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Xenbase

Xenbase is a web-accessible resource that integrates all the diverse biological, genomic, genotype and phenotype data available from Xenopus research.

Xenbase Bulk Data Xenbase FTP

Gene to Phenotype

This ingest is built against a one-off OBAN formatted file, which makes for a transformation which only requries adding a curie prefix and connecting column names to biolink attributes. Evidence codes are provided as ECO terms but not yet captured in the output.

Biolink captured

  • biolink:Gene

    • id

  • biolink:PhenotypicFeature

    • id

  • biolink:GeneToPhenotypicFeatureAssociation

    • id (random uuid)
    • subject (gene.id)
    • predicate (has_phenotype)
    • object (phenotypicFeature.id)
    • publications
    • aggregating_knowledge_source (["infores:monarchinitiative"])
    • primary_knowledge_source (infores:xenbase)

Gene Literature

This ingest reads from Xenbase's Genes Associated with Literature file to capture associations between Xenbase's XB-GENEPAGE ids and PMIDs, then relies on a map built from Xenbase's GenepageToGeneId file to create associations from XB-GENE records to PMID records.

Biolink captured

  • Gene

    • id

  • Publication

    • id

  • InformationContentEntityToNamedThingAssociation

    • id (random uuid)
    • subject (gene.id)
    • predicate (mentions)
    • object (publication.id)
    • aggregating_knowledge_source (["infores:monarchinitiative"])
    • primary_knowledge_source (infores:xenbase)

Citation

Fisher et al. 2023, Genetics, 2023;, iyad018, doi:10.1093/genetics/iyad018 (Xenbase / PubMed / Genetics)