Index

A

ABBREVIATION (hpotk.model.SynonymType attribute) absent_annotations() (hpotk.annotations.AnnotatedItem method) ALLELIC_REQUIREMENT (hpotk.model.SynonymType attribute) alt_term_ids (hpotk.MinimalTerm property) (hpotk.model.MinimalTerm property) AnnotatedItem (class in hpotk.annotations) AnnotatedItemContainer (class in hpotk.annotations)

AnnotationIcContainer (class in hpotk.algorithm.similarity) AnnotationPropagationValidator (class in hpotk.validate) AnnotationReference (class in hpotk.annotations) annotations (hpotk.annotations.AnnotatedItem property) (hpotk.annotations.SimpleHpoDisease property) argsort() (hpotk.util.sort.HierarchicalIcTermIdSorting method) (hpotk.util.sort.TermIdSorting method)

B

BROAD (hpotk.model.SynonymCategory attribute)

C

calculate_ic_for_annotated_items() (in module hpotk.algorithm.similarity) category (hpotk.model.Synonym property) (hpotk.validate.ValidationResult attribute) check_numerator_and_denominator() (hpotk.model.FrequencyAwareFeature static method) clear() (hpotk.OntologyStore method) (hpotk.store.OntologyStore method) CLINICAL_MODIFIER (in module hpotk.constants.hpo.base) cohort_size (hpotk.annotations.load.hpoa.SimpleHpoaDiseaseLoader property) comment (hpotk.model.Term property) (hpotk.Term property) configure_ontology_store() (in module hpotk) (in module hpotk.store)

create_graph() (hpotk.graph.CsrIndexedGraphFactory method) (hpotk.graph.GraphFactory method) create_minimal_ontology() (in module hpotk.ontology) create_minimal_term() (hpotk.MinimalTerm static method) (hpotk.model.MinimalTerm static method) create_ontology() (in module hpotk.ontology) create_term() (hpotk.model.Term static method) (hpotk.ontology.load.obographs.MinimalTermFactory method) (hpotk.ontology.load.obographs.TermFactory method) (hpotk.Term static method) CsrIndexedGraphFactory (class in hpotk.graph) current_synonyms() (hpotk.model.Term method) (hpotk.Term method)

D

Definition (class in hpotk.model) definition (hpotk.model.Definition property) (hpotk.model.Term property) (hpotk.Term property)

denominator (hpotk.annotations.SimpleHpoDiseaseAnnotation property) (hpotk.model.FrequencyAwareFeature property) disease_ids (hpotk.annotations.SimpleHpoDiseases property) diseases (hpotk.annotations.SimpleHpoDiseases property)

E

ERROR (hpotk.validate.ValidationLevel attribute) evidence_code (hpotk.annotations.AnnotationReference property)

EvidenceCode (class in hpotk.annotations) EXACT (hpotk.model.SynonymCategory attribute)

F

FEMALE (hpotk.annotations.Sex attribute) fetch_ontology() (hpotk.store.GitHubRemoteOntologyService method) (hpotk.store.RemoteOntologyService method) fetch_tags() (hpotk.store.GitHubOntologyReleaseService method) (hpotk.store.OntologyReleaseService method)

frequency (hpotk.constants.hpo.frequency.HpoFrequency property) frequency() (hpotk.model.FrequencyAwareFeature method) FrequencyAwareFeature (class in hpotk.model) from_csv() (hpotk.algorithm.similarity.SimilarityContainer static method) from_curie() (hpotk.model.TermId static method) (hpotk.TermId static method)

G

get_ancestor_idx() (hpotk.graph.IndexedOntologyGraph method) get_ancestors() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) get_children() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) get_children_idx() (hpotk.graph.IndexedOntologyGraph method) get_descendant_idx() (hpotk.graph.IndexedOntologyGraph method) get_descendants() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) get_parents() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method)

get_parents_idx() (hpotk.graph.IndexedOntologyGraph method) get_similarity() (hpotk.algorithm.similarity.SimilarityContainer method) get_term() (hpotk.MinimalOntology method) (hpotk.ontology.MinimalOntology method) get_term_name() (hpotk.MinimalOntology method) (hpotk.ontology.MinimalOntology method) GitHubOntologyReleaseService (class in hpotk.store) GitHubRemoteOntologyService (class in hpotk.store) graph (hpotk.graph.GraphAware property) (hpotk.GraphAware property) GraphAware (class in hpotk) (class in hpotk.graph) GraphFactory (class in hpotk.graph)

H

HierarchicalEdgeTermIdSorting (class in hpotk.util.sort) HierarchicalIcTermIdSorting (class in hpotk.util.sort) HierarchicalSimilaritySorting (class in hpotk.util.sort) HPO (hpotk.OntologyType attribute) (hpotk.store.OntologyType attribute) HpoDisease (class in hpotk.annotations) HpoDiseaseAnnotation (class in hpotk.annotations) HpoDiseases (class in hpotk.annotations) HpoFrequency (class in hpotk.constants.hpo.frequency) hpotk module hpotk.algorithm module hpotk.algorithm.similarity module hpotk.annotations module hpotk.annotations.load module hpotk.annotations.load.hpoa module hpotk.constants module hpotk.constants.hpo module hpotk.constants.hpo.base module hpotk.constants.hpo.frequency module

hpotk.constants.hpo.inheritance module hpotk.constants.hpo.onset module hpotk.constants.hpo.organ_system module hpotk.constants.hpo.severity module hpotk.graph module hpotk.graph.csr module hpotk.model module hpotk.ontology module hpotk.ontology.load module hpotk.ontology.load.obographs module hpotk.store module hpotk.util module hpotk.util.sort module hpotk.validate module

I

id (hpotk.model.TermId property) (hpotk.TermId property) Identified (class in hpotk.model) identifier (hpotk.annotations.AnnotationReference property) (hpotk.annotations.SimpleHpoDisease property) (hpotk.annotations.SimpleHpoDiseaseAnnotation property) (hpotk.constants.hpo.frequency.HpoFrequency property) (hpotk.model.Identified property) (hpotk.OntologyType property) (hpotk.store.OntologyType property) idx_to_node() (hpotk.graph.IndexedOntologyGraph method) IEA (hpotk.annotations.EvidenceCode attribute) IncrementalCsrGraphFactory (class in hpotk.graph) IndexedOntologyGraph (class in hpotk.graph) is_absent (hpotk.model.ObservableFeature property) is_ancestor_of() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) is_ancestor_of_idx() (hpotk.graph.IndexedOntologyGraph method) is_child_of() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) is_child_of_idx() (hpotk.graph.IndexedOntologyGraph method) is_current (hpotk.MinimalTerm property) (hpotk.model.MinimalTerm property)

is_current() (hpotk.model.SynonymType method) is_descendant_of() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) is_descendant_of_idx() (hpotk.graph.IndexedOntologyGraph method) is_excluded (hpotk.model.FrequencyAwareFeature property) (hpotk.model.ObservableFeature property) is_leaf() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) is_obsolete (hpotk.MinimalTerm property) (hpotk.model.MinimalTerm property) is_obsolete() (hpotk.model.SynonymType method) is_ok() (hpotk.validate.ValidationResults method) is_parent_of() (hpotk.graph.IndexedOntologyGraph method) (hpotk.graph.OntologyGraph method) (hpotk.OntologyGraph method) is_parent_of_idx() (hpotk.graph.IndexedOntologyGraph method) is_present (hpotk.model.FrequencyAwareFeature property) (hpotk.model.ObservableFeature property) item_ids() (hpotk.annotations.AnnotatedItemContainer method) items (hpotk.annotations.AnnotatedItemContainer property) (hpotk.annotations.SimpleHpoDiseases property) items() (hpotk.algorithm.similarity.SimilarityContainer method)

L

LAYPERSON_TERM (hpotk.model.SynonymType attribute) level (hpotk.validate.ValidationResult attribute) load() (hpotk.annotations.load.hpoa.SimpleHpoaDiseaseLoader method) load_hpo() (hpotk.OntologyStore method) (hpotk.store.OntologyStore method) load_minimal_hpo() (hpotk.OntologyStore method) (hpotk.store.OntologyStore method) load_minimal_ontology() (hpotk.OntologyStore method) (hpotk.store.OntologyStore method) (in module hpotk.ontology.load.obographs)

load_ontology() (hpotk.OntologyStore method) (hpotk.store.OntologyStore method) (in module hpotk.ontology.load.obographs) looks_gzipped() (in module hpotk.util) looks_like_url() (in module hpotk.util) lower_bound (hpotk.constants.hpo.frequency.HpoFrequency property)

M

MALE (hpotk.annotations.Sex attribute) MAxO (hpotk.OntologyType attribute) (hpotk.store.OntologyType attribute) message (hpotk.validate.ValidationResult attribute) metadata (hpotk.algorithm.similarity.SimilarityContainer property) (hpotk.algorithm.similarity.SimpleAnnotationIcContainer property) (hpotk.model.MetadataAware property) metadata_from_str() (hpotk.model.MetadataAware static method) metadata_to_str() (hpotk.model.MetadataAware method) MetadataAware (class in hpotk.model) MinimalOntology (class in hpotk) (class in hpotk.ontology) MinimalTerm (class in hpotk) (class in hpotk.model) MinimalTermFactory (class in hpotk.ontology.load.obographs) MODE_OF_INHERITANCE (in module hpotk.constants.hpo.base) modes_of_inheritance (hpotk.annotations.HpoDisease property) (hpotk.annotations.SimpleHpoDisease property) modifiers (hpotk.annotations.HpoDiseaseAnnotation property) (hpotk.annotations.SimpleHpoDiseaseAnnotation property) module hpotk hpotk.algorithm hpotk.algorithm.similarity hpotk.annotations hpotk.annotations.load hpotk.annotations.load.hpoa hpotk.constants hpotk.constants.hpo hpotk.constants.hpo.base hpotk.constants.hpo.frequency hpotk.constants.hpo.inheritance hpotk.constants.hpo.onset hpotk.constants.hpo.organ_system hpotk.constants.hpo.severity hpotk.graph hpotk.graph.csr hpotk.model hpotk.ontology hpotk.ontology.load hpotk.ontology.load.obographs hpotk.store hpotk.util hpotk.util.sort hpotk.validate

MONDO (hpotk.OntologyType attribute) (hpotk.store.OntologyType attribute)

N

name (hpotk.annotations.SimpleHpoDisease property) (hpotk.model.Named property) (hpotk.model.Synonym property) Named (class in hpotk.model)

NARROW (hpotk.model.SynonymCategory attribute) node_to_idx() (hpotk.graph.IndexedOntologyGraph method) numerator (hpotk.annotations.SimpleHpoDiseaseAnnotation property) (hpotk.model.FrequencyAwareFeature property)

O

ObservableFeature (class in hpotk.model) OBSOLETE_SYNONYM (hpotk.model.SynonymType attribute) obsolete_synonyms() (hpotk.model.Term method) (hpotk.Term method) ObsoleteTermIdsValidator (class in hpotk.validate) Ontology (class in hpotk) (class in hpotk.ontology) OntologyGraph (class in hpotk) (class in hpotk.graph)

OntologyReleaseService (class in hpotk.store) OntologyStore (class in hpotk) (class in hpotk.store) OntologyType (class in hpotk) (class in hpotk.store) open_text_io_handle_for_reading() (in module hpotk.util) open_text_io_handle_for_writing() (in module hpotk.util)

P

parse() (hpotk.annotations.EvidenceCode static method) (hpotk.annotations.Sex static method) parse_hpo_frequency() (in module hpotk.constants.hpo.frequency) PCS (hpotk.annotations.EvidenceCode attribute) PHENOTYPIC_ABNORMALITY (in module hpotk.constants.hpo.base)

PhenotypicAbnormalityValidator (class in hpotk.validate) PLURAL_FORM (hpotk.model.SynonymType attribute) precalculate_ic_mica_for_hpo_concept_pairs() (in module hpotk.algorithm.similarity) prefix (hpotk.model.TermId property) (hpotk.TermId property) present_annotations() (hpotk.annotations.AnnotatedItem method)

R

references (hpotk.annotations.HpoDiseaseAnnotation property) (hpotk.annotations.SimpleHpoDiseaseAnnotation property) RELATED (hpotk.model.SynonymCategory attribute) RemoteOntologyService (class in hpotk.store) resolve_store_path() (hpotk.OntologyStore method) (hpotk.store.OntologyStore method)

results (hpotk.validate.ValidationResults property) root (hpotk.graph.IndexedOntologyGraph property) (hpotk.graph.OntologyGraph property) (hpotk.OntologyGraph property) root_idx (hpotk.graph.IndexedOntologyGraph property) RuleValidator (class in hpotk.validate)

S

set_similarity() (hpotk.algorithm.similarity.SimilarityContainer method) setup_logging() (in module hpotk.util) Sex (class in hpotk.annotations) SimilarityContainer (class in hpotk.algorithm.similarity) SimpleAnnotationIcContainer (class in hpotk.algorithm.similarity) SimpleHpoaDiseaseLoader (class in hpotk.annotations.load.hpoa) SimpleHpoDisease (class in hpotk.annotations) SimpleHpoDiseaseAnnotation (class in hpotk.annotations)

SimpleHpoDiseases (class in hpotk.annotations) store_dir (hpotk.OntologyStore property) (hpotk.store.OntologyStore property) Synonym (class in hpotk.model) synonym_type (hpotk.model.Synonym property) SynonymCategory (class in hpotk.model) synonyms (hpotk.model.Term property) (hpotk.Term property) SynonymType (class in hpotk.model)

T

TAS (hpotk.annotations.EvidenceCode attribute) Term (class in hpotk) (class in hpotk.model) term_ids (hpotk.MinimalOntology property) (hpotk.ontology.MinimalOntology property) TermFactory (class in hpotk.ontology.load.obographs)

TermId (class in hpotk) (class in hpotk.model) TermIdSorting (class in hpotk.util.sort) terms (hpotk.MinimalOntology property) (hpotk.ontology.MinimalOntology property) to_csv() (hpotk.algorithm.similarity.AnnotationIcContainer method) (hpotk.algorithm.similarity.SimilarityContainer method)

U

UK_SPELLING (hpotk.model.SynonymType attribute)

UNKNOWN (hpotk.annotations.Sex attribute) upper_bound (hpotk.constants.hpo.frequency.HpoFrequency property)

V

validate() (hpotk.validate.AnnotationPropagationValidator method) (hpotk.validate.ObsoleteTermIdsValidator method) (hpotk.validate.PhenotypicAbnormalityValidator method) (hpotk.validate.RuleValidator method) validate_all() (hpotk.validate.ValidationRunner method) validate_instance() (in module hpotk.util) validate_optional_instance() (in module hpotk.util) ValidationLevel (class in hpotk.validate)

ValidationResult (class in hpotk.validate) ValidationResults (class in hpotk.validate) ValidationRunner (class in hpotk.validate) value (hpotk.model.TermId property) (hpotk.TermId property) version (hpotk.annotations.SimpleHpoDiseases property) (hpotk.model.Versioned property) Versioned (class in hpotk.model)

W

WARNING (hpotk.validate.ValidationLevel attribute)

X

xrefs (hpotk.model.Definition property) (hpotk.model.Synonym property) (hpotk.model.Term property) (hpotk.Term property)