resourceDescriptors.yaml

# AGR Schema Resource Descriptors YAML.
# When submitting identifiers, please use the appropriate example_id/gid field listed below.

#
# MGI
#

- db_prefix: MGI
  name: MGI
  example_id: MGI:80863
  gid_pattern: "^MGI:\d+$"
  default_url: 
  pages:
    - name: gene  
      url: http://www.informatics.jax.org/accession/MGI:[%s]

# MGI
#

- db_prefix: MGD_old
  name: MGD_old
  example_id: MGD_old:MGD-MRK-11588
  gid_pattern: "^MGD_old:MGD-[A-Z]+-\d+$"
  default_url:   
  pages:
    - name: gene
      url: http://www.informatics.jax.org/accession/[%s]

- db_prefix: WIKIP
  name: Wikipedia
  example_id: WIKIP:BRCA2
  gid_pattern: "^WIKIP:\S+$"
  default_url: https://en.wikipedia.org/wiki/[%s]


#
# RGD
#

- db_prefix: RGD
  name: RGD
  example_gid: RGD:1311419
  gid_pattern: "^RGD:\d+$"
  default_url: 
  pages:
    - name: gene
      url: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=RGD:[%s]

#
# ZFIN
#

- db_prefix: ZFIN
  name: ZFIN
  example_gid: ZFIN:ZDB-GENE-030131-9438
  gid_pattern: "^ZFIN:\S+$"
  default_url: 
  pages:
    - name: gene
      url: https://zfin.org/[%s]
    - name: gene/expression
      url: https://zfin.org/action/marker/[%s]/expression
    - name: gene/wild_type_expression
      description: "Wild type expression data"
      url: https://zfin.org/action/marker/[%s]/wt_expression
    - name: gene/references
      url: https://zfin.org/[%s]
    - name: allele
      url: https://zfin.org/[%s]
    - name: genotype
      url: https://zfin.org/[%s]
 
#
# FlyBase
#

- db_prefix: FB
  name: FlyBase
  example_gid: FB:FBgn0000490
  gid_pattern: "^FB:FB\w+$"
  default_url: 
  pages:
    - name: gene
      url: http://flybase.org/reports/[%s].html
    - name: gene/expression
      url: http://flybase.org/reports/[%s].html#expression_data
    - name: gene/references
      url: http://flybase.org/reports/[%s].html#pubs
    - name: allele
      url: http://flybase.org/reports/[%s].html
    - name: strain
      url: http://flybase.org/reports/[%s].html

#
# WormBase
#

- db_prefix: WB
  name: WormBase genes
  example_gid: WB:WBGene00000064
  gid_pattern: "^WB:WB\w+$"
  default_url: http://www.wormbase.org/db/get?name=[%s];class=Gene
  pages:
    - name: gene
      url: http://www.wormbase.org/db/get?name=[%s];class=Gene
    - name: gene/expression
      url: http://www.wormbase.org/db/get?name=[%s];class=Gene;widget=expression
    - name: gene/interactions
      url: http://www.wormbase.org/db/get?name=[%s];class=Gene;widget=interactions
    - name: gene/references
      url: http://www.wormbase.org/db/get?name=[%s];class=Gene;widget=references

- db_prefix: WBRef
  name: WormBase references
  example_gid: WBRef:WBPaper00050597
  gid_pattern: "^WBRef:WBPaper\d+$"
  default_url: http://www.wormbase.org/db/get?name=[%s];class=Paper
  pages:
    - name: reference
      url: http://www.wormbase.org/db/get?name=[%s];class=Paper

- db_prefix: WBVar
  name: WormBase variations
  example_gid: WBVar:WBVar:WBVar00000001
  gid_pattern: "^WBVar:WBVar\d+$"
  default_url: http://www.wormbase.org/db/get?name=[%s];class=Variation
  pages:
    - name: variation
      url: http://www.wormbase.org/db/get?name=[%s];class=Variation

- db_prefix: WBStrain
  name: WormBase strains
  example_gid: WBStrain:N2
  gid_pattern: "^WBStrain:\S+$"
  default_url: http://www.wormbase.org/db/get?name=[%s];class=Strain
  pages:
    - name: strain
      url: http://www.wormbase.org/db/get?name=[%s];class=Strain

- db_prefix: WBTransgene
  name: WormBase Transgenes
  example_gid: WBTransgene:xxxxxx
  gid_pattern: "^WBTransgene:\S+$"
  default_url: http://www.wormbase.org/db/get?name=[%s];class=Transgene
  pages:
    - name: transgene  
      url: http://www.wormbase.org/db/get?name=[%s];class=Transgene

- db_prefix: WBls
  name: WormBase life-stage Ontology
  example_gid: WBls:0000001
  gid_pattern: "^WBls:\d+$"
  default_url: http://www.wormbase.org/db/get?name=WBls:[%s];class=Life_stage
  pages:
    - name: ontology_term
      url: http://www.wormbase.org/db/get?name=WBls:[%s];class=Life_stage

- db_prefix: WBbt
  name: WormBase anatomy Ontology
  example_gid: WBbt:0008611
  gid_pattern: "^WBbt:\d+$"
  default_url: http://www.wormbase.org/db/get?name=WBbt:[%s];class=Anatomy
  pages:
    - name: ontology_term
      url: http://www.wormbase.org/db/get?name=WBbt:[%s];class=Anatomy

- db_prefix: WBPhenotype
  name: WormBase Phenotype Ontology
  example_gid: WBPhenotype:0000517
  gid_pattern: "^WBPhenotype:\d+$"
  default_url: http://www.wormbase.org/db/get?name=WBPhenotype:[%s];class=Phenotype
  pages:
    - name: ontology_term
      url: http://www.wormbase.org/db/get?name=WBPhenotype:[%s];class=Phenotype

- db_prefix: WB_SPELL
  name: WormBase SPELL
  example_gid: WB_SPELL:eat-4
  gid_pattern: "^WB_SPELL:\w+$"
  default_url: 
  pages:
    - name: gene/spell
      url: http://spell.caltech.edu:3000/search/show_listing?search_string=[%s]


#
# SGD
#

- db_prefix: SGD
  name: SGD genes
  example_gid: SGD:S000001855
  gid_pattern: "^SGD:\w+$"
  default_url: 
  pages:
  - name: gene
    url: http://www.yeastgenome.org/locus/[%s]
  - name: gene/expression
    url: http://www.yeastgenome.org/locus/[%s]/expression
  - name: gene/interactions
    url: http://www.yeastgenome.org/locus/[%s]/interaction
  - name: spell
    url: http://spell.yeastgenome.org/search/show_listing?search_string=[%s]

#
# GO
#

- db_prefix: GO
  name: Gene Ontology
  example_gid: GO:0045860
  gid_pattern: "^GO:\d+$"
  default_url: http://amigo.geneontology.org/amigo/term/GO:[%s] 

#
# External resources
#

- db_prefix: HGNC
  name: HGNC
  example_gid: HGNC:33510
  gid_pattern: "^HGNC:\d+$"
  default_url: http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:[%s]
  pages:
  - name: gene
    url: http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:[%s]

- db_prefix: NCBI_Gene
  name: NCBI Gene
  example_gid: NCBI_Gene:33432
  gid_pattern: "^NCBI_Gene:\d+$"
  default_url: https://www.ncbi.nlm.nih.gov/gene/[%s]

- db_prefix: UniProtKB
  name: UniProtKB
  example_gid: UniProtKB:P07713
  gid_pattern: "^UniProtKB:\w+$"
  default_url: http://www.uniprot.org/uniprot/[%s]

- db_prefix: ENSEMBL
  name: Ensembl
  example_id: ENSEMBL:FBgn0000490
  gid_pattern: "^ENSEMBL:\w+$"
  default_url: http://www.ensembl.org/id/[%s] 

- db_prefix: RNAcentral
  name: RNAcentral
  example_gid: RNAcentral:URS000075C808
  gid_pattern: "^RNAcentral:\w+$"
  default_url: http://rnacentral.org/rna/[%s]

- db_prefix: PMID
  name: PubMed
  example_gid: PMID:26447131
  gid_pattern: "^PMID:\d+$"
  default_url: https://www.ncbi.nlm.nih.gov/pubmed/[%s]

- db_prefix: DRSC
  name: DRSC
  example_gid: DRSC:FBgn0000490
  gid_pattern: "^DRSC:\S+$"
  default_url: 
    
- db_prefix: NCBITaxon
  name: NCBI Taxonomy
  example_gid: NCBITaxon:7227
  gid_pattern: "^NCBITaxon:\d+$"
  default_url: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[%s]

- db_prefix: SO
  name: Sequence Ontology
  example_gid: SO:0001217
  gid_pattern: "^SO:\d+$"
  default_url: http://www.sequenceontology.org/browser/current_svn/term/SO:[%s]

- db_prefix: DOID
  name: Disease Ontology
  example_gid: DOID:820
  gid_pattern: "^DOID:\d+$"
  default_url: 

- db_prefix: ZECO
  name: Zebrafish Environment Condition Ontology
  example_gid: ZECO:0000103
  gid_pattern: "^ZECO:\d+$"
  default_url: https://zfin.org/action/ontology/term-detail/ZECO:[%s]

- db_prefix: CHEBI
  name: Chemical Entities of Biological Interest Ontology
  example_gid: CHEBI:53438
  gid_pattern: "^CHEBI:\d+$"
  default_url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=[%s]

- db_prefix: ZFA
  name: Zebrafish Anatomy Ontology
  example_id: ZFA:0001327
  gid_pattern: "^ZFA:\d+$"
  default_url: http://zfin.org/action/ontology/term-detail/ZFA:[%s]

- db_prefix: PANTHER
  name: PANTHER
  example_id: PANTHER:PTHR11662
  gid_pattern: "^PANTHER:PTHR\d+$"
  default_url: http://pantherdb.org/panther/family.do?clsAccession=[%s]