Index

Symbols

--directory pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option --eager-versions pyobo-database-build command line option --force pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option --force-process pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option --identifier pyobo-lookup-alts command line option pyobo-lookup-definitions command line option pyobo-lookup-names command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option --include-has-member pyobo-lookup-hierarchy command line option --include-part-of pyobo-lookup-hierarchy command line option --index-force pyobo-obo-lexical-review command line option --index-url pyobo-obo-lexical-review command line option --key pyobo-lookup-properties command line option --location pyobo-obo-lexical-review command line option --no-strict pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option --relation pyobo-lookup-relations command line option --remove-obo pyobo-clean command line option --show-passed pyobo-obo-lexical-review command line option --skip-below pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option --skip-pyobo pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option --skip-upper pyobo-obo-lexical-review command line option --strict pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option

--summarize pyobo-lookup-relations command line option --target pyobo-lookup-mappings command line option pyobo-lookup-xrefs command line option --uri-prefix pyobo-obo-lexical-review command line option --verbose pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option --version pyobo command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option --zenodo pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option -f pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option -i pyobo-lookup-alts command line option pyobo-lookup-definitions command line option pyobo-lookup-names command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option -k pyobo-lookup-properties command line option -t pyobo-lookup-mappings command line option pyobo-lookup-xrefs command line option -v pyobo-database-alts command line option pyobo-database-build command line option pyobo-database-cache command line option pyobo-database-definitions command line option pyobo-database-edges command line option pyobo-database-mappings command line option pyobo-database-metadata command line option pyobo-database-names command line option pyobo-database-properties command line option pyobo-database-relations command line option pyobo-database-species command line option pyobo-database-synonyms command line option pyobo-database-typedefs command line option pyobo-lookup-alts command line option pyobo-lookup-ancestors command line option pyobo-lookup-definitions command line option pyobo-lookup-descendants command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-species command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option

A

ancestors() (Obo method) Annotation (class in pyobo) annotations (Synonym attribute) append_broad_match() (Term method)

append_exact_match() (Term method) append_narrow_match() (Term method) append_related_match() (Term method) append_see_also_uri() (Term method) auto_generated_by (Obo attribute)

B

bioversions_key (Obo attribute) build_ontology() (in module pyobo)

builtin (Term attribute) (TypeDef attribute)

C

check_bioregistry_prefix (Obo attribute) check_should_cache() (in module pyobo.constants) check_should_force() (in module pyobo.constants) check_should_use_tqdm() (in module pyobo.constants) cli() (Obo class method)

comment (TypeDef attribute) created_by (TypeDef attribute) creation_date (TypeDef attribute) CURIE pyobo-lookup-ancestors command line option pyobo-lookup-descendants command line option

D

data_version (Obo attribute) DatabaseKwargs (typeddict in pyobo.constants) date (Obo attribute) date_formatted (Obo attribute) default() (Term class method) (TypeDef class method) default_reference() (in module pyobo)

definition (Term attribute) (TypeDef attribute) descendants() (Obo method) disjoint_from (Term attribute) (TypeDef attribute) disjoint_over (TypeDef attribute) domain (TypeDef attribute) dynamic_version (Obo attribute)

E

edges_header (Obo attribute) ensure_path() (in module pyobo) equivalent_to (Term attribute) (TypeDef attribute)

equivalent_to_chain (TypeDef attribute) extend_parents() (Term method) extend_relationship() (Term method)

F

float() (Annotation class method) force (Obo attribute) format (OntologyPathPack attribute)

from_obo_path() (in module pyobo) from_obonet() (in module pyobo) from_triple() (Term class method) (TypeDef class method)

G

get_alts_to_id() (in module pyobo) get_ancestors() (in module pyobo) get_children() (in module pyobo) get_cls_cli() (Obo class method) get_definition() (in module pyobo) get_descendants() (in module pyobo) get_edges() (in module pyobo) get_edges_df() (in module pyobo) (Obo method) get_filtered_multixrefs_mapping() (Obo method) get_filtered_properties_df() (in module pyobo) (Obo method) get_filtered_properties_mapping() (in module pyobo) (Obo method) get_filtered_properties_multimapping() (in module pyobo) (Obo method) get_filtered_relations_df() (in module pyobo) (Obo method) get_filtered_xrefs() (in module pyobo) get_filtered_xrefs_mapping() (Obo method) get_graph() (in module pyobo) get_graph_embeddings_df() (in module pyobo) get_grounder() (in module pyobo) (Obo method) get_hierarchical_predicates() (Obo class method) get_hierarchy() (in module pyobo) get_id_alts_mapping() (Obo method) get_id_definition_mapping() (in module pyobo) (Obo method) get_id_multirelations_mapping() (in module pyobo) (Obo method) get_id_name_mapping() (in module pyobo) (Obo method) get_id_species_mapping() (in module pyobo) (Obo method) get_id_synonyms_mapping() (in module pyobo) (Obo method) get_id_to_alts() (in module pyobo) get_ids() (in module pyobo) (Obo method) get_literal_mappings() (in module pyobo) (Obo method) get_literal_mappings_df() (in module pyobo) (Obo method) get_literal_mappings_subset() (in module pyobo) get_literal_properties() (in module pyobo) get_literal_properties_df() (in module pyobo) (Obo method) get_mappings_df() (in module pyobo) (Obo method) get_metadata() (in module pyobo) (Obo method) get_name() (in module pyobo) get_name_by_curie() (in module pyobo) get_name_id_mapping() (in module pyobo)

get_object_properties() (in module pyobo) get_object_properties_df() (in module pyobo) (Obo method) get_obsolete() (in module pyobo) (Obo method) get_ofn_from_obo() (in module pyobo.struct.functional) get_ontology() (in module pyobo) get_ontology_annotations() (in module pyobo.struct.functional) get_ontology_axioms() (in module pyobo.struct.functional) get_primary_curie() (in module pyobo) get_primary_identifier() (in module pyobo) get_primary_reference() (in module pyobo) get_properties() (in module pyobo) get_properties_df() (in module pyobo) (Obo method) get_property() (in module pyobo) (Term method) get_property_literals() (Term method) get_references() (in module pyobo) get_relation() (in module pyobo) (Obo method) get_relation_mapping() (in module pyobo) (Obo method) get_relation_multimapping() (Obo method) get_relations_df() (in module pyobo) (Obo method) get_scispacy_entities() (in module pyobo) (in module pyobo.ner.scispacy_utils) get_scispacy_entity_linker() (in module pyobo) (in module pyobo.ner.scispacy_utils) get_scispacy_knowledgebase() (in module pyobo) (in module pyobo.ner.scispacy_utils) get_semantic_mapping_metadata() (in module pyobo) (in module pyobo.constants) get_semantic_mappings() (in module pyobo) (Obo method) get_species() (in module pyobo) (Term method) get_sssom_df() (in module pyobo) get_subhierarchy() (in module pyobo) get_synonyms() (in module pyobo) get_term_axioms() (in module pyobo.struct.functional) get_text_embedding() (in module pyobo) get_text_embedding_similarity() (in module pyobo) get_text_embeddings_df() (in module pyobo) get_typedef_axioms() (in module pyobo.struct.functional) get_typedef_df() (in module pyobo) (Obo method) get_typedef_id_name_mapping() (Obo method) get_version() (in module pyobo) get_xref() (in module pyobo) get_xrefs() (in module pyobo) get_xrefs_df() (in module pyobo) GetOntologyKwargs (typeddict in pyobo.constants) ground() (in module pyobo)

H

has_ancestor() (in module pyobo) has_nomenclature_plugin() (in module pyobo)

hierarchy (Obo attribute) holds_over_chain (TypeDef attribute)

I

idspaces (Obo attribute) imports (Obo attribute) intersection_of (Term attribute) (TypeDef attribute) inverse (TypeDef attribute) is_anonymous (Term attribute) (TypeDef attribute) is_anti_symmetric (TypeDef attribute) is_class_level (TypeDef attribute) is_cyclic (TypeDef attribute) is_descendant() (Obo method) is_descendent() (in module pyobo) is_functional (TypeDef attribute) is_inverse_functional (TypeDef attribute) is_metadata_tag (TypeDef attribute) is_obsolete (Term attribute) (TypeDef attribute) is_reflexive (TypeDef attribute) is_symmetric (TypeDef attribute) is_transitive (TypeDef attribute) iter_literal_properties() (Obo method) iter_nomenclature_plugins() (in module pyobo) iter_object_properties() (Obo method) iter_only (Obo attribute) iter_relation_rows() (Obo method)

iter_terms() (Obo method) iter_typedef_id_name() (Obo method) iterate_alt_rows() (Obo method) iterate_alts() (Obo method) iterate_edge_rows() (Obo method) iterate_edges() (Obo method) iterate_filtered_properties() (Obo method) iterate_filtered_relations() (Obo method) iterate_filtered_relations_filtered_targets() (Obo method) iterate_filtered_xrefs() (Obo method) iterate_id_definition() (Obo method) iterate_id_name() (Obo method) iterate_id_species() (Obo method) iterate_ids() (Obo method) iterate_literal_mapping_rows() (Obo method) iterate_node_rows() (Obo method) iterate_obo_lines() (Obo method) (Term method) (TypeDef method) iterate_properties() (Obo method) iterate_references() (Obo method) iterate_relations() (Obo method) iterate_synonym_rows() (Obo method) iterate_synonyms() (Obo method) iterate_xrefs() (Obo method) IterHelperHelperDict (typeddict in pyobo.constants)

L

language (Synonym attribute)

literal_properties_header (Obo attribute)

M

module pyobo pyobo.constants pyobo.ner.scispacy_utils pyobo.struct.functional

N

name (Obo attribute) (Synonym attribute)

namespace (Term attribute) (TypeDef attribute) nodes_header (Obo attribute)

O

object_properties_header (Obo attribute) Obo (class in pyobo) ontology (Obo attribute)

ontology_iri (Obo attribute) ontology_version_iri (Obo attribute) OntologyPathPack (class in pyobo.constants)

P

parents (Term attribute) (TypeDef attribute) path (OntologyPathPack attribute) predicate (Annotation attribute) (Synonym attribute) PREFIX pyobo-lookup-alts command line option pyobo-lookup-definitions command line option pyobo-lookup-hierarchy command line option pyobo-lookup-ids command line option pyobo-lookup-mappings command line option pyobo-lookup-metadata command line option pyobo-lookup-names command line option pyobo-lookup-prefixes command line option pyobo-lookup-properties command line option pyobo-lookup-relations command line option pyobo-lookup-synonyms command line option pyobo-lookup-typedefs command line option pyobo-lookup-xrefs command line option pyobo-obo-lexical-review command line option properties (Term attribute) (TypeDef attribute) properties_header (Obo attribute) property_values (Obo attribute) provenance (Synonym attribute) pyobo module pyobo command line option --version pyobo-clean command line option --remove-obo pyobo-database-alts command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-build command line option --directory --eager-versions --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-cache command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-definitions command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-edges command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-mappings command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-metadata command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-names command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-properties command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-relations command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-species command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-synonyms command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-database-typedefs command line option --directory --force --force-process --no-strict --skip-below --skip-pyobo --strict --verbose --zenodo -f -v pyobo-lookup-alts command line option --force --force-process --identifier --no-strict --strict --verbose --version -f -i -v PREFIX

pyobo-lookup-ancestors command line option --force --force-process --no-strict --strict --verbose --version -f -v CURIE pyobo-lookup-definitions command line option --force --force-process --identifier --no-strict --strict --verbose --version -f -i -v PREFIX pyobo-lookup-descendants command line option --force --force-process --no-strict --strict --verbose --version -f -v CURIE pyobo-lookup-hierarchy command line option --force --force-process --include-has-member --include-part-of --no-strict --strict --verbose --version -f -v PREFIX pyobo-lookup-ids command line option --force --force-process --no-strict --strict --verbose --version -f -v PREFIX pyobo-lookup-mappings command line option --force --force-process --no-strict --strict --target --verbose --version -f -t -v PREFIX pyobo-lookup-metadata command line option --force --force-process --no-strict --strict --verbose --version -f -v PREFIX pyobo-lookup-names command line option --force --force-process --identifier --no-strict --strict --verbose --version -f -i -v PREFIX pyobo-lookup-prefixes command line option --force --force-process --no-strict --strict --verbose --version -f -v PREFIX pyobo-lookup-properties command line option --force --force-process --key --no-strict --strict --verbose --version -f -k -v PREFIX pyobo-lookup-relations command line option --force --force-process --no-strict --relation --strict --summarize --verbose --version -f -v PREFIX pyobo-lookup-species command line option --force --force-process --identifier --no-strict --strict --verbose --version -f -i -v pyobo-lookup-synonyms command line option --force --force-process --identifier --no-strict --strict --verbose --version -f -i -v PREFIX pyobo-lookup-typedefs command line option --force --force-process --no-strict --strict --verbose --version -f -v PREFIX pyobo-lookup-xrefs command line option --force --force-process --no-strict --strict --target --verbose --version -f -t -v PREFIX pyobo-obo-lexical-review command line option --index-force --index-url --location --show-passed --skip-upper --uri-prefix PREFIX pyobo.constants module pyobo.ner.scispacy_utils module pyobo.struct.functional module

R

range (TypeDef attribute) rdf_format (OntologyPathPack attribute) Reference (in module pyobo) reference (SynonymTypeDef attribute) (Term attribute) (TypeDef attribute)

relations_header (Obo attribute) relationships (Term attribute) (TypeDef attribute) root_terms (Obo attribute) run_nomenclature_plugin() (in module pyobo)

S

set_species() (Term method) skip_maintainers (Obo attribute) SlimGetOntologyKwargs (typeddict in pyobo.constants) specificity (Synonym attribute) (SynonymTypeDef attribute) static_version (Obo attribute) string() (Annotation class method)

subsetdefs (Obo attribute) subsets (Term attribute) (TypeDef attribute) Synonym (class in pyobo) synonym_typedefs (Obo attribute) synonyms (Term attribute) (TypeDef attribute) SynonymTypeDef (class in pyobo)

T

Term (class in pyobo) to_obo() (Synonym method) (SynonymTypeDef method) to_obonet() (Obo method) transitive_over (TypeDef attribute)

type (Synonym attribute) (Term attribute) (TypeDef attribute) TypeDef (class in pyobo) typedefs (Obo attribute)

U

union_of (Term attribute) (TypeDef attribute)

uri() (Annotation class method)

V

value (Annotation attribute)

W

write_cache() (Obo method) write_default() (Obo method) write_edges() (Obo method) write_metadata() (Obo method) write_nodes() (Obo method) write_obo() (Obo method)

write_obograph() (Obo method) write_obonet_gz() (Obo method) write_ofn() (Obo method) write_owl() (Obo method) write_prefix_map() (Obo method) write_rdf() (Obo method) write_skos() (Obo method)

X

xrefs (Term attribute) (TypeDef attribute)