Man pages for xu-hong/rphenoscape
Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase
| 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_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_data | Get data from an API endpoint |
| get_KBinfo | Summary and metadata about the Phenoscape KB |
| 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... |
| 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_relation | Test which candidate terms are ancestors or descendants of a... |
| mutual_exclusivity_pairwise | Determine whether two phenotypes are mutually exclusive |
| mutually_exclusive | Determine mutual exclusivity between two or more phenotypes |
| nexml_drop | Drop parts of a nexml object |
| obo_prefix | Extract the OBO ontology prefix from IRIs |
| owl | OWL Objects |
| pa_dep_matrix | Obtains a presence-absence dependency matrix |
| phenotype | Phenotype Objects |
| phenotype_matches | Which phenotypes match filter |
| pkb_args_to_query | Creates a list of named query parameters |
| profile_similarity | 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... |
| rphenoscape-deprecated | Deprecated functions in 'rphenoscape'. |
| 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 |
| terminfo | Terminfo Objects |
| term_iri | Obtain IRI(s) for canonical terms and properties |
| terms | Get term details (ID, label, definition) |
