All functions

add_provenance_record()

Generate and add provenance record to nexml

anatomy_ontology_iris()

Get IRIs of ontologies with anatomy terms

corpus_size()

Obtain the size of different corpora

find_term()

Find terms matching a query text

get_KBinfo() print(<KBinfo>)

Summary and metadata about the Phenoscape KB

get_json_data() get_csv_data() get_nexml_data()

Get data from an API endpoint

get_phenotypes()

Retrieve phenotypes by entity, quality, taxon, and study

get_term_label()

Obtains the labels for a list of terms

nexml_drop_otu() nexml_drop_char() is_unused_char() is_unused_otu()

Drop parts of a nexml object

obo_prefix()

Extract the OBO ontology prefix from IRIs

pa_dep_matrix()

Obtains a presence-absence dependency matrix

as.phenotype() is.phenotype() is_valid_phenotype() charstates() chars() print(<phenotype>)

Phenotype Objects

phenotype_matches()

Which phenotypes match filter

pk_taxon_class() pk_anatomical_class() pk_phenotype_class()

Get term classification

pk_get_iri()

Resolve a text query to IRI

pk_get_ontotrace_xml()

Obtain a synthetic presence/absence matrix

pk_get_study()

pk_get_study

pk_get_study_list()

Query the list of studies by taxa, anatomical entities, and qualities.

pk_get_study_meta()

pk_get_study_meta

pk_get_study_xml()

pk_get_study_xml

pk_is_descendant() pk_is_ancestor()

Test which candidate terms are ancestors or descendants of a term

pk_is_extinct()

Determine which taxa are extinct

pk_get_ontotrace() pk_get_ontotrace_meta()

Returns a NeXML-format evolutionary character matrix.

pk_taxon_detail() pk_anatomical_detail() pk_phenotype_detail() pk_gene_detail()

Get term details (ID, label, definition)

pkb_args_to_query()

Creates a list of named query parameters

profile_similarity() bestPairs() reduce.ignoringDiag()

Semantic similarity between profiles

tanimoto_similarity() jaccard_similarity() cosine_similarity() resnik_similarity()

Compute semantic similarity metrics between terms

subsumer_matrix()

Obtains a subsumer matrix

taxon_ontology_iris()

Get IRIs of ontologies with taxonomy terms

term_category()

Determine the general category of terms

term_freqs()

Obtains term frequencies for the Phenoscape KB

partOf_iri() hasPart_iri() term_iri()

Obtain IRI(s) for canonical terms and properties