Retrieve details about a taxon, an anatomical structure, a gene, or a phenotypic quality.
taxon_info(term, verbose = FALSE)
anatomy_term_info(term, verbose = FALSE)
phenotypic_quality_term_info(term, verbose = FALSE)
gene_info(term, taxon = NA, verbose = FALSE)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).
logical, whether informative messages should be printed. The
default is FALSE.
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 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').
taxon_info("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>
anatomy_term_info("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_0011618
gene_info("socs5")
#> id label matchType
#> 1 http://www.informatics.jax.org/accession/MGI:2385459 Socs5 exact
#> 2 http://zfin.org/ZDB-GENE-061013-408 socs5a partial
#> 3 http://zfin.org/ZDB-GENE-080722-18 socs5b partial
#> taxon.id taxon.label
#> 1 http://purl.obolibrary.org/obo/NCBITaxon_10090 Mus musculus
#> 2 http://purl.obolibrary.org/obo/NCBITaxon_7955 Danio rerio
#> 3 http://purl.obolibrary.org/obo/NCBITaxon_7955 Danio rerio