terms: Get term details (ID, label, definition)

In xu-hong/rphenoscape: Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase

Get term details (ID, label, definition)

Description

Retrieve details about a taxon, an anatomical structure, a gene, or a phenotypic quality.

Usage

taxon_info(term, includeRelatedSynonyms = FALSE, verbose = FALSE)

anatomy_term_info(term, verbose = FALSE)

phenotypic_quality_term_info(term, verbose = FALSE)

gene_info(term, taxon = NA, verbose = FALSE)

Arguments

term	character, the query term, either as name or IRI. Names are looked up against taxonomies, anatomy ontologies, and PATO for taxon_info, anatomy_term_info, and phenotypic_quality_term_info, respectively. For taxon_info this can also be a list (or vector) of terms (taxa).
includeRelatedSynonyms	logical: optional. If TRUE when looking up the IRI for a term label, matches against related synonyms will be included.
verbose	logical, whether informative messages should be printed. The default is FALSE.
taxon	character, the NCBI taxon name or corresponding NCBITaxon ontology IRI for which to match the gene name.

Value

A data.frame, with at least columns "id" and "label".

For taxon_info, additional columns are "extinct" (logical), "rank.id", "rank.label", and where available "common_name". The rows corresponding to taxon names that failed to be resolved to IRIs will be NA.

For anatomy_term_info and phenotypic_quality_term_info, the additional column is "definition".

For gene_info, the additional columns are "taxon.id" and "taxon.label" for the corresponding NCBI Taxonomy ID and name, and "matchType" ('exact' or 'partial').

Examples

taxon_info("Coralliozetus")
taxon_info("Chrosomus eos", includeRelatedSynonyms = TRUE)
anatomy_term_info("basihyal bone")
gene_info("socs5")

xu-hong/rphenoscape documentation built on Oct. 30, 2024, 8:43 a.m.