kg_covid_19.transform_utils.chembl package

Submodules

kg_covid_19.transform_utils.chembl.chembl_transform module

class kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform(input_dir: str = None, output_dir: str = None)

Bases: kg_covid_19.transform_utils.transform.Transform

Parse ChEMBL and transform them into a property graph representation.

parse_chembl_activity(data: List)

Parse ChEMBL Activity records.

An activity document links 4 entities,

• assay

• document

• target

• molecule

Each of the activity document will be converted to an edge that links a molecule to a target with biolink:interacts_with edge_label. The edge itself will have additional properties like ‘publications’ and ‘assay’ that references the publication and assay, respectively. The edge will also have measurements as edge properties that describe the activity/interaction further.

Args:

data: A list of ChEMBL Activity records

Returns:

A list

parse_chembl_assay(data: List)

Parse ChEMBL Assay records.

Args:

data: A list of ChEMBL Assay records

Returns:

A list

parse_chembl_document(data: List)

Parse ChEMBL Document records.

Args:

data: A list of ChEMBL Document records

Returns:

A list

parse_chembl_molecules(data: List)

Parse ChEMBL Molecule records.

Args:

data: A list of ChEMBL Molecule records

Returns:

A list

parse_doc_fields(record: dict, allowed_properties: set, remap: dict = None)

Parse a record from the API.

Args:

record: The record or document from the API allowed_properties: properties that are to be parsed remap: properties that are to be remapped from one name to another

Returns:

A dict of properties

read_json(json_file)

Read in json files

Args:

data_file: json_file to parse

Returns:

A list of records

run(data_file: Optional[str] = None, chembl_data_files: Optional[dict] = None) → None

Method is called and performs needed transformations to process SARS-CoV-2 subset of ChEMBL.

http://chembl.blogspot.com/2020/05/chembl27-sars-cov-2-release.html

Args:

data_file: NOT USED - preserves to placate mypy. Use “data_files” instead chembl_data_files: data files to parse

Returns:

None.

Module contents

class kg_covid_19.transform_utils.chembl.ChemblTransform(input_dir: str = None, output_dir: str = None)

Bases: kg_covid_19.transform_utils.transform.Transform

Parse ChEMBL and transform them into a property graph representation.

parse_chembl_activity(data: List)

Parse ChEMBL Activity records.

An activity document links 4 entities,

• assay

• document

• target

• molecule

Each of the activity document will be converted to an edge that links a molecule to a target with biolink:interacts_with edge_label. The edge itself will have additional properties like ‘publications’ and ‘assay’ that references the publication and assay, respectively. The edge will also have measurements as edge properties that describe the activity/interaction further.

Args:

data: A list of ChEMBL Activity records

Returns:

A list

parse_chembl_assay(data: List)

Parse ChEMBL Assay records.

Args:

data: A list of ChEMBL Assay records

Returns:

A list

parse_chembl_document(data: List)

Parse ChEMBL Document records.

Args:

data: A list of ChEMBL Document records

Returns:

A list

parse_chembl_molecules(data: List)

Parse ChEMBL Molecule records.

Args:

data: A list of ChEMBL Molecule records

Returns:

A list

parse_doc_fields(record: dict, allowed_properties: set, remap: dict = None)

Parse a record from the API.

Args:

record: The record or document from the API allowed_properties: properties that are to be parsed remap: properties that are to be remapped from one name to another

Returns:

A dict of properties

read_json(json_file)

Read in json files

Args:

data_file: json_file to parse

Returns:

A list of records

run(data_file: Optional[str] = None, chembl_data_files: Optional[dict] = None) → None

Method is called and performs needed transformations to process SARS-CoV-2 subset of ChEMBL.

http://chembl.blogspot.com/2020/05/chembl27-sars-cov-2-release.html

Args:

data_file: NOT USED - preserves to placate mypy. Use “data_files” instead chembl_data_files: data files to parse

Returns:

None.