oaklib
Contents:
Introduction
Tutorial
The OAK Guide
OAK Library Documentation
Command Line
Datamodels
How-To Guides
Jupyter Notebooks
Glossary
FAQ
oaklib
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
add_associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
add_metadata() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
add_missing_property_values() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
AggregatorImplementation (class in oaklib.implementations.aggregator.aggregator_implementation)
alias_map_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
aliases_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
all_by_all_pairwise_similarity() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
all_entity_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
all_obsolete_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
all_ontology_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
all_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
all_sssom_mappings() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
all_subset_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Ancestor
ancestor_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
ancestors() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
annotate_file() (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface method)
annotate_tabular_file() (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface method)
annotate_text() (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface method)
Annotation
annotation_assertion_axioms() (oaklib.interfaces.owl_interface.OwlInterface method)
AnnotationProperty
apply_patch() (oaklib.interfaces.patcher_interface.PatcherInterface method)
as_obograph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
Asserted
Association
association_counts() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
association_pairwise_coassociations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
association_subject_counts() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
AssociationProviderInterface (class in oaklib.interfaces.association_provider_interface)
associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
associations_subject_search() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
associations_subjects() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
auto_add_contributor_using (oaklib.interfaces.patcher_interface.PatcherInterface attribute)
auto_relax_axioms (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute)
autosave (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute)
(oaklib.interfaces.differ_interface.DifferInterface attribute)
(oaklib.interfaces.mapping_provider_interface.MappingProviderInterface attribute)
(oaklib.interfaces.relation_graph_interface.RelationGraphInterface attribute)
(oaklib.interfaces.search_interface.SearchInterface attribute)
(oaklib.interfaces.subsetter_interface.SubsetterInterface attribute)
(oaklib.interfaces.validator_interface.ValidatorInterface attribute)
axiom_is_about() (oaklib.interfaces.owl_interface.OwlInterface method)
axiom_references() (oaklib.interfaces.owl_interface.OwlInterface method)
B
basic_search() (oaklib.interfaces.search_interface.SearchInterface method)
BasicOntologyInterface (class in oaklib.interfaces.basic_ontology_interface)
Bioportal
branch_summary_statistics() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method)
C
cache_directory (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface attribute)
cache_lookups (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute)
cached_information_content_map (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface attribute)
Category
Class
clone() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Closure
comments() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
compare_ontology_term_lists() (oaklib.interfaces.differ_interface.DifferInterface method)
Concept
converter (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property)
create_entity() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
create_normalization_map() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
create_search_configuration() (in module oaklib.datamodels.search)
CURIE
curie_to_uri() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
curies_by_label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
curies_by_subset() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
D
dangling() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Datamodel
DatatypeProperty
default_language (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property)
defined_by() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
defined_bys() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
definition() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
definitions() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
delete_entity() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Descendant
descendant_count() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
descendant_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
descendants() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
Diff
diff() (oaklib.interfaces.differ_interface.DifferInterface method)
diff_summary() (oaklib.interfaces.differ_interface.DifferInterface method)
DifferInterface (class in oaklib.interfaces.differ_interface)
direct_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
disable_transitive_query_cache() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
disjoint_class_expressions_axioms() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
disjoint_pairs() (oaklib.interfaces.owl_interface.OwlInterface method)
E
Edge
(class in semsql.sqla.semsql)
edge_index (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property)
edges() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
enable_transitive_query_cache() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
Entailed
entailed_edge_index (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property)
entailed_incoming_relationships() (oaklib.interfaces.relation_graph_interface.RelationGraphInterface method)
entailed_outgoing_relationships() (oaklib.interfaces.relation_graph_interface.RelationGraphInterface method)
entailed_relationships_between() (oaklib.interfaces.relation_graph_interface.RelationGraphInterface method)
EntailedEdge (class in semsql.sqla.semsql)
entities() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
entities_metadata_statements() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
entity_alias_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
entity_aliases() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
entity_metadata_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
equivalence_axioms() (oaklib.interfaces.owl_interface.OwlInterface method)
exclude_owl_top_and_bottom (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute)
(oaklib.interfaces.differ_interface.DifferInterface attribute)
(oaklib.interfaces.mapping_provider_interface.MappingProviderInterface attribute)
(oaklib.interfaces.relation_graph_interface.RelationGraphInterface attribute)
(oaklib.interfaces.search_interface.SearchInterface attribute)
(oaklib.interfaces.subsetter_interface.SubsetterInterface attribute)
(oaklib.interfaces.validator_interface.ValidatorInterface attribute)
expand_change() (oaklib.interfaces.patcher_interface.PatcherInterface method)
expand_changes() (oaklib.interfaces.patcher_interface.PatcherInterface method)
extract_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
extract_subset_ontology() (oaklib.interfaces.subsetter_interface.SubsetterInterface method)
F
Functional Syntax
FunOWL
G
gap_fill_relationships() (oaklib.interfaces.subsetter_interface.SubsetterInterface method)
get_curies_by_label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
get_definition_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
get_information_content() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
get_label_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
get_labels_for_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
get_prefix_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
get_sssom_mappings_by_curie() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
get_transitive_mappings_by_curie() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
global_summary_statistics() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method)
Graph
Graph Traversal
grouped_diff() (oaklib.interfaces.differ_interface.DifferInterface method)
H
hierarchical_parents() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
I
Identifier
ignore_invalid_changes (oaklib.interfaces.patcher_interface.PatcherInterface attribute)
Implementation
incoming_relationship_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
incoming_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Information Content
information_content_scores() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
Input Selector
Interface
IS_A:
is_coherent() (oaklib.interfaces.validator_interface.ValidatorInterface method)
is_disjoint() (oaklib.interfaces.owl_interface.OwlInterface method)
is_satisfiable() (oaklib.interfaces.owl_interface.OwlInterface method)
Iterator
K
KGCL
L
Label
label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
labels() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
languages() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
leafs() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
lexical_index (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface attribute)
load_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
Logical Definition
logical_definitions() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
lookup_references() (oaklib.interfaces.validator_interface.ValidatorInterface method)
M
map_associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
Mapping
MappingProviderInterface (class in oaklib.interfaces.mapping_provider_interface)
metadata_property_summary_statistics() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method)
migrate_curies() (oaklib.interfaces.patcher_interface.PatcherInterface method)
module
oaklib.datamodels.search
oaklib.utilities.apikey_manager
oaklib.utilities.graph.networkx_bridge
oaklib.utilities.graph.relationship_walker
oaklib.utilities.lexical.lexical_indexer
oaklib.utilities.obograph_utils
oaklib.utilities.subsets.slimmer_utils
oaklib.utilities.taxon.taxon_constraint_utils
most_recent_common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
multilingual (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface property)
multilingual_labels() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
multiset_most_recent_common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
multiterm_search() (oaklib.interfaces.search_interface.SearchInterface method)
N
Name
Named Individual
Node
node() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
nodes() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
non_redundant_entailed_relationships() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
normalize() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
normalize_association() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
normalize_associations() (oaklib.interfaces.association_provider_interface.AssociationProviderInterface method)
normalize_prefix() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
O
oaklib.datamodels.search
module
oaklib.utilities.apikey_manager
module
oaklib.utilities.graph.networkx_bridge
module
oaklib.utilities.graph.relationship_walker
module
oaklib.utilities.lexical.lexical_indexer
module
oaklib.utilities.obograph_utils
module
oaklib.utilities.subsets.slimmer_utils
module
oaklib.utilities.taxon.taxon_constraint_utils
module
Object
Object Closure
ObjectProperty
OBO Format
OBO Graphs
OboGraphInterface (class in oaklib.interfaces.obograph_interface)
obsoletes() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
obsoletes_migration_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
OLS
Ontobee
OntoGPT
ontologies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Ontology
Ontology Element
Ontology Format
Ontology Graph Projection
ontology_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
ontology_metadata_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
ontology_metamodel_mapper (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute)
ontology_versions() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
OntoPortal
outgoing_relationship_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
outgoing_relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
OWL
OWL Annotation
owl_type() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
owl_types() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
OwlInterface (class in oaklib.interfaces.owl_interface)
P
pairwise_similarity() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
Part Of
Patch
PatcherInterface (class in oaklib.interfaces.patcher_interface)
paths() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
precompute_lookups() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Predicate
prefix_map() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Pronto
Property
property_characteristics() (oaklib.interfaces.owl_interface.OwlInterface method)
Q
query() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
R
RDF
Reasoner
reasoner_configurations() (oaklib.interfaces.owl_interface.OwlInterface method)
Reasoning
Reflexive
Relation Graph
RelationGraphInterface (class in oaklib.interfaces.relation_graph_interface)
Relationship
Relationship Type
relationships() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
relationships_metadata() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
relationships_to_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
repair() (oaklib.interfaces.validator_interface.ValidatorInterface method)
reverse_changes() (oaklib.interfaces.patcher_interface.PatcherInterface method)
roots() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
rule_collection (oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface attribute)
S
save() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
(oaklib.interfaces.patcher_interface.PatcherInterface method)
SearchConfiguration (class in oaklib.datamodels.search)
(class in oaklib.interfaces.search_interface)
SearchInterface (class in oaklib.interfaces.search_interface)
Semantic Similarity
Semantic SQL
SemanticSimilarityInterface (class in oaklib.interfaces.semsim_interface)
set_label() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
set_metamodel_mappings() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
setwise_most_recent_common_ancestors() (oaklib.interfaces.semsim_interface.SemanticSimilarityInterface method)
simple_mappings() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
simple_mappings_by_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
simple_subproperty_of_chains() (oaklib.interfaces.owl_interface.OwlInterface method)
singletons() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
SPARQL
SQL
SSSOM
sssom_mappings() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
sssom_mappings_by_source() (oaklib.interfaces.mapping_provider_interface.MappingProviderInterface method)
Statements (class in semsql.sqla.semsql)
strict (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface attribute)
subclass_axioms() (oaklib.interfaces.owl_interface.OwlInterface method)
subgraph_from_traversal() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
Subject
Subject Closure
Subset
subset_curies() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
subset_members() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
subsets() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
SubsetterInterface (class in oaklib.interfaces.subsetter_interface)
summary_statistic_description() (oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface method)
SummaryStatisticsInterface (class in oaklib.interfaces.summary_statistics_interface)
synonym_map_for_curies() (oaklib.interfaces.obograph_interface.OboGraphInterface method)
T
Tautology
Term
term_curies_without_definitions() (oaklib.interfaces.validator_interface.ValidatorInterface method)
terms_categories() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
terms_subsets() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
Text Annotation
TextAnnotation (class in oaklib.datamodels.text_annotator)
TextAnnotatorInterface (class in oaklib.interfaces.text_annotator_interface)
transitive_object_properties() (oaklib.interfaces.owl_interface.OwlInterface method)
TraversalConfiguration (class in oaklib.interfaces.obograph_interface)
Triple
Triplestore
U
Ubergraph
undo() (oaklib.interfaces.patcher_interface.PatcherInterface method)
unsatisfiable_classes() (oaklib.interfaces.validator_interface.ValidatorInterface method)
URI
uri_to_curie() (oaklib.interfaces.basic_ontology_interface.BasicOntologyInterface method)
V
validate() (oaklib.interfaces.validator_interface.ValidatorInterface method)
validate_definitions() (oaklib.interfaces.validator_interface.ValidatorInterface method)
validate_mappings() (oaklib.interfaces.validator_interface.ValidatorInterface method)
validate_synonyms() (oaklib.interfaces.validator_interface.ValidatorInterface method)
ValidatorInterface (class in oaklib.interfaces.validator_interface)
W
walk_up_relationship_graph() (oaklib.interfaces.obograph_interface.OboGraphInterface method)