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More updates for the new BridgeDb Datasources release
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-218
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11 files changed

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‎dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -743,7 +743,7 @@
743743
%{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'],
744744
'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'",
745745
"\'ID\|\'", "\'\|$species\|\'", "\'\'",
746-
"\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'",
746+
"\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'",
747747
"\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"],
748748
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
749749
'PRIMARY KEY (ID)'
@@ -863,7 +863,7 @@
863863
%{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'],
864864
'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'",
865865
"\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
866-
"\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'",
866+
"\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'",
867867
"\'ftp://rgd.mcw.edu/pub/\'"],
868868
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
869869
'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
@@ -916,8 +916,8 @@
916916
%{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'],
917917
'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'",
918918
"\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
919-
"\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
920-
"\'http://www.gramene.org\'"],
919+
"\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'",
920+
"\'https://www.gramene.org\'"],
921921
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
922922
'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'',
923923
'Description VARCHAR(255) DEFAULT NULL',
@@ -926,8 +926,8 @@
926926
%{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'],
927927
'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'",
928928
"\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'",
929-
"\'http://www.gramene.org/pathway\'", "\'\'",
930-
"\'http://www.gramene.org/pathway\'"],
929+
"\'https://www.gramene.org/pathway\'", "\'\'",
930+
"\'https://www.gramene.org/pathway\'"],
931931
'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'',
932932
'Description VARCHAR(255) DEFAULT NULL',
933933
'PRIMARY KEY (ID)'

‎org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge
3434
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
3535
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
3636
GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
37-
Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
37+
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
3838
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
39-
Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
39+
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
4040
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
41-
Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
42-
Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
41+
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
42+
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
4343
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
4444
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
4545
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
@@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI
7878
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
7979
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
8080
miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
81-
miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
81+
miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
8282
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
8383
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
8484
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene
@@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
112112
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
113113
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
114114
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
115-
Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
115+
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
116116
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
117117
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
118118
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

‎org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge
3434
GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene
3535
Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene
3636
GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology
37-
Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
37+
Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene
3838
Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene
39-
Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
39+
Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene
4040
Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene
41-
Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
42-
Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
41+
Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway
42+
Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene
4343
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
4444
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
4545
HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene
@@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI
7878
MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene
7979
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
8080
miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene
81-
miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
81+
miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene
8282
Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease
8383
NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material
8484
NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene
@@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?
112112
Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene
113113
RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene
114114
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
115-
Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
115+
Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene
116116
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
117117
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
118118
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

‎org.bridgedb.rdf/resources/BioDataSource.ttl‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ;
3535
bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
3636
bridgeDB:fullName "BioCyc" ;
3737
bridgeDB:systemCode "Bc" ;
38-
bridgeDB:mainUrl "http://biocyc.org" ;
38+
bridgeDB:mainUrl "https://biocyc.org" ;
3939
bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ;
4040
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
4141
bridgeDB:type "gene" ;
@@ -45,7 +45,7 @@ bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ;
4545
bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
4646
bridgeDB:fullName "BioGrid" ;
4747
bridgeDB:systemCode "Bg" ;
48-
bridgeDB:mainUrl "http://thebiogrid.org/" ;
48+
bridgeDB:mainUrl "https://thebiogrid.org/" ;
4949
bridgeDB:idExample "31623" ;
5050
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
5151
bridgeDB:type "interaction" ;
@@ -55,7 +55,7 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ;
5555
bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ;
5656
bridgeDB:fullName "BioModels Database" ;
5757
bridgeDB:systemCode "Bm" ;
58-
bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ;
58+
bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ;
5959
bridgeDB:idExample "BIOMD0000000048" ;
6060
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
6161
bridgeDB:type "pathway" ;
@@ -105,7 +105,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ;
105105
bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ;
106106
bridgeDB:fullName "ChEBI" ;
107107
bridgeDB:systemCode "Ce" ;
108-
bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ;
108+
bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ;
109109
bridgeDB:idExample "CHEBI:36927" ;
110110
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
111111
bridgeDB:type "metabolite" ;
@@ -473,7 +473,7 @@ bridgeDB:DataSource_GeneOntology a bridgeDB:DataSource ;
473473
bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
474474
bridgeDB:fullName "Gramene Arabidopsis" ;
475475
bridgeDB:systemCode "EnAt" ;
476-
bridgeDB:mainUrl "http://www.gramene.org/" ;
476+
bridgeDB:mainUrl "https://www.gramene.org/" ;
477477
bridgeDB:idExample "ATMG01360-TAIR-G" ;
478478
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
479479
bridgeDB:type "gene" ;
@@ -484,7 +484,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ;
484484
bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
485485
bridgeDB:fullName "Gramene Genes DB" ;
486486
bridgeDB:systemCode "Gg" ;
487-
bridgeDB:mainUrl "http://www.gramene.org/" ;
487+
bridgeDB:mainUrl "https://www.gramene.org/" ;
488488
bridgeDB:idExample "GR:0060184" ;
489489
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
490490
bridgeDB:type "gene" ;
@@ -494,7 +494,7 @@ bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ;
494494
bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
495495
bridgeDB:fullName "Gramene Literature" ;
496496
bridgeDB:systemCode "Gl" ;
497-
bridgeDB:mainUrl "http://www.gramene.org/" ;
497+
bridgeDB:mainUrl "https://www.gramene.org/" ;
498498
bridgeDB:idExample "6200" ;
499499
bridgeDB:primary "false"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
500500
bridgeDB:type "gene" ;
@@ -503,7 +503,7 @@ bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ;
503503
bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
504504
bridgeDB:fullName "Gramene Maize" ;
505505
bridgeDB:systemCode "EnZm" ;
506-
bridgeDB:mainUrl "http://www.ensembl.org" ;
506+
bridgeDB:mainUrl "https://www.ensembl.org" ;
507507
bridgeDB:idExample "GRMZM2G174107" ;
508508
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
509509
bridgeDB:type "gene" ;
@@ -512,7 +512,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ;
512512
bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
513513
bridgeDB:fullName "Gramene Pathway" ;
514514
bridgeDB:systemCode "Gp" ;
515-
bridgeDB:mainUrl "http://www.gramene.org/pathway" ;
515+
bridgeDB:mainUrl "https://www.gramene.org/pathway" ;
516516
bridgeDB:idExample "AAH72400" ;
517517
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
518518
bridgeDB:type "pathway" ;
@@ -521,7 +521,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ;
521521
bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ;
522522
bridgeDB:fullName "Gramene Rice" ;
523523
bridgeDB:systemCode "EnOj" ;
524-
bridgeDB:mainUrl "http://www.gramene.org/" ;
524+
bridgeDB:mainUrl "https://www.gramene.org/" ;
525525
bridgeDB:idExample "osa-MIR171a" ;
526526
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
527527
bridgeDB:type "gene" ;
@@ -780,7 +780,7 @@ bridgeDB:DataSource_MINT a bridgeDB:DataSource ;
780780
bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ;
781781
bridgeDB:fullName "miRBase mature sequence" ;
782782
bridgeDB:systemCode "Mbm" ;
783-
bridgeDB:mainUrl "http://www.mirbase.org/" ;
783+
bridgeDB:mainUrl "https://www.mirbase.org/" ;
784784
bridgeDB:idExample "MIMAT0000001" ;
785785
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
786786
bridgeDB:type "gene" ;
@@ -1032,7 +1032,7 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ;
10321032
bridgeDB:DataSource_RGD a bridgeDB:DataSource ;
10331033
bridgeDB:fullName "RGD" ;
10341034
bridgeDB:systemCode "R" ;
1035-
bridgeDB:mainUrl "http://rgd.mcw.edu/" ;
1035+
bridgeDB:mainUrl "https://rgd.mcw.edu/" ;
10361036
bridgeDB:idExample "2018" ;
10371037
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
@@ -1053,7 +1053,7 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ;
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bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ;
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bridgeDB:fullName "Rice Ensembl Gene" ;
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bridgeDB:systemCode "Os" ;
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bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ;
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bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ;
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bridgeDB:idExample "LOC_Os04g54800" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;
@@ -1175,7 +1175,7 @@ bridgeDB:DataSource_Systems_Biology_Ontology a bridgeDB:DataSource ;
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bridgeDB:DataSource_TAIR a bridgeDB:DataSource ;
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bridgeDB:fullName "TAIR" ;
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bridgeDB:systemCode "A" ;
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bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ;
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bridgeDB:mainUrl "https://www.arabidopsis.org/" ;
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bridgeDB:idExample "AT1G01030" ;
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bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
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bridgeDB:type "gene" ;

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