Function reference • rphenoscape

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_char_matrix()`	Obtains a character-state matrix from a nexml object
`get_char_matrix_meta()`	Obtains taxa and character metadata from a nexml object
`get_json_data()` `get_csv_data()` `get_nexml_data()` `get_plain_text()`	Get data from an API endpoint
`get_ontotrace_data()`	Obtain a synthetic presence/absence matrix
`get_phenotypes()`	Retrieve phenotypes by entity, quality, taxon, and study
`get_studies()`	Query the list of studies by taxa, anatomical entities, and qualities.
`get_study_data()`	get_study_data
`get_term_iri()`	Find the IRI of the term matching a text query
`get_term_label()`	Obtains the labels for a list of terms
`is_extinct()`	Determine which taxa are extinct
`is_descendant()` `is_ancestor()`	Test which candidate terms are ancestors or descendants of a term
`mutual_exclusivity_pairwise()`	Determine whether two phenotypes are mutually exclusive
`mutually_exclusive()`	Determine mutual exclusivity between two or more phenotypes
`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
`as.owl()` `is.owl()` `is.manchester_owl()`	OWL Objects
`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
`pkb_args_to_query()`	Creates a list of named query parameters
`profile_similarity()` `bestPairs()` `reduce.ignoringDiag()`	Semantic similarity between profiles
`rclean_jsonld_names()`	Clean JSON-LD names in a list/data.frame
`resolve_label_expression()`	Convert a label-based class expression in OWL Manchester syntax into an expression composed of IRIs.
`tanimoto_similarity()` `jaccard_similarity()` `cosine_similarity()` `resnik_similarity()`	Compute semantic similarity metrics between terms
`state_symbols2labels()`	Translates state symbols to labels in a character matrix
`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_classification()`	Get term classification
`term_freqs()`	Obtains term frequencies for the Phenoscape KB
`partOf_iri()` `hasPart_iri()` `developsFrom_iri()` `term_iri()`	Obtain IRI(s) for canonical terms and properties
`as.terminfo()` `is.terminfo()` `is_valid_terminfo()` `print(<terminfo>)`	Terminfo Objects
`taxon_info()` `anatomy_term_info()` `phenotypic_quality_term_info()` `gene_info()`	Get term details (ID, label, definition)

Reference

All functions