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Dictybase

Dictybase is a comprehensive database for the ameboid protozoan Dictyostelium discoideum, which is a powerful model system for genetic and functional analysis of gene function.

Gene Information

Dictybase genes in the Gene to Phenotype ingest (below) are either directly identified from their gene identifier, mapped directly to NCBI Dictyostelium discoideum gene identifier mappings or mapped indirectly from the Dictybase identifier, names and synonyms mappings, with synonyms being populated as available (Note: full gene product information is not captured at this time).

Gene to Phenotype

Data is available in a well-documented easy-to-parse GAF-like format with associations to an UPHENO-compliant ontology. Phenotypes are linked to Strains, and the Strains are linked to Genes.

Biolink Captured

  • biolink:Gene

    • 'id' (NCBI or Dictybase)
    • 'category'
    • 'name'
    • 'symbol'
    • 'in_taxon'
    • 'source'

  • biolink:PhenotypicFeature

    • id

  • biolink:GeneToPhenotypicFeatureAssociation

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

Citation

Fey, P., Dodson, R., Basu, S., Chisholm, R. L. (2013). 'One Stop Shop for Everything Dictyostelium: dictyBase and the Dicty Stock Center'. Dictyostelium discoideum Protocols. Methods Mol. Biol. 983:59-92, edited by Ludwig Eichinger and Francisco Rivero.