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More updates for the new BridgeDb Datasources release
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egonw committed Jul 25, 2024
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12 changes: 6 additions & 6 deletions dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl
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Expand Up @@ -743,7 +743,7 @@
%{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'],
'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'",
"\'ID\|\'", "\'\|$species\|\'", "\'\'",
"\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'",
"\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'",
"\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'PRIMARY KEY (ID)'
Expand Down Expand Up @@ -863,7 +863,7 @@
%{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'],
'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'",
"\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
"\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'",
"\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'",
"\'ftp://rgd.mcw.edu/pub/\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
Expand Down Expand Up @@ -916,8 +916,8 @@
%{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'],
'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'",
"\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
"\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
"\'http://www.gramene.org\'"],
"\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
"\'https://www.gramene.org\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
'Description VARCHAR(255) DEFAULT NULL',
Expand All @@ -926,8 +926,8 @@
%{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'],
'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'",
"\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
"\'http://www.gramene.org/pathway\'", "\'\'",
"\'http://www.gramene.org/pathway\'"],
"\'https://www.gramene.org/pathway\'", "\'\'",
"\'https://www.gramene.org/pathway\'"],
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
'Description VARCHAR(255) DEFAULT NULL',
'PRIMARY KEY (ID)'
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12 changes: 6 additions & 6 deletions org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene
Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
Expand Down Expand Up @@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction
miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene
Expand Down Expand Up @@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction
Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene
Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway
SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein
Expand Down
12 changes: 6 additions & 6 deletions org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene
Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
Expand Down Expand Up @@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction
miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene
Expand Down Expand Up @@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction
Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene
Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway
SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein
Expand Down
28 changes: 14 additions & 14 deletions org.bridgedb.rdf/resources/BioDataSource.ttl
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ;
bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
bridgeDB:fullName "BioCyc" ;
bridgeDB:systemCode "Bc" ;
bridgeDB:mainUrl "http://biocyc.org" ;
bridgeDB:mainUrl "https://biocyc.org" ;
bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand All @@ -45,7 +45,7 @@ bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
bridgeDB:fullName "BioGrid" ;
bridgeDB:systemCode "Bg" ;
bridgeDB:mainUrl "http://thebiogrid.org/" ;
bridgeDB:mainUrl "https://thebiogrid.org/" ;
bridgeDB:idExample "31623" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "interaction" ;
Expand All @@ -55,7 +55,7 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ;
bridgeDB:fullName "BioModels Database" ;
bridgeDB:systemCode "Bm" ;
bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ;
bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ;
bridgeDB:idExample "BIOMD0000000048" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "pathway" ;
Expand Down Expand Up @@ -105,7 +105,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ;
bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ;
bridgeDB:fullName "ChEBI" ;
bridgeDB:systemCode "Ce" ;
bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ;
bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ;
bridgeDB:idExample "CHEBI:36927" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "metabolite" ;
Expand Down Expand Up @@ -473,7 +473,7 @@ bridgeDB:DataSource_GeneOntology a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Arabidopsis" ;
bridgeDB:systemCode "EnAt" ;
bridgeDB:mainUrl "http://www.gramene.org/" ;
bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "ATMG01360-TAIR-G" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand All @@ -484,7 +484,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Genes DB" ;
bridgeDB:systemCode "Gg" ;
bridgeDB:mainUrl "http://www.gramene.org/" ;
bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "GR:0060184" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand All @@ -494,7 +494,7 @@ bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Literature" ;
bridgeDB:systemCode "Gl" ;
bridgeDB:mainUrl "http://www.gramene.org/" ;
bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "6200" ;
bridgeDB:primary "false"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand All @@ -503,7 +503,7 @@ bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Maize" ;
bridgeDB:systemCode "EnZm" ;
bridgeDB:mainUrl "http://www.ensembl.org" ;
bridgeDB:mainUrl "https://www.ensembl.org" ;
bridgeDB:idExample "GRMZM2G174107" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand All @@ -512,7 +512,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Pathway" ;
bridgeDB:systemCode "Gp" ;
bridgeDB:mainUrl "http://www.gramene.org/pathway" ;
bridgeDB:mainUrl "https://www.gramene.org/pathway" ;
bridgeDB:idExample "AAH72400" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "pathway" ;
Expand All @@ -521,7 +521,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ;
bridgeDB:fullName "Gramene Rice" ;
bridgeDB:systemCode "EnOj" ;
bridgeDB:mainUrl "http://www.gramene.org/" ;
bridgeDB:mainUrl "https://www.gramene.org/" ;
bridgeDB:idExample "osa-MIR171a" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand Down Expand Up @@ -780,7 +780,7 @@ bridgeDB:DataSource_MINT a bridgeDB:DataSource ;
bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ;
bridgeDB:fullName "miRBase mature sequence" ;
bridgeDB:systemCode "Mbm" ;
bridgeDB:mainUrl "http://www.mirbase.org/" ;
bridgeDB:mainUrl "https://www.mirbase.org/" ;
bridgeDB:idExample "MIMAT0000001" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand Down Expand Up @@ -1032,7 +1032,7 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ;
bridgeDB:DataSource_RGD a bridgeDB:DataSource ;
bridgeDB:fullName "RGD" ;
bridgeDB:systemCode "R" ;
bridgeDB:mainUrl "http://rgd.mcw.edu/" ;
bridgeDB:mainUrl "https://rgd.mcw.edu/" ;
bridgeDB:idExample "2018" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand All @@ -1053,7 +1053,7 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ;
bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ;
bridgeDB:fullName "Rice Ensembl Gene" ;
bridgeDB:systemCode "Os" ;
bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ;
bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ;
bridgeDB:idExample "LOC_Os04g54800" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand Down Expand Up @@ -1175,7 +1175,7 @@ bridgeDB:DataSource_Systems_Biology_Ontology a bridgeDB:DataSource ;
bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
bridgeDB:fullName "TAIR" ;
bridgeDB:systemCode "A" ;
bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ;
bridgeDB:mainUrl "https://www.arabidopsis.org/" ;
bridgeDB:idExample "AT1G01030" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "gene" ;
Expand Down
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