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  1. NIF
  2. NIF-11839

Refactor views to use NCBIGene as prefix for those gene ids

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    • NIF
    • Issues closed as MONARCH has transitioned from UCSD services

    Description

      We want to standardize the id prefixes used in the Monarch and NIF sources, with a first sweep to be on NCBI gene identifiers.

      I know in some places we use NCBI_Gene, others NCBI_gene or NCBIgene, and still others have no prefix.

      We need to review and curate all resources with NCBI gene identifiers with the appropriate prefix, and document our method.

      Chris M suggests eliminating the underscore in the prefix so as to make sure we don't run into any issues with id conversion (particularly with owl/rdf), however, note that the GO.xref_abbs does use an underscore:
      https://neuinfo.org/mynif/search.php?q=NCBI_gene&t=indexable&nif=nif-0000-02915-4&b=0&r=20

      abbreviation: NCBI_Gene
      database: NCBI Gene
      object: Identifier
      synonym: GeneID
      synonym: LocusID
      example_id: NCBI_Gene:4771
      local_id_syntax: ^\d+$
      generic_url: http://www.ncbi.nlm.nih.gov/
      url_syntax: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=[example_id]
      url_example: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=4771
      !entity_type: SO:0000704 ! gene
      

      Chris and Anita, please comment to finalize the idspace designation, and then I will begin reviewing/reindexing.

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            nlw Nicole Washington
            nlw Nicole Washington
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