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Generify OBO Classes/Properties (INTERNAL)

generify_obo.Rd

format_axiom() internal helper that replaces URI/CURIEs defined by OBO ontologies with namespace-prefixed descriptions/types, where defined internally, or just the namespace. Will not modify non-OBO class URI/CURIEs.

Usage

generify_obo(x)

Arguments

x

Complete logical axioms in OWL functional syntax, as a character vector.

Internally-defined OBO namespace-types

The following namespaces have 'namespace:types' defined by this function:

  • CL: 'CL:cell'

  • CHEBI: 'CHEBI:chemical'

  • DISDRIV: 'DISDRIV:disease_driver'

  • DOID: 'DOID:disease'

  • FOODON: 'FOODON:food_material'

  • ECO: 'ECO:evidence'

  • GENO: 'GENO:inheritance_pattern'

  • NCBITaxon: 'NCBITaxon:organism'

  • MIM: 'MIM:susceptibility'

  • OMIM: 'MIM:susceptibility'

  • UBERON: 'UBERON:anatomy'

  • UPHENO: 'UPHENO:phenotype'

  • SO: 'SO:sequence'

  • SYMP: 'SYMP:symptom'

  • TRANS: 'TRANS:pathogen_transmission'

Ontologies with multiple object types used by the DO (e.g. HP, onset or phenotype), that are imported via DISDRIV (e.g. ExO), or used for their properties (e.g. RO) are not defined internally and will be formatted namespace only. .