Index

Symbols

--directory pyobo-database-alts command line option pyobo-database-build 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-database-xrefs command line option --force pyobo-database-alts command line option pyobo-database-build 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-database-xrefs 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-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-database-xrefs 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-names pyobo-lookup-mappings command line option --include-part-of pyobo-lookup-hierarchy command line option --key pyobo-lookup-properties command line option --no-strict pyobo-database-alts command line option pyobo-database-build 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-database-xrefs 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 --skip-below pyobo-database-alts command line option pyobo-database-build 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-database-xrefs command line option --skip-pyobo pyobo-database-alts command line option pyobo-database-build 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-database-xrefs command line option --strict pyobo-database-alts command line option pyobo-database-build 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-database-xrefs 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-relations command line option pyobo-lookup-xrefs command line option --verbose pyobo-database-alts command line option pyobo-database-build 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-database-xrefs 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-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-database-xrefs command line option -f pyobo-database-alts command line option pyobo-database-build 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-database-xrefs 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-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-database-xrefs 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

AltMacro (class in pyobo.struct.functional.macros) ancestors() (Obo method) Annotation (class in pyobo.struct.functional.dsl) annotation_property (AltMacro attribute) (DescriptionMacro attribute) (IsAnonymousMacro attribute) (IsObsoleteMacro attribute) (LabelMacro attribute) AnnotationAssertion (class in pyobo.struct.functional.dsl) AnnotationAxiom (class in pyobo.struct.functional.dsl)

AnnotationProperty (class in pyobo.struct.functional.dsl) AnnotationPropertyDomain (class in pyobo.struct.functional.dsl) AnnotationPropertyRange (class in pyobo.struct.functional.dsl) annotations (Synonym attribute) append_exact_match() (Term method) append_see_also_uri() (Term method) Assertion (class in pyobo.struct.functional.dsl) AsymmetricObjectProperty (class in pyobo.struct.functional.dsl) auto_generated_by (Obo attribute) Axiom (class in pyobo.struct.functional.dsl)

B

Box (class in pyobo.struct.functional.dsl)

C

check_bioregistry_prefix (Obo attribute) ClassAssertion (class in pyobo.struct.functional.dsl)

ClassAxiom (class in pyobo.struct.functional.dsl) ClassExpression (class in pyobo.struct.functional.dsl) cli() (Obo class method)

D

data_version (Obo attribute) DataAllValuesFrom (class in pyobo.struct.functional.dsl) DataComplementOf (class in pyobo.struct.functional.dsl) DataExactCardinality (class in pyobo.struct.functional.dsl) DataHasValue (class in pyobo.struct.functional.dsl) DataIntersectionOf (class in pyobo.struct.functional.dsl) DataMaxCardinality (class in pyobo.struct.functional.dsl) DataMinCardinality (class in pyobo.struct.functional.dsl) DataOneOf (class in pyobo.struct.functional.dsl) DataPropertyAssertion (class in pyobo.struct.functional.dsl) DataPropertyAxiom (class in pyobo.struct.functional.dsl) DataPropertyDomain (class in pyobo.struct.functional.dsl) DataPropertyExpression (class in pyobo.struct.functional.dsl) DataPropertyRange (class in pyobo.struct.functional.dsl) DataRange (class in pyobo.struct.functional.dsl) DataSomeValuesFrom (class in pyobo.struct.functional.dsl) DatatypeDefinition (class in pyobo.struct.functional.dsl) DatatypeRestriction (class in pyobo.struct.functional.dsl)

DataUnionOf (class in pyobo.struct.functional.dsl) date (Obo attribute) date_formatted (Obo property) Declaration (class in pyobo.struct.functional.dsl) declare_wrapped_ope() (ObjectInverseOf method) default() (Term class method) (TypeDef class method) default_reference() (in module pyobo) definition (Term attribute) (TypeDef attribute) descendants() (Obo method) DescriptionMacro (class in pyobo.struct.functional.macros) DifferentIndividuals (class in pyobo.struct.functional.dsl) disjoint_over (TypeDef attribute) DisjointClasses (class in pyobo.struct.functional.dsl) DisjointDataProperties (class in pyobo.struct.functional.dsl) DisjointObjectProperties (class in pyobo.struct.functional.dsl) DisjointUnion (class in pyobo.struct.functional.dsl) dynamic_version (Obo attribute)

E

edges_header (Obo property) ensure_path() (in module pyobo) EquivalentClasses (class in pyobo.struct.functional.dsl)

EquivalentDataProperties (class in pyobo.struct.functional.dsl) EquivalentObjectProperties (class in pyobo.struct.functional.dsl) extend_parents() (Term method) extend_relationship() (Term method)

F

force (Obo attribute) from_obo_path() (in module pyobo) from_obonet() (in module pyobo)

from_triple() (Term class method) (TypeDef class method) FunctionalDataProperty (class in pyobo.struct.functional.dsl) FunctionalObjectProperty (class in pyobo.struct.functional.dsl)

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) (Obo method) get_grounder() (in module pyobo) 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_ontology() (in module pyobo) get_primary_curie() (in module pyobo) get_primary_identifier() (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_species() (in module pyobo) (Term method) get_sssom_df() (in module pyobo) get_subhierarchy() (in module pyobo) get_synonyms() (in module pyobo) 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) ground() (in module pyobo)

H

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

HasKey (class in pyobo.struct.functional.dsl) hierarchy (Obo property)

I

IDENTIFIER pyobo-lookup-ancestors command line option pyobo-lookup-descendants command line option idspaces (Obo attribute) InverseFunctionalObjectProperty (class in pyobo.struct.functional.dsl) InverseObjectProperties (class in pyobo.struct.functional.dsl) IrreflexiveObjectProperty (class in pyobo.struct.functional.dsl) is_descendant() (Obo method) is_descendent() (in module pyobo) is_metadata_tag (TypeDef attribute) is_obsolete (Term attribute) (TypeDef attribute) IsAnonymousMacro (class in pyobo.struct.functional.macros) IsObsoleteMacro (class in pyobo.struct.functional.macros) 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_mapping_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)

L

l() (in module pyobo.struct.functional.dsl) LabelMacro (class in pyobo.struct.functional.macros)

language (Synonym attribute) literal_properties_header (Obo property)

M

MappingMacro (class in pyobo.struct.functional.macros) module pyobo pyobo.struct.functional.dsl pyobo.struct.functional.macros

N

name (Obo attribute) (Synonym attribute)

namespace (Term attribute) NegativeDataPropertyAssertion (class in pyobo.struct.functional.dsl) NegativeObjectPropertyAssertion (class in pyobo.struct.functional.dsl)

O

object_properties_header (Obo property) ObjectAllValuesFrom (class in pyobo.struct.functional.dsl) ObjectComplementOf (class in pyobo.struct.functional.dsl) ObjectExactCardinality (class in pyobo.struct.functional.dsl) ObjectHasSelf (class in pyobo.struct.functional.dsl) ObjectHasValue (class in pyobo.struct.functional.dsl) ObjectIntersectionOf (class in pyobo.struct.functional.dsl) ObjectInverseOf (class in pyobo.struct.functional.dsl) ObjectMaxCardinality (class in pyobo.struct.functional.dsl) ObjectMinCardinality (class in pyobo.struct.functional.dsl)

ObjectOneOf (class in pyobo.struct.functional.dsl) ObjectPropertyAssertion (class in pyobo.struct.functional.dsl) ObjectPropertyAxiom (class in pyobo.struct.functional.dsl) ObjectPropertyChain (class in pyobo.struct.functional.dsl) ObjectPropertyDomain (class in pyobo.struct.functional.dsl) ObjectPropertyExpression (class in pyobo.struct.functional.dsl) ObjectPropertyRange (class in pyobo.struct.functional.dsl) ObjectSomeValuesFrom (class in pyobo.struct.functional.dsl) ObjectUnionOf (class in pyobo.struct.functional.dsl) Obo (class in pyobo) ontology (Obo attribute)

P

parents (Term attribute) parse_results_from_obo() (in module pyobo) predicate (Synonym property) PREFIX 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 properties_header (Obo property) property_qualified (DataExactCardinality attribute) (DataMaxCardinality attribute) (DataMinCardinality attribute) (ObjectExactCardinality attribute) (ObjectMaxCardinality attribute) (ObjectMinCardinality attribute) property_type (AnnotationPropertyDomain attribute) (AnnotationPropertyRange attribute) (AsymmetricObjectProperty attribute) (DataAllValuesFrom attribute) (DataHasValue attribute) (DataIntersectionOf attribute) (DataPropertyDomain attribute) (DataPropertyRange attribute) (DataSomeValuesFrom attribute) (DataUnionOf attribute) (FunctionalObjectProperty attribute) (InverseFunctionalObjectProperty attribute) (IrreflexiveObjectProperty attribute) (ObjectIntersectionOf attribute) (ObjectOneOf attribute) (ObjectPropertyDomain attribute) (ObjectPropertyRange attribute) (ObjectUnionOf attribute) (ReflexiveObjectProperty attribute) (SymmetricObjectProperty attribute) (TransitiveObjectProperty attribute) property_unqualified (DataExactCardinality attribute) (DataMaxCardinality attribute) (DataMinCardinality attribute) (ObjectExactCardinality attribute) (ObjectMaxCardinality attribute) (ObjectMinCardinality 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 --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-database-xrefs 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 IDENTIFIER PREFIX 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 IDENTIFIER PREFIX 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 --include-names --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 --target --verbose --version -f -v PREFIX pyobo-lookup-species command line option --force --force-process --identifier --no-strict --strict --verbose --version -f -i -v PREFIX 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.struct.functional.dsl module pyobo.struct.functional.macros module

R

Reference (in module pyobo) reference (Term attribute) ReflexiveObjectProperty (class in pyobo.struct.functional.dsl) relations_header (Obo property) RelationshipMacro (class in pyobo.struct.functional.macros)

relationships (Term attribute) restriction_predicate (ObjectAllValuesFrom attribute) (ObjectSomeValuesFrom attribute) root_terms (Obo attribute) run_nomenclature_plugin() (in module pyobo)

S

safe() (ClassExpression class method) (DataPropertyExpression class method) (DataRange class method) (ObjectPropertyExpression class method) SameIndividual (class in pyobo.struct.functional.dsl) set_species() (Term method) specificity (Synonym attribute) static_version (Obo attribute) SubAnnotationPropertyOf (class in pyobo.struct.functional.dsl)

SubClassOf (class in pyobo.struct.functional.dsl) SubDataPropertyOf (class in pyobo.struct.functional.dsl) SubObjectPropertyOf (class in pyobo.struct.functional.dsl) SymmetricObjectProperty (class in pyobo.struct.functional.dsl) Synonym (class in pyobo) synonym_typedefs (Obo attribute) SynonymMacro (class in pyobo.struct.functional.macros) synonyms (Term attribute) SynonymTypeDef (class in pyobo)

T

Term (class in pyobo) to_funowl_args() (Annotation method) (Axiom method) (DataComplementOf method) (DataHasValue method) (DataOneOf method) (DatatypeRestriction method) (Declaration method) (ObjectComplementOf method) (ObjectHasSelf method) (ObjectHasValue method) (ObjectInverseOf method) (ObjectOneOf method) (ObjectPropertyChain method) to_obo() (Synonym method) (SynonymTypeDef method) to_obonet() (Obo method) to_rdflib_node() (Annotation method) (AnnotationAssertion method) (AnnotationProperty method) (ClassAssertion method) (DataComplementOf method) (DataHasValue method) (DataOneOf method) (DataPropertyAssertion method) (DatatypeDefinition method) (DatatypeRestriction method) (Declaration method) (DifferentIndividuals method) (DisjointClasses method) (DisjointDataProperties method) (DisjointObjectProperties method) (DisjointUnion method) (EquivalentClasses method) (EquivalentDataProperties method) (EquivalentObjectProperties method) (FunctionalDataProperty method) (HasKey method) (InverseObjectProperties method) (NegativeDataPropertyAssertion method) (NegativeObjectPropertyAssertion method) (ObjectComplementOf method) (ObjectHasSelf method) (ObjectHasValue method) (ObjectInverseOf method) (ObjectOneOf method) (ObjectPropertyAssertion method) (ObjectPropertyChain method) (SameIndividual method) (SubAnnotationPropertyOf method) (SubClassOf method) (SubDataPropertyOf method) (SubObjectPropertyOf method)

TransitiveObjectProperty (class in pyobo.struct.functional.dsl) type (Synonym attribute) TypeDef (class in pyobo) typedefs (Obo 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_prefix_map() (Obo method) write_rdf() (Obo method)

X

XrefMacro (class in pyobo.struct.functional.macros)

xrefs (Term attribute)