_hgvs` (
CREATE TABLE `variation_set` (
`variation_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`short_name_attrib_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`variation_set_id`),
KEY `name_idx` (`name`)
diff --git a/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
index ca3b8453df7ac64a36df345caa5a8a4eee1240a1..26756a3d6f695abfd784527fcfe7b4624d00b38d 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:38 2019
+-- Created on Fri Nov 1 15:19:32 2019
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
index a37a4be27525a9506d5f433ee450b3f45d35584a..2ba190a233fe5be4d14ef1b1b41ec54630a0037a 100644
--- a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:43 2019
+-- Created on Fri Nov 1 15:19:53 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/mapping/core/meta.txt b/modules/t/test-genome-DBs/mapping/core/meta.txt
index 72983dd7a1338bc958399d868988f302f658c3d9..ee84ac3b6b8fafb2801e0a305f22fd3f3445533d 100644
--- a/modules/t/test-genome-DBs/mapping/core/meta.txt
+++ b/modules/t/test-genome-DBs/mapping/core/meta.txt
@@ -74,3 +74,4 @@
167 \N patch patch_97_98_a.sql|schema_version
168 \N patch patch_98_99_a.sql|schema_version
169 \N patch patch_99_100_a.sql|schema_version
+170 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/mapping/core/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index 244ca00107704525ebe44f3bb74797676d2daf53..ccf60eb44a3d48f2b6aff5b91d5362e07ea3a149 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=170 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=171 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql b/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
index 5371036922c646047a5e0cc221dafc4f5a35a739..19cd3934098563599067643fc8d60bea408374fc 100644
--- a/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:47 2019
+-- Created on Fri Nov 1 15:20:09 2019
--
BEGIN TRANSACTION;
@@ -384,7 +384,7 @@ CREATE TABLE "hmm_curated_annot" (
"seq_member_stable_id" varchar(40) NOT NULL,
"model_id" varchar(40),
"library_version" varchar(40) NOT NULL,
- "annot_date" timestamp NOT NULL DEFAULT 'current_timestamp()',
+ "annot_date" timestamp NOT NULL DEFAULT current_timestamp,
"reason" mediumtext,
PRIMARY KEY ("seq_member_stable_id")
);
@@ -442,7 +442,7 @@ CREATE TABLE "homology_member" (
CREATE TABLE "mapping_session" (
"mapping_session_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"type" enum,
- "when_mapped" timestamp NOT NULL DEFAULT 'current_timestamp()',
+ "when_mapped" timestamp NOT NULL DEFAULT current_timestamp,
"rel_from" integer,
"rel_to" integer,
"prefix" char(4) NOT NULL
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
index 3a4ca4ad9f4c93f9f33867f57c0984b03fb0ef6d..3b8e1a832938520b161ab1fb0006f12f1b09509f 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:52 2019
+-- Created on Fri Nov 1 15:20:31 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
index 2a48dd477ef3418bbf3d4f762a9d3167f7e61914..64df46e580a146dfcd0fcc49f1607deed5de81a1 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
@@ -191,3 +191,4 @@
1703 \N patch patch_97_98_a.sql|schema_version
1704 \N patch patch_98_99_a.sql|schema_version
1705 \N patch patch_99_100_a.sql|schema_version
+1706 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index 28a5dbe7c10023e0e5e312aab9d6e016135c894b..d4c3867375d62ba48453d55a13353ce73ed956de 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=40 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=508 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=1706 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1707 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=13705556 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
index 71720063d08302781f777a070daa54e4ff171f0d..186af1589382f06eb049ce6937c849cbb4d3face 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
@@ -1,5 +1,5 @@
1 \N schema_type variation
-2 \N schema_version 99
+2 \N schema_version 100
6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
@@ -71,3 +71,8 @@
77 \N patch patch_96_97_c.sql|add an unique index on the name column
78 \N patch patch_97_98_a.sql|schema version
79 \N patch patch_98_99_a.sql|schema_version
+80 \N patch patch_98_99_b.sql|Add the column data_source_attrib in the table variation_citation
+81 \N patch patch_98_99_c.sql|Increase the size of the title and doi columns in the publication table
+82 \N patch patch_98_99_d.sql|add key data_source_attrib
+83 \N patch patch_98_99_e.sql|Fix attrib ids in table variation_citation
+84 \N patch patch_99_100_a.sql|schema version
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
index 454fa14adc06d9271524b0064fef617d8123d232..cb7051359fbeeb697b18c7a0d55f9221d1ce18f4 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` (
CREATE TABLE `attrib` (
`attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
PRIMARY KEY (`attrib_id`),
UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
) ENGINE=MyISAM AUTO_INCREMENT=419 DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_set` (
- `attrib_set_id` int(11) unsigned NOT NULL DEFAULT 0,
- `attrib_id` int(11) unsigned NOT NULL DEFAULT 0,
+ `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
+ `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
KEY `attrib_idx` (`attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` (
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` (
`seq_region_start` int(11) NOT NULL,
`seq_region_end` int(11) NOT NULL,
`seq_region_strand` tinyint(4) NOT NULL,
- `genotypes` blob DEFAULT NULL,
+ `genotypes` blob,
KEY `pos_idx` (`seq_region_id`,`seq_region_start`),
KEY `sample_idx` (`sample_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` (
CREATE TABLE `compressed_genotype_var` (
`variation_id` int(11) unsigned NOT NULL,
`subsnp_id` int(11) unsigned DEFAULT NULL,
- `genotypes` blob DEFAULT NULL,
+ `genotypes` blob,
KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` (
CREATE TABLE `individual` (
`individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown',
`father_individual_id` int(10) unsigned DEFAULT NULL,
`mother_individual_id` int(10) unsigned DEFAULT NULL,
- `individual_type_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `individual_type_id` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`individual_id`),
KEY `father_individual_idx` (`father_individual_id`),
KEY `mother_individual_idx` (`mother_individual_id`)
@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` (
CREATE TABLE `individual_type` (
`individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) NOT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`individual_type_id`)
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=80 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` (
`variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL,
`motif_feature_id` int(11) unsigned NOT NULL,
- `allele_string` text DEFAULT NULL,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `allele_string` text,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`motif_start` int(11) unsigned DEFAULT NULL,
`motif_end` int(11) unsigned DEFAULT NULL,
`motif_score_delta` float DEFAULT NULL,
- `in_informative_position` tinyint(1) NOT NULL DEFAULT 0,
+ `in_informative_position` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`motif_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
@@ -233,7 +233,7 @@ CREATE TABLE `phenotype_feature` (
`study_id` int(11) unsigned DEFAULT NULL,
`type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') DEFAULT NULL,
`object_id` varchar(255) DEFAULT NULL,
- `is_significant` tinyint(1) unsigned DEFAULT 1,
+ `is_significant` tinyint(1) unsigned DEFAULT '1',
`seq_region_id` int(11) unsigned DEFAULT NULL,
`seq_region_start` int(11) unsigned DEFAULT NULL,
`seq_region_end` int(11) unsigned DEFAULT NULL,
@@ -267,8 +267,8 @@ CREATE TABLE `population` (
`population_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
`size` int(10) DEFAULT NULL,
- `description` text DEFAULT NULL,
- `collection` tinyint(1) DEFAULT 0,
+ `description` text,
+ `collection` tinyint(1) DEFAULT '0',
`freqs_from_gts` tinyint(1) DEFAULT NULL,
`display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
`display_group_id` tinyint(1) DEFAULT NULL,
@@ -310,7 +310,7 @@ CREATE TABLE `population_synonym` (
CREATE TABLE `protein_function_predictions` (
`translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL,
- `prediction_matrix` mediumblob DEFAULT NULL,
+ `prediction_matrix` mediumblob,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -318,18 +318,18 @@ CREATE TABLE `protein_function_predictions_attrib` (
`translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL,
`attrib_type_id` int(11) unsigned NOT NULL,
- `position_values` blob DEFAULT NULL,
+ `position_values` blob,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `publication` (
`publication_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `title` varchar(255) DEFAULT NULL,
+ `title` varchar(300) DEFAULT NULL,
`authors` varchar(255) CHARACTER SET latin2 DEFAULT NULL,
`pmid` int(10) DEFAULT NULL,
`pmcid` varchar(255) DEFAULT NULL,
`year` int(10) unsigned DEFAULT NULL,
- `doi` varchar(50) DEFAULT NULL,
+ `doi` varchar(80) DEFAULT NULL,
`ucsc_id` varchar(50) DEFAULT NULL,
PRIMARY KEY (`publication_id`),
KEY `pmid_idx` (`pmid`),
@@ -350,9 +350,9 @@ CREATE TABLE `regulatory_feature_variation` (
`regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL,
- `feature_type` text DEFAULT NULL,
- `allele_string` text DEFAULT NULL,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `feature_type` text,
+ `allele_string` text,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL,
PRIMARY KEY (`regulatory_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
@@ -365,10 +365,10 @@ CREATE TABLE `sample` (
`sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`individual_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`study_id` int(10) unsigned DEFAULT NULL,
`display` enum('REFERENCE','DEFAULT','DISPLAYABLE','UNDISPLAYABLE','LD','MARTDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
- `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT 0,
+ `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT '0',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') DEFAULT NULL,
PRIMARY KEY (`sample_id`),
KEY `individual_idx` (`individual_id`),
@@ -431,11 +431,11 @@ CREATE TABLE `structural_variation` (
`alias` varchar(255) DEFAULT NULL,
`source_id` int(10) unsigned NOT NULL,
`study_id` int(10) unsigned DEFAULT NULL,
- `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
- `is_evidence` tinyint(4) DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `is_evidence` tinyint(4) DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`copy_number` tinyint(2) DEFAULT NULL,
PRIMARY KEY (`structural_variation_id`),
UNIQUE KEY `variation_name` (`variation_name`),
@@ -466,11 +466,11 @@ CREATE TABLE `structural_variation_feature` (
`variation_name` varchar(255) DEFAULT NULL,
`source_id` int(10) unsigned NOT NULL,
`study_id` int(10) unsigned DEFAULT NULL,
- `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
- `allele_string` longtext DEFAULT NULL,
- `is_evidence` tinyint(1) NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `allele_string` longtext,
+ `is_evidence` tinyint(1) NOT NULL DEFAULT '0',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`breakpoint_order` tinyint(4) DEFAULT NULL,
`length` int(10) DEFAULT NULL,
PRIMARY KEY (`structural_variation_feature_id`),
@@ -496,7 +496,7 @@ CREATE TABLE `study` (
`study_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`url` varchar(255) DEFAULT NULL,
`external_reference` varchar(255) DEFAULT NULL,
`study_type` varchar(255) DEFAULT NULL,
@@ -545,8 +545,8 @@ CREATE TABLE `transcript_variation` (
`transcript_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL,
- `allele_string` text DEFAULT NULL,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `allele_string` text,
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
`cds_start` int(11) unsigned DEFAULT NULL,
`cds_end` int(11) unsigned DEFAULT NULL,
@@ -555,16 +555,16 @@ CREATE TABLE `transcript_variation` (
`translation_start` int(11) unsigned DEFAULT NULL,
`translation_end` int(11) unsigned DEFAULT NULL,
`distance_to_transcript` int(11) unsigned DEFAULT NULL,
- `codon_allele_string` text DEFAULT NULL,
- `pep_allele_string` text DEFAULT NULL,
- `hgvs_genomic` text DEFAULT NULL,
- `hgvs_transcript` text DEFAULT NULL,
- `hgvs_protein` text DEFAULT NULL,
+ `codon_allele_string` text,
+ `pep_allele_string` text,
+ `hgvs_genomic` text,
+ `hgvs_transcript` text,
+ `hgvs_protein` text,
`polyphen_prediction` enum('unknown','benign','possibly damaging','probably damaging') DEFAULT NULL,
`sift_prediction` enum('tolerated','deleterious','tolerated - low confidence','deleterious - low confidence') DEFAULT NULL,
`polyphen_score` float DEFAULT NULL,
`sift_score` float DEFAULT NULL,
- `display` int(1) DEFAULT 1,
+ `display` int(1) DEFAULT '1',
PRIMARY KEY (`transcript_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`),
@@ -583,14 +583,14 @@ CREATE TABLE `variation` (
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
`flipped` tinyint(1) unsigned DEFAULT NULL,
- `class_attrib_id` int(10) unsigned DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`minor_allele` varchar(50) DEFAULT NULL,
`minor_allele_freq` float DEFAULT NULL,
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
- `display` int(1) DEFAULT 1,
+ `display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_id`),
UNIQUE KEY `name` (`name`),
KEY `source_idx` (`source_id`)
@@ -607,7 +607,9 @@ CREATE TABLE `variation_attrib` (
CREATE TABLE `variation_citation` (
`variation_id` int(10) unsigned NOT NULL,
`publication_id` int(10) unsigned NOT NULL,
- PRIMARY KEY (`variation_id`,`publication_id`)
+ `data_source_attrib` set('615','616','617') DEFAULT NULL,
+ PRIMARY KEY (`variation_id`,`publication_id`),
+ KEY `data_source_attrib_idx` (`data_source_attrib`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `variation_feature` (
@@ -625,15 +627,15 @@ CREATE TABLE `variation_feature` (
`source_id` int(10) unsigned NOT NULL,
`consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
- `class_attrib_id` int(10) unsigned DEFAULT 0,
- `somatic` tinyint(1) NOT NULL DEFAULT 0,
+ `class_attrib_id` int(10) unsigned DEFAULT '0',
+ `somatic` tinyint(1) NOT NULL DEFAULT '0',
`minor_allele` varchar(50) DEFAULT NULL,
`minor_allele_freq` float DEFAULT NULL,
`minor_allele_count` int(10) unsigned DEFAULT NULL,
`alignment_quality` double DEFAULT NULL,
`evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
`clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
- `display` int(1) DEFAULT 1,
+ `display` int(1) DEFAULT '1',
PRIMARY KEY (`variation_feature_id`),
KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
KEY `variation_idx` (`variation_id`),
@@ -657,7 +659,7 @@ CREATE TABLE `variation_hgvs` (
CREATE TABLE `variation_set` (
`variation_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`short_name_attrib_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`variation_set_id`),
KEY `name_idx` (`name`)
diff --git a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
index 1c8f1a1af127fd6d0c836ceb6acbc344fc7e2d27..1068f1bc41d6f9a10d34ce3d17ae944626e652a4 100644
--- a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:07:57 2019
+-- Created on Fri Nov 1 15:20:53 2019
--
BEGIN TRANSACTION;
@@ -314,7 +314,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index 7979ed3e6182f52b3fe1bcf03e16f9f037b766a0..39c312be17e285bdae1d9ae15117d148ee68f4df 100644
--- a/modules/t/test-genome-DBs/nameless/core/meta.txt
+++ b/modules/t/test-genome-DBs/nameless/core/meta.txt
@@ -112,3 +112,4 @@
166 \N patch patch_97_98_a.sql|schema_version
167 \N patch patch_98_99_a.sql|schema_version
168 \N patch patch_99_100_a.sql|schema_version
+169 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index 103748b1765a88f55eb15b05c80c4d17516a765a..63c28b3252d2ac9afff804afde2592db1a997fc6 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -247,8 +247,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -259,31 +259,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -299,8 +299,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -316,13 +316,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -330,8 +330,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -342,8 +342,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -351,14 +351,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -381,7 +381,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -389,9 +389,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -429,8 +429,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -440,11 +440,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -452,10 +452,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -464,7 +464,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -474,24 +474,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=169 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=170 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -501,17 +501,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -521,14 +521,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -540,7 +540,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -601,13 +601,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -617,10 +617,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -630,18 +630,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -655,19 +655,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -681,7 +681,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -691,14 +691,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -724,8 +724,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -737,7 +737,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -745,16 +745,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -781,12 +781,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -799,18 +799,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -826,8 +826,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -843,8 +843,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -862,9 +862,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -886,8 +886,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -904,7 +904,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -927,7 +927,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
index 6dadabe9d56f71a35408b65bb3d1540bc955651e..fc3a0b12f01890fe912532f4a11726029d371408 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:08:00 2019
+-- Created on Fri Nov 1 15:20:59 2019
--
BEGIN TRANSACTION;
diff --git a/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
index 15d4825479370fc33619766fa3c4852710c50dd5..3480d6548c88d9ea1c7fdbcd35ea3c8908a02836 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:08:05 2019
+-- Created on Fri Nov 1 15:21:20 2019
--
BEGIN TRANSACTION;
@@ -325,7 +325,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta.txt b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
index fdc128efbfb6416d2f92ee52c6b464e1469c11e0..2c867489de5b99efc7bb3287f09e15afaf75d729 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/meta.txt
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
@@ -167,3 +167,4 @@
247 \N patch patch_97_98_a.sql|schema_version
248 \N patch patch_98_99_a.sql|schema_version
249 \N patch patch_99_100_a.sql|schema_version
+250 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index a6fb1ea5ef18c9ff4d48e76cdab79ca95ee1efd4..dd3f8de10ab17fab204f4405dfd2d74c4eb632ae 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=201 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=437 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -257,8 +257,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -269,31 +269,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=382467 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -309,8 +309,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -326,13 +326,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -340,8 +340,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -352,8 +352,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -361,14 +361,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -391,7 +391,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -399,9 +399,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -439,8 +439,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -450,11 +450,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -462,10 +462,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -474,7 +474,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -484,24 +484,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=250 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=251 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -511,17 +511,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -531,14 +531,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=24 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -550,7 +550,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -611,13 +611,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -627,10 +627,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -640,18 +640,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -665,19 +665,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -691,7 +691,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -701,14 +701,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -734,8 +734,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -747,7 +747,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -755,16 +755,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=3495795 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -791,12 +791,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -809,18 +809,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -836,8 +836,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -853,8 +853,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -872,9 +872,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -896,8 +896,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -914,7 +914,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -937,7 +937,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
index d5980140d0c5e680c932e49e6baf6e042c8af119..1c1a0ac1ccb190a3ef3ce10480bceaa47f20cf1e 100644
--- a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
@@ -1,6 +1,6 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Mon Sep 16 14:08:10 2019
+-- Created on Fri Nov 1 15:21:42 2019
--
BEGIN TRANSACTION;
@@ -314,7 +314,7 @@ CREATE TABLE "external_db" (
"status" enum NOT NULL DEFAULT 'KNOWNXREF',
"priority" integer NOT NULL DEFAULT 0,
"db_display_name" varchar(255),
- "type" enum,
+ "type" enum NOT NULL,
"secondary_db_name" varchar(255),
"secondary_db_table" varchar(255),
"description" text
diff --git a/modules/t/test-genome-DBs/test_collection/core/meta.txt b/modules/t/test-genome-DBs/test_collection/core/meta.txt
index 85b613e3b479ec679b5fa1962b54c1d77e850692..be72c192df2aae7974da9261b8c01661779b82da 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/modules/t/test-genome-DBs/test_collection/core/meta.txt
@@ -187,3 +187,4 @@
229 \N patch patch_97_98_a.sql|schema_version
230 \N patch patch_98_99_a.sql|schema_version
231 \N patch patch_99_100_a.sql|schema_version
+232 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
diff --git a/modules/t/test-genome-DBs/test_collection/core/table.sql b/modules/t/test-genome-DBs/test_collection/core/table.sql
index 6661529d26cb5567a91276338e46dcf87ee64051..d7ba949c27b8d3217b9601b664e92ca6e49bf572 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -28,7 +28,7 @@ CREATE TABLE `analysis` (
`program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
- `parameters` text COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
`module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
`module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
@@ -38,22 +38,22 @@ CREATE TABLE `analysis` (
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `displayable` tinyint(1) NOT NULL DEFAULT 1,
- `web_data` text COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
UNIQUE KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `assembly` (
- `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `asm_start` int(10) NOT NULL DEFAULT 0,
- `asm_end` int(10) NOT NULL DEFAULT 0,
- `cmp_start` int(10) NOT NULL DEFAULT 0,
- `cmp_end` int(10) NOT NULL DEFAULT 0,
- `ori` tinyint(4) NOT NULL DEFAULT 0,
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
@@ -61,14 +61,14 @@ CREATE TABLE `assembly` (
CREATE TABLE `assembly_exception` (
`assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
`exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
- `exc_seq_region_id` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_start` int(11) NOT NULL DEFAULT 0,
- `exc_seq_region_end` int(11) NOT NULL DEFAULT 0,
- `ori` int(11) NOT NULL DEFAULT 0,
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
@@ -82,12 +82,12 @@ CREATE TABLE `associated_group` (
CREATE TABLE `associated_xref` (
`associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`source_xref_id` int(10) unsigned DEFAULT NULL,
`condition_type` varchar(128) DEFAULT NULL,
`associated_group_id` int(10) unsigned DEFAULT NULL,
- `rank` int(10) unsigned DEFAULT 0,
+ `rank` int(10) unsigned DEFAULT '0',
PRIMARY KEY (`associated_xref_id`),
UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
KEY `associated_source_idx` (`source_xref_id`),
@@ -100,7 +100,7 @@ CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -111,7 +111,7 @@ CREATE TABLE `biotype` (
`object_type` enum('gene','transcript') NOT NULL DEFAULT 'gene',
`db_type` set('cdna','core','coreexpressionatlas','coreexpressionest','coreexpressiongnf','funcgen','otherfeatures','rnaseq','variation','vega','presite','sangervega') NOT NULL DEFAULT 'core',
`attrib_type_id` int(11) DEFAULT NULL,
- `description` text DEFAULT NULL,
+ `description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
@@ -121,7 +121,7 @@ CREATE TABLE `biotype` (
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned NOT NULL DEFAULT 1,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
`name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL,
@@ -137,9 +137,9 @@ CREATE TABLE `data_file` (
`coord_system_id` int(10) unsigned NOT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
`name` varchar(100) NOT NULL,
- `version_lock` tinyint(1) NOT NULL DEFAULT 0,
- `absolute` tinyint(1) NOT NULL DEFAULT 0,
- `url` text DEFAULT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
@@ -149,11 +149,11 @@ CREATE TABLE `data_file` (
CREATE TABLE `density_feature` (
`density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
- `density_type_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_id` int(11) NOT NULL DEFAULT 0,
- `seq_region_start` int(11) NOT NULL DEFAULT 0,
- `seq_region_end` int(11) NOT NULL DEFAULT 0,
- `density_value` float NOT NULL DEFAULT 0,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
@@ -161,9 +161,9 @@ CREATE TABLE `density_feature` (
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
- `analysis_id` int(11) NOT NULL DEFAULT 0,
- `block_size` int(11) NOT NULL DEFAULT 0,
- `region_features` int(11) NOT NULL DEFAULT 0,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
@@ -182,24 +182,24 @@ CREATE TABLE `ditag` (
`ditag_id` int(10) NOT NULL AUTO_INCREMENT,
`name` varchar(30) DEFAULT NULL,
`type` varchar(30) DEFAULT NULL,
- `tag_count` smallint(6) DEFAULT 1,
- `sequence` text DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `ditag_id` int(10) unsigned NOT NULL DEFAULT 0,
- `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_start` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_end` int(10) unsigned NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
- `cigar_line` text DEFAULT NULL,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
`ditag_side` char(1) DEFAULT '',
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
@@ -208,26 +208,26 @@ CREATE TABLE `ditag_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`sequence` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
CREATE TABLE `dna_align_feature` (
`dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
- `hit_start` int(11) NOT NULL DEFAULT 0,
- `hit_end` int(11) NOT NULL DEFAULT 0,
- `hit_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -247,8 +247,8 @@ CREATE TABLE `exon` (
`seq_region_strand` tinyint(2) NOT NULL,
`phase` tinyint(2) NOT NULL,
`end_phase` tinyint(2) NOT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
- `is_constitutive` tinyint(1) NOT NULL DEFAULT 0,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
`created_date` datetime DEFAULT NULL,
@@ -259,31 +259,31 @@ CREATE TABLE `exon` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
- `exon_id` int(10) unsigned NOT NULL DEFAULT 0,
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `rank` int(10) NOT NULL DEFAULT 0,
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
KEY `transcript` (`transcript_id`),
KEY `exon` (`exon_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_db` (
- `external_db_id` int(11) NOT NULL DEFAULT 0,
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
`db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
`db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
- `priority` int(11) NOT NULL DEFAULT 0,
+ `priority` int(11) NOT NULL DEFAULT '0',
`db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin NOT NULL,
`secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `external_synonym` (
- `xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`,`synonym`),
KEY `name_index` (`synonym`)
@@ -299,8 +299,8 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -316,13 +316,13 @@ CREATE TABLE `gene` (
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `gene_version` smallint(6) NOT NULL DEFAULT 0,
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
`transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `transcript_version` smallint(6) NOT NULL DEFAULT 0,
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
`translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
- `translation_version` smallint(6) NOT NULL DEFAULT 0,
- `peptide_archive_id` int(11) NOT NULL DEFAULT 0,
- `mapping_session_id` int(11) NOT NULL DEFAULT 0,
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
KEY `gene_idx` (`gene_stable_id`,`gene_version`),
KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
KEY `translation_idx` (`translation_stable_id`,`translation_version`),
@@ -330,8 +330,8 @@ CREATE TABLE `gene_archive` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `gene_attrib` (
- `gene_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -342,8 +342,8 @@ CREATE TABLE `gene_attrib` (
CREATE TABLE `genome_statistics` (
`genome_statistics_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`statistic` varchar(128) NOT NULL,
- `value` bigint(11) unsigned NOT NULL DEFAULT 0,
- `species_id` int(10) unsigned DEFAULT 1,
+ `value` bigint(11) unsigned NOT NULL DEFAULT '0',
+ `species_id` int(10) unsigned DEFAULT '1',
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime DEFAULT NULL,
PRIMARY KEY (`genome_statistics_id`),
@@ -351,14 +351,14 @@ CREATE TABLE `genome_statistics` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`xref_identity` int(5) DEFAULT NULL,
`ensembl_identity` int(5) DEFAULT NULL,
`xref_start` int(11) DEFAULT NULL,
`xref_end` int(11) DEFAULT NULL,
`ensembl_start` int(11) DEFAULT NULL,
`ensembl_end` int(11) DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
PRIMARY KEY (`object_xref_id`)
@@ -381,7 +381,7 @@ CREATE TABLE `intron_supporting_evidence` (
`hit_name` varchar(100) NOT NULL,
`score` decimal(10,3) DEFAULT NULL,
`score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
- `is_splice_canonical` tinyint(1) NOT NULL DEFAULT 0,
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
PRIMARY KEY (`intron_supporting_evidence_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
@@ -389,9 +389,9 @@ CREATE TABLE `intron_supporting_evidence` (
CREATE TABLE `karyotype` (
`karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) NOT NULL DEFAULT 0,
- `seq_region_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
`band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
@@ -429,8 +429,8 @@ CREATE TABLE `marker` (
`display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
`left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
- `min_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
- `max_primer_dist` int(10) unsigned NOT NULL DEFAULT 0,
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
`priority` int(11) DEFAULT NULL,
`type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_id`),
@@ -440,11 +440,11 @@ CREATE TABLE `marker` (
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`map_weight` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -452,10 +452,10 @@ CREATE TABLE `marker_feature` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
- `map_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
`chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
- `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
`position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
`lod_score` double DEFAULT NULL,
PRIMARY KEY (`marker_id`,`map_id`),
@@ -464,7 +464,7 @@ CREATE TABLE `marker_map_location` (
CREATE TABLE `marker_synonym` (
`marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `marker_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
`source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
`name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`marker_synonym_id`),
@@ -474,24 +474,24 @@ CREATE TABLE `marker_synonym` (
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
- `species_id` int(10) unsigned DEFAULT 1,
+ `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=232 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=233 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `coord_system_id` int(11) NOT NULL DEFAULT 0,
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
`max_length` int(11) DEFAULT NULL,
UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_attrib` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -501,17 +501,17 @@ CREATE TABLE `misc_attrib` (
CREATE TABLE `misc_feature` (
`misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
- `misc_feature_id` int(10) unsigned NOT NULL DEFAULT 0,
- `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -521,14 +521,14 @@ CREATE TABLE `misc_set` (
`code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
`name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`description` text COLLATE latin1_bin NOT NULL,
- `max_length` int(10) unsigned NOT NULL DEFAULT 0,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
- `ensembl_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
@@ -540,7 +540,7 @@ CREATE TABLE `object_xref` (
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
- `object_xref_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
`linkage_type` varchar(3) DEFAULT NULL,
`source_xref_id` int(10) unsigned DEFAULT NULL,
UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
@@ -601,13 +601,13 @@ CREATE TABLE `peptide_archive` (
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `exon_rank` smallint(5) unsigned NOT NULL DEFAULT 0,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
- `start_phase` tinyint(4) NOT NULL DEFAULT 0,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`p_value` double DEFAULT NULL,
PRIMARY KEY (`prediction_exon_id`),
@@ -617,10 +617,10 @@ CREATE TABLE `prediction_exon` (
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(4) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
`analysis_id` int(11) DEFAULT NULL,
`display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`prediction_transcript_id`),
@@ -630,18 +630,18 @@ CREATE TABLE `prediction_transcript` (
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
`external_db_id` smallint(5) unsigned DEFAULT NULL,
`hcoverage` double DEFAULT NULL,
`align_type` enum('ensembl','cigar','vulgar','mdtag') COLLATE latin1_bin DEFAULT 'ensembl',
@@ -655,19 +655,19 @@ CREATE TABLE `protein_align_feature` (
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `translation_id` int(11) NOT NULL DEFAULT 0,
- `seq_start` int(10) NOT NULL DEFAULT 0,
- `seq_end` int(10) NOT NULL DEFAULT 0,
- `hit_start` int(10) NOT NULL DEFAULT 0,
- `hit_end` int(10) NOT NULL DEFAULT 0,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
- `score` double NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
`perc_ident` float DEFAULT NULL,
- `external_data` text COLLATE latin1_bin DEFAULT NULL,
- `hit_description` text COLLATE latin1_bin DEFAULT NULL,
- `cigar_line` text COLLATE latin1_bin DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ `cigar_line` text COLLATE latin1_bin,
`align_type` enum('ensembl','cigar','cigarplus','vulgar','mdtag') COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`protein_feature_id`),
UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`,`analysis_id`),
@@ -681,7 +681,7 @@ CREATE TABLE `repeat_consensus` (
`repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
`repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `repeat_consensus` text COLLATE latin1_bin DEFAULT NULL,
+ `repeat_consensus` text COLLATE latin1_bin,
PRIMARY KEY (`repeat_consensus_id`),
KEY `name` (`repeat_name`),
KEY `class` (`repeat_class`),
@@ -691,14 +691,14 @@ CREATE TABLE `repeat_consensus` (
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 1,
- `repeat_start` int(10) NOT NULL DEFAULT 0,
- `repeat_end` int(10) NOT NULL DEFAULT 0,
- `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT 0,
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`repeat_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -724,8 +724,8 @@ CREATE TABLE `rnaproduct` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `rnaproduct_attrib` (
- `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text NOT NULL,
UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -737,7 +737,7 @@ CREATE TABLE `rnaproduct_type` (
`rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
- `description` text DEFAULT NULL,
+ `description` text,
PRIMARY KEY (`rnaproduct_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -745,16 +745,16 @@ CREATE TABLE `rnaproduct_type` (
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
- `coord_system_id` int(10) NOT NULL DEFAULT 0,
- `length` int(10) NOT NULL DEFAULT 0,
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -781,12 +781,12 @@ CREATE TABLE `seq_region_synonym` (
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `seq_region_id` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_start` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_end` int(10) unsigned NOT NULL DEFAULT 0,
- `seq_region_strand` tinyint(1) NOT NULL DEFAULT 0,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
`display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
- `analysis_id` int(10) unsigned NOT NULL DEFAULT 0,
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL,
PRIMARY KEY (`simple_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
@@ -799,18 +799,18 @@ CREATE TABLE `stable_id_event` (
`old_version` smallint(6) DEFAULT NULL,
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
- `mapping_session_id` int(10) NOT NULL DEFAULT 0,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
`type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
- `score` float NOT NULL DEFAULT 0,
+ `score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
KEY `old_idx` (`old_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `supporting_feature` (
- `exon_id` int(11) NOT NULL DEFAULT 0,
+ `exon_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -826,8 +826,8 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
- `description` text DEFAULT NULL,
- `is_current` tinyint(1) NOT NULL DEFAULT 1,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
`stable_id` varchar(128) DEFAULT NULL,
`version` smallint(5) unsigned DEFAULT NULL,
@@ -843,8 +843,8 @@ CREATE TABLE `transcript` (
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
- `transcript_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -862,9 +862,9 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_supporting_feature` (
- `transcript_id` int(11) NOT NULL DEFAULT 0,
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
`feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
- `feature_id` int(11) NOT NULL DEFAULT 0,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
KEY `feature_idx` (`feature_type`,`feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
@@ -886,8 +886,8 @@ CREATE TABLE `translation` (
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
- `translation_id` int(10) unsigned NOT NULL DEFAULT 0,
- `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
`value` text COLLATE latin1_bin NOT NULL,
UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
@@ -904,7 +904,7 @@ CREATE TABLE `unmapped_object` (
`unmapped_reason_id` int(10) unsigned NOT NULL,
`query_score` double DEFAULT NULL,
`target_score` double DEFAULT NULL,
- `ensembl_id` int(10) unsigned DEFAULT 0,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
@@ -927,7 +927,7 @@ CREATE TABLE `xref` (
`dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
`display_label` varchar(512) COLLATE latin1_bin NOT NULL,
`version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
- `description` text COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
`info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
`info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`xref_id`),
diff --git a/sql/patch_99_100_b.sql b/sql/patch_99_100_b.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a0add3b87e6cad51ce32b2bd7788f182521d1e15
--- /dev/null
+++ b/sql/patch_99_100_b.sql
@@ -0,0 +1,27 @@
+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2019] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+-- http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_99_100_b.sql
+#
+# Title: Update external_db.type to NOT NULL
+#
+# Description:
+# Update external_db.type column to NOT NULL.
+
+ALTER TABLE external_db MODIFY COLUMN type ENUM('ARRAY', 'ALT_TRANS', 'ALT_GENE', 'MISC', 'LIT', 'PRIMARY_DB_SYNONYM', 'ENSEMBL') NOT NULL;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_99_100_b.sql|alter_externaldb_type_notnull');
diff --git a/sql/table.sql b/sql/table.sql
index cb14e89646e8b89711b028357f3b00f4bbd6d35e..568a5337cb5a04cd9dd4d59b793872569b6ab7fb 100755
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -316,6 +316,8 @@ INSERT INTO meta (species_id, meta_key, meta_value) VALUES
INSERT INTO meta (species_id, meta_key, meta_value)
VALUES (NULL, 'patch', 'patch_99_100_a.sql|schema_version');
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_99_100_b.sql|alter_externaldb_type_notnull');
/**
@table meta_coord
@@ -2159,7 +2161,7 @@ CREATE TABLE external_db (
status ENUM('KNOWNXREF','KNOWN','XREF','PRED','ORTH', 'PSEUDO') NOT NULL,
priority INT NOT NULL,
db_display_name VARCHAR(255),
- type ENUM('ARRAY', 'ALT_TRANS', 'ALT_GENE', 'MISC', 'LIT', 'PRIMARY_DB_SYNONYM', 'ENSEMBL'),
+ type ENUM('ARRAY', 'ALT_TRANS', 'ALT_GENE', 'MISC', 'LIT', 'PRIMARY_DB_SYNONYM', 'ENSEMBL') NOT NULL,
secondary_db_name VARCHAR(255) DEFAULT NULL,
secondary_db_table VARCHAR(255) DEFAULT NULL,
description TEXT,