Update db-xrefs.yaml

metadata/db-xrefs.schema.yaml

@@ -28,6 +28,7 @@ sequence:
         required: false
       "rdf_uri_prefix":
         type: str
+        pattern: /.+[_/[[:punct:]]]$/
         required: false
       "generic_urls":
         type: seq

metadata/db-xrefs.yaml

@@ -813,16 +813,16 @@
   synonyms:
     - FlyBase
     - FLYBASE
-  rdf_uri_prefix: http://identifiers.org/flybase/
+  rdf_uri_prefix: https://registry.identifiers.org/registry/fb/
   generic_urls:
     - http://flybase.org/
   entity_types:
     - type_name: gene
       type_id: SO:0000704
       id_syntax: FBgn[0-9]{7}
-      url_syntax: http://flybase.org/reports/[example_id].html
+      url_syntax: https://www.alliancegenome.org/gene/FB:[example_id]
       example_id: FB:FBgn0000024
-      example_url: http://flybase.org/reports/FBgn0000024.html
+      example_url: https://www.alliancegenome.org/gene/FB:FBgn0000024
 - database: FBbt
   name: Drosophila gross anatomy
   rdf_uri_prefix: http://purl.obolibrary.org/obo/FBbt_
@@ -1259,7 +1259,7 @@
       example_url: http://www.ebi.ac.uk/complexportal/complex/EBI-10205244
 - database: InterPro
   name: InterPro database of protein domains and motifs
-  rdf_uri_prefix: https://registry.identifiers.org/registry/interpro
+  rdf_uri_prefix: https://registry.identifiers.org/registry/interpro/
   synonyms:
     - INTERPRO
     - IPR
@@ -1477,7 +1477,7 @@
       example_url: https://maizegdb.org/gene_center/gene/12098
 - database: MaizeGDB_Locus
   name: MaizeGDB
-  rdf_uri_prefix: https://identifiers.org/maizegdb.locus
+  rdf_uri_prefix: https://identifiers.org/maizegdb.locus/
   generic_urls:
     - https://www.maizegdb.org/
   entity_types:
@@ -1570,7 +1570,7 @@
   name: Metabolic Encyclopedia of metabolic and other pathways
   synonyms:
     - METACYC
-  rdf_uri_prefix: https://identifiers.org/metacyc.reaction
+  rdf_uri_prefix: https://identifiers.org/metacyc.reaction/
   generic_urls:
     - https://metacyc.org/
   entity_types:
@@ -1600,7 +1600,7 @@
       example_id: MGD:Adcy9
 - database: MGI
   name: Mouse Genome Informatics
-  rdf_uri_prefix: https://identifiers.org/MGI
+  rdf_uri_prefix: https://registry.identifiers.org/registry/mgi/
   generic_urls:
     - http://www.informatics.jax.org/
   entity_types:
@@ -1675,7 +1675,7 @@
     - GeneID
     - LocusID
     - NCBI_Gene
-  rdf_uri_prefix: https://identifiers.org/ncbigene
+  rdf_uri_prefix: https://identifiers.org/ncbigene/
   generic_urls:
     - http://www.ncbi.nlm.nih.gov/
   entity_types:
@@ -1797,7 +1797,7 @@
       type_id: BET:0000000
 - database: PANTHER
   name: Protein ANalysis THrough Evolutionary Relationships Classification System
-  rdf_uri_prefix: https://identifiers.org/panther.family
+  rdf_uri_prefix: https://identifiers.org/panther.family/
   generic_urls:
     - http://www.pantherdb.org/
   entity_types:
@@ -2011,7 +2011,7 @@
       example_url: http://planteome.org/po_ref/00001
 - database: PlasmoDB
   name: PlasmoDB
-  rdf_uri_prefix: https://identifiers.org/plasmodb
+  rdf_uri_prefix: https://identifiers.org/plasmodb/
   generic_urls:
     - https://plasmodb.org
   entity_types:
@@ -2030,7 +2030,7 @@
       type_id: BET:0000000
 - database: PomBase
   name: PomBase
-  rdf_uri_prefix: https://identifiers.org/pombase
+  rdf_uri_prefix: https://identifiers.org/pombase/
   generic_urls:
     - https://www.pombase.org/
   entity_types:
@@ -2201,7 +2201,7 @@
   synonyms:
     - REACTOME
     - REAC
-  rdf_uri_prefix: https://identifiers.org/reactome
+  rdf_uri_prefix: https://identifiers.org/reactome/
   generic_urls:
     - https://www.reactome.org/
   entity_types:
@@ -2273,16 +2273,16 @@
   synonyms:
     - RAD
     - RGDID
-  rdf_uri_prefix: https://identifiers.org/rgd
+  rdf_uri_prefix: https://registry.identifiers.org/registry/rgd/
   generic_urls:
     - https://rgd.mcw.edu/
   entity_types:
     - type_name: gene
       type_id: SO:0000704
       id_syntax: '[0-9]{4,7}'
-      url_syntax: https://rgd.mcw.edu/rgdweb/search/search.html?term=[example_id]
+      url_syntax: https://www.alliancegenome.org/gene/RGD:[example_id]
       example_id: RGD:2004
-      example_url: https://rgd.mcw.edu/rgdweb/search/search.html?term=2004
+      example_url: https://www.alliancegenome.org/gene/RGD:2004
 - database: RHEA
   name: Rhea, the Annotated Reactions Database
   description: Rhea is a manually annotated database of chemical reactions. All data in Rhea is freely accessible and available for anyone to use.
@@ -2373,26 +2373,26 @@
   name: Saccharomyces Genome Database
   synonyms:
     - SGDID
-  rdf_uri_prefix: https://identifiers.org/sgd
+  rdf_uri_prefix: https://registry.identifiers.org/registry/sgd/
   generic_urls:
     - http://www.yeastgenome.org/
   entity_types:
     - type_name: gene
       type_id: SO:0000704
       id_syntax: S[0-9]{9}
-      url_syntax:  https://www.yeastgenome.org/locus/[example_id]
+      url_syntax:  https://www.alliancegenome.org/gene/SGD:[example_id]
       example_id: SGD:S000006169
-      example_url: https://www.yeastgenome.org/locus/S000006169
+      example_url: https://www.alliancegenome.org/gene/SGD:S000006169
 - database: SGD_LOCUS
   name: Saccharomyces Genome Database
   generic_urls:
     - http://www.yeastgenome.org/
   entity_types:
     - type_name: entity
       type_id: BET:0000000
-      url_syntax: https://www.yeastgenome.org/search?q=[example_id]&is_quick=true
+      url_syntax: https://www.alliancegenome.org/gene/SGD:[example_id]
       example_id: SGD_LOCUS:GAL4
-      example_url: https://www.yeastgenome.org/search?q=S000006169&is_quick=true
+      example_url: https://www.alliancegenome.org/gene/SGD:S000006169
 - database: SGD_REF
   name: Saccharomyces Genome Database
   generic_urls:
@@ -2407,7 +2407,7 @@
   name: Sol Genomics Network
   synonyms:
     - SGN_gene
-  rdf_uri_prefix: https://identifiers.org/sgn
+  rdf_uri_prefix: https://identifiers.org/sgn/
   generic_urls:
     - https://www.sgn.cornell.edu/
   entity_types:
@@ -2535,7 +2535,7 @@
       type_id: BET:0000000
 - database: TAIR
   name: The Arabidopsis Information Resource
-  rdf_uri_prefix: https://identifiers.org/tair.locus
+  rdf_uri_prefix: https://identifiers.org/tair.locus/
   generic_urls:
     - http://www.arabidopsis.org/
   entity_types:
@@ -2584,7 +2584,7 @@
       example_url: http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1
 - database: TGD
   name: Tetrahymena Genome Database
-  rdf_uri_prefix: https://identifiers.org/tgd
+  rdf_uri_prefix: https://identifiers.org/tgd/
   generic_urls:
     - http://www.ciliate.org/
   entity_types:
@@ -2639,7 +2639,7 @@
       example_url: http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=254
 - database: TriTrypDB
   name: TriTrypDB
-  rdf_uri_prefix: https://identifiers.org/tritrypdb
+  rdf_uri_prefix: https://identifiers.org/tritrypdb/
   generic_urls:
     - https://tritrypdb.org/
   entity_types:
@@ -2749,7 +2749,7 @@
 - database: UniProtKB
   name: Universal Protein Knowledgebase
   description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database
-  rdf_uri_prefix: https://identifiers.org/uniprot
+  rdf_uri_prefix: https://identifiers.org/uniprot/
   generic_urls:
     - http://www.uniprot.org
   entity_types:
@@ -2808,7 +2808,7 @@
   name: WormBase database of nematode biology
   synonyms:
     - WormBase
-  rdf_uri_prefix: https://identifiers.org/wb
+  rdf_uri_prefix: https://registry.identifiers.org/registry/wb/
   generic_urls:
     - http://www.wormbase.org/
   entity_types:
@@ -2915,16 +2915,16 @@
       example_url: https://en.wikipedia.org/w/index.php?title=Fallopian_tube&oldid=998395727
 - database: Xenbase
   name: Xenbase
-  rdf_uri_prefix: https://identifiers.org/xenbase
+  rdf_uri_prefix: https://registry.identifiers.org/registry/xenbase/
   generic_urls:
     - http://www.xenbase.org/
   entity_types:
     - type_name: gene
       type_id: SO:0000704
       id_syntax: XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+
-      url_syntax: http://www.xenbase.org/entry/[example_id]
+      url_syntax: https://www.alliancegenome.org/gene/Xenbase:[example_id]
       example_id: Xenbase:XB-GENE-6255962
-      example_url: http://www.xenbase.org/entry/XB-GENE-6255962
+      example_url: https://www.alliancegenome.org/gene/Xenbase:XB-GENE-6255962
     - type_name: morpholino oligo
       type_id: SO:0000034
       id_syntax: XB-(GENE|LINE|TRANSGENE|MORPHOLINO)-[0-9]+
@@ -2957,22 +2957,22 @@
     - http://citgenedb.yubiolab.org
 - database: ZFIN
   name: Zebrafish Information Network
-  rdf_uri_prefix: https://identifiers.org/zfin
+  rdf_uri_prefix: https://registry.identifiers.org/registry/zfin/
   generic_urls:
     - http://zfin.org/
   entity_types:
     - type_name: gene
       type_id: SO:0000704
       id_syntax: ZDB-(TRNAG|LINCRNAG|MIRNAG|NCRNAG|SNORNAG|GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+
-      url_syntax: http://zfin.org/[example_id]
+      url_syntax: https://www.alliancegenome.org/gene/ZFIN:[example_id]
       example_id: ZDB-GENE-990415-103
-      example_url: http://zfin.org/ZDB-GENE-990415-103
+      example_url: https://www.alliancegenome.org/gene/ZFIN:ZDB-GENE-990415-103
     - type_name: variation
       type_id: VariO:0001
       id_syntax: ZDB-(TRNAG|LINCRNAG|MIRNAG|NCRNAG|SNORNAG|GENE|GENO|MRPHLNO)-[0-9]{6}-[0-9]+
-      url_syntax: http://zfin.org/[example_id]
+      url_syntax: https://www.alliancegenome.org/gene/ZFIN:[example_id]
       example_id: ZDB-GENE-990415-103
-      example_url: http://zfin.org/ZDB-GENE-990415-103
+      example_url: https://www.alliancegenome.org/gene/ZFIN:ZDB-GENE-990415-103
 - database: TFClass
   name: TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains
   generic_urls: