chembl Processor (indra_cogex.sources.chembl)

Processor for ChEMBL.

class ChemblIndicationsProcessor(version=None)

Bases: Processor

A processor for ChEMBL indications.

get_nodes()

Iterate over ChEMBL chemicals and indications

Return type:

Iterable[Node]

get_relations()

Iterate over ChEMBL indication annotations.

Return type:

Iterable[Relation]

MOLECULE_SQL = '\nSELECT DISTINCT\n    MOLECULE_DICTIONARY.chembl_id,\n    MOLECULE_DICTIONARY.pref_name\nFROM MOLECULE_DICTIONARY\nJOIN DRUG_INDICATION ON MOLECULE_DICTIONARY.molregno == DRUG_INDICATION.molregno\n'

SQL for ChEMBL to get molecules that have indications

SQL = '\nSELECT\n    MOLECULE_DICTIONARY.chembl_id,\n    DRUG_INDICATION.mesh_id,\n    DRUG_INDICATION.max_phase_for_ind\nFROM MOLECULE_DICTIONARY\nJOIN DRUG_INDICATION ON MOLECULE_DICTIONARY.molregno == DRUG_INDICATION.molregno\n'

SQL for ChEMBL to get indications