Index

_

__init__() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) (metabograph.biopax.query_manager.BiopaxQueryManager method) (metabograph.cache.CacheManager method) (metabograph.config.BiopaxData method) (metabograph.config.CacheData method) (metabograph.config.Config method) (metabograph.config.ConfigData method) (metabograph.owl.OwlLoader method)

A

asdict() (metabograph.config.Config method)

B

biopax (metabograph.config.ConfigData attribute) biopax_dir (metabograph.biopax.query_manager.BiopaxQueryManager property)

BiopaxData (class in metabograph.config) BiopaxGraphGenerator (class in metabograph.biopax.graph_generator) BiopaxQueryManager (class in metabograph.biopax.query_manager)

C

cache (metabograph.config.ConfigData attribute) cache_dir (metabograph.cache.CacheManager property) CacheData (class in metabograph.config) CacheManager (class in metabograph.cache) canonicalize() (in module metabograph.sparql)

clear() (metabograph.cache.CacheManager method) Config (class in metabograph.config) ConfigData (class in metabograph.config) configure_logging() (in module metabograph.logging) custom_owl_files (metabograph.config.BiopaxData attribute)

D

dict_from_dataframe_columns() (in module metabograph.utils)

Direction (class in metabograph.biopax.graph_generator) download() (in module metabograph.common)

E

endpoint (metabograph.biopax.query_manager.BiopaxQueryManager property) (metabograph.config.BiopaxData attribute) entity_to_location_name_mapper (metabograph.biopax.query_manager.BiopaxQueryManager property)

entity_to_names_mappers (metabograph.biopax.query_manager.BiopaxQueryManager property) entity_to_simplified_id (metabograph.biopax.query_manager.BiopaxQueryManager property) entity_to_type_mapper (metabograph.biopax.query_manager.BiopaxQueryManager property) extract_species_owl_file() (metabograph.biopax.query_manager.BiopaxQueryManager method)

F

FIELD_DELIMITER (metabograph.biopax.query_manager.BiopaxQueryManager attribute) filter_by_location() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) filter_by_pathway() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method)

filter_complexes() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) filter_controls() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) filter_member_entities() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) from_str() (metabograph.biopax.graph_generator.Direction class method)

G

get_common_prefix() (in module metabograph.utils) get_custom_node_attributes() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) get_documented_yaml() (metabograph.config.Config method) get_graph() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method) get_node_identifier() (metabograph.biopax.graph_generator.BiopaxGraphGenerator method)

get_owl_files() (metabograph.biopax.query_manager.BiopaxQueryManager method) get_path() (metabograph.cache.CacheManager method) get_protein_entities() (in module metabograph.biopax.protein) (metabograph.biopax.query_manager.BiopaxQueryManager method) get_uniprot_id() (in module metabograph.biopax.protein)

H

hash_data() (in module metabograph.utils)

hash_file() (in module metabograph.utils) hash_query() (in module metabograph.sparql)

I

id_mapper_context() (in module metabograph.uniprot.id_mapping) include_complexes (metabograph.config.BiopaxData attribute) include_default_owl_files (metabograph.config.BiopaxData attribute)

include_member_entities (metabograph.config.BiopaxData attribute) is_older_or_missing() (in module metabograph.utils) ITEM_DELIMITER (metabograph.biopax.query_manager.BiopaxQueryManager attribute)

K

keep_unknown (metabograph.config.BiopaxData attribute)

L

LEFT_TO_RIGHT (metabograph.biopax.graph_generator.Direction attribute) level_3_owl_file (metabograph.biopax.query_manager.BiopaxQueryManager property) list_locations() (metabograph.biopax.query_manager.BiopaxQueryManager method) list_pathways() (metabograph.biopax.query_manager.BiopaxQueryManager method)

list_species() (metabograph.biopax.query_manager.BiopaxQueryManager method) load() (metabograph.config.Config method) (metabograph.owl.OwlLoader method) location_data (metabograph.biopax.graph_generator.BiopaxGraphGenerator property) locations (metabograph.config.BiopaxData attribute)

M

main() (in module metabograph.fuseki) (in module metabograph.main) map_members_to_uniprot_ids() (in module metabograph.biopax.protein) map_uniprot_ids_to_gene_ids() (in module metabograph.biopax.protein) metabograph module metabograph.biopax module metabograph.biopax.graph_generator module metabograph.biopax.protein module metabograph.biopax.query_manager module metabograph.cache module metabograph.common module metabograph.config module metabograph.exception module metabograph.fuseki module metabograph.logging module metabograph.main module metabograph.owl module

metabograph.sparql module metabograph.uniprot module metabograph.uniprot.id_mapping module metabograph.utils module MetabographConfigError MetabographException MetabographIdMapperError MetabographIOError MetabographRuntimeError module metabograph metabograph.biopax metabograph.biopax.graph_generator metabograph.biopax.protein metabograph.biopax.query_manager metabograph.cache metabograph.common metabograph.config metabograph.exception metabograph.fuseki metabograph.logging metabograph.main metabograph.owl metabograph.sparql metabograph.uniprot metabograph.uniprot.id_mapping metabograph.utils

O

owl_file() (in module metabograph.biopax.query_manager)

OwlLoader (class in metabograph.owl) owlready2_world (metabograph.owl.OwlLoader property)

P

path (metabograph.config.CacheData attribute)

pathway_data (metabograph.biopax.graph_generator.BiopaxGraphGenerator property) pathways (metabograph.config.BiopaxData attribute)

Q

query() (metabograph.biopax.query_manager.BiopaxQueryManager method) (metabograph.owl.OwlLoader method) query_complex_components() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_controls() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_conversion_directions() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_entities() (metabograph.biopax.query_manager.BiopaxQueryManager method)

query_interaction_participants() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_interactions() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_locations() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_member_entities() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_participants() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_pathways() (metabograph.biopax.query_manager.BiopaxQueryManager method) query_physical_entities() (metabograph.biopax.query_manager.BiopaxQueryManager method)

R

rdflib_graph (metabograph.owl.OwlLoader property) reactome_archive_path (metabograph.biopax.query_manager.BiopaxQueryManager property) resolve_path() (metabograph.config.Config method) REVERSIBLE (metabograph.biopax.graph_generator.Direction attribute)

RIGHT_TO_LEFT (metabograph.biopax.graph_generator.Direction attribute) run_fuseki_server() (in module metabograph.fuseki) run_main() (in module metabograph.fuseki) (in module metabograph.main)

S

species (metabograph.biopax.query_manager.BiopaxQueryManager property) (metabograph.config.BiopaxData attribute)

T

timeout (metabograph.config.CacheData attribute)