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)
term | character, the query term, either as name or IRI. Names are looked
up against taxonomies, anatomy ontologies, and PATO for For |
---|---|
verbose | logical, whether informative messages should be printed. The
default is |
taxon | character, the NCBI taxon name or corresponding NCBITaxon ontology IRI for which to match the gene name. |
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').
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 isDefinedBy #> 1 basihyal bone http://purl.obolibrary.org/obo/uberon.owl #> 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_0011618pk_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