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)