Index

A

annotate() (in module kg_bacdive.utils.ner_utils)

B

BacDiveTransform (class in kg_bacdive.transform_utils.bacdive) (class in kg_bacdive.transform_utils.bacdive.bacdive)

C

convert_to_json() (in module kg_bacdive.utils.robot_utils)

D

DATA_DIR (kg_bacdive.transform_utils.transform.Transform attribute) decompress() (kg_bacdive.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_bacdive.transform_utils.ontology.OntologyTransform method) DEFAULT_INPUT_DIR (kg_bacdive.transform_utils.transform.Transform attribute) DEFAULT_OUTPUT_DIR (kg_bacdive.transform_utils.transform.Transform attribute)

download() (in module kg_bacdive) (in module kg_bacdive.download) download_yaml_and_get_json() (kg_bacdive.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_bacdive.transform_utils.mediadive.MediaDiveTransform method) drop_duplicates() (in module kg_bacdive.utils.pandas_utils)

E

establish_transitive_relationship() (in module kg_bacdive.utils.pandas_utils)

extract_convert_to_json() (in module kg_bacdive.utils.robot_utils)

G

get_compounds_of_solution() (kg_bacdive.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_bacdive.transform_utils.mediadive.MediaDiveTransform method)

I

initialize_robot() (in module kg_bacdive.utils.robot_utils)

K

kg_bacdive module kg_bacdive.download module kg_bacdive.merge_utils module kg_bacdive.merge_utils.merge_kg module kg_bacdive.query module kg_bacdive.run module kg_bacdive.transform module kg_bacdive.transform_utils module kg_bacdive.transform_utils.bacdive module kg_bacdive.transform_utils.bacdive.bacdive module kg_bacdive.transform_utils.constants module kg_bacdive.transform_utils.example_transform module

kg_bacdive.transform_utils.mediadive module kg_bacdive.transform_utils.mediadive.mediadive module kg_bacdive.transform_utils.ontology module kg_bacdive.transform_utils.ontology.ontology_transform module kg_bacdive.transform_utils.traits module kg_bacdive.transform_utils.traits.traits module kg_bacdive.transform_utils.transform module kg_bacdive.utils module kg_bacdive.utils.ner_utils module kg_bacdive.utils.pandas_utils module kg_bacdive.utils.robot_utils module

L

load_and_merge() (in module kg_bacdive.merge_utils) (in module kg_bacdive.merge_utils.merge_kg)

M

MediaDiveTransform (class in kg_bacdive.transform_utils.mediadive) (class in kg_bacdive.transform_utils.mediadive.mediadive) module kg_bacdive kg_bacdive.download kg_bacdive.merge_utils kg_bacdive.merge_utils.merge_kg kg_bacdive.query kg_bacdive.run kg_bacdive.transform kg_bacdive.transform_utils kg_bacdive.transform_utils.bacdive kg_bacdive.transform_utils.bacdive.bacdive kg_bacdive.transform_utils.constants kg_bacdive.transform_utils.example_transform kg_bacdive.transform_utils.mediadive kg_bacdive.transform_utils.mediadive.mediadive kg_bacdive.transform_utils.ontology kg_bacdive.transform_utils.ontology.ontology_transform kg_bacdive.transform_utils.traits kg_bacdive.transform_utils.traits.traits kg_bacdive.transform_utils.transform kg_bacdive.utils kg_bacdive.utils.ner_utils kg_bacdive.utils.pandas_utils kg_bacdive.utils.robot_utils tests

O

OntologyTransform (class in kg_bacdive.transform_utils.ontology) (class in kg_bacdive.transform_utils.ontology.ontology_transform)

P

parse() (kg_bacdive.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_bacdive.transform_utils.ontology.OntologyTransform method) parse_load_config() (in module kg_bacdive.merge_utils) (in module kg_bacdive.merge_utils.merge_kg)

parse_query_yaml() (in module kg_bacdive.query) pass_through() (kg_bacdive.transform_utils.transform.Transform method)

R

remove_convert_to_json() (in module kg_bacdive.utils.robot_utils) result_dict_to_tsv() (in module kg_bacdive.query) run() (kg_bacdive.transform_utils.bacdive.bacdive.BacDiveTransform method) (kg_bacdive.transform_utils.bacdive.BacDiveTransform method) (kg_bacdive.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_bacdive.transform_utils.mediadive.MediaDiveTransform method) (kg_bacdive.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_bacdive.transform_utils.ontology.OntologyTransform method) (kg_bacdive.transform_utils.traits.traits.TraitsTransform method) (kg_bacdive.transform_utils.traits.TraitsTransform method) (kg_bacdive.transform_utils.transform.Transform method)

run_query() (in module kg_bacdive.query)

S

standardize_compound_id() (kg_bacdive.transform_utils.mediadive.mediadive.MediaDiveTransform method) (kg_bacdive.transform_utils.mediadive.MediaDiveTransform method)

T

tests module TraitsTransform (class in kg_bacdive.transform_utils.traits) (class in kg_bacdive.transform_utils.traits.traits)

Transform (class in kg_bacdive.transform_utils.transform) transform() (in module kg_bacdive.transform)