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

pk_taxon_detail(term, verbose = FALSE)

pk_anatomical_detail(term, verbose = FALSE)

pk_phenotype_detail(term, verbose = FALSE)

pk_gene_detail(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 pk_taxon_detail, pk_anatomical_detail, and pk_phenotype_detail, respectively.

For pk_taxon_detail this can also be a list (or vector) of terms (taxa).

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 pk_taxon_detail, 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 pk_anatomical_detail and pk_phenotype_detail, the additional column is "definition".

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

Examples

pk_taxon_detail("Coralliozetus")
#> id label extinct #> 1 http://purl.obolibrary.org/obo/VTO_0042955 Coralliozetus FALSE #> rank.id rank.label common_name #> 1 http://purl.obolibrary.org/obo/TAXRANK_0000005 genus <NA>
pk_anatomical_detail("basihyal bone")
#> label #> 1 basihyal bone #> definition #> 1 Replacement bone that is median and is the anterior-most bone of the ventral hyoid arch. #> id #> 1 http://purl.obolibrary.org/obo/UBERON_0011618
pk_gene_detail("socs5")
#> id label matchType #> 1 http://xenbase.org/XB-GENEPAGE-479592 socs5 exact #> 2 http://www.informatics.jax.org/marker/MGI:2385459 Socs5 exact #> 3 http://zfin.org/ZDB-GENE-061013-408 socs5a partial #> 4 http://zfin.org/ZDB-GENE-080722-18 socs5b partial #> taxon.id taxon.label #> 1 http://purl.obolibrary.org/obo/NCBITaxon_8353 Xenopus #> 2 http://purl.obolibrary.org/obo/NCBITaxon_10090 Mus musculus #> 3 http://purl.obolibrary.org/obo/NCBITaxon_7955 Danio rerio #> 4 http://purl.obolibrary.org/obo/NCBITaxon_7955 Danio rerio