Target, drug and association queries: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

Retrieve drug mechanisms by name or identifier¶

dnakit.databases.ch_embl_get_drug_mechanisms(*, limit=None, offset=None, drug_chembl_id=None, drug_name=None, molecule_chembl_id=None, chembl_id=None, drug_chembl_id__exact=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`limit`	integer	None	Maximum results for the current request, not a database-wide total.
`offset`	integer	None	Pagination offset within the current query.
`drug_chembl_id`	string	None	ChEMBL drug/molecule ID (e.g., "CHEMBL1201580" for adalimumab, "CHEMBL4535757" for sotorasib).
`drug_name`	string	None	Drug name for automatic ChEMBL ID lookup (e.g., "trastuzumab", "lapatinib", "aspirin"). Case-insensitive. Triggers internal ChEMBL molecule search — use drug_chembl_id if you already know the ID.
`molecule_chembl_id`	string	None	Alias for drug_chembl_id. ChEMBL molecule ID (e.g., "CHEMBL25" for aspirin).
`chembl_id`	string	None	Alias for drug_chembl_id. ChEMBL ID (e.g., "CHEMBL3301622").
`drug_chembl_id__exact`	string	None	DNAKit optional alias for drug_chembl_id
`verbose`	bool	True	Progress flag.

Retrieve ChEMBL molecular structures and properties¶

dnakit.databases.ch_embl_get_molecule(*, chembl_id=None, format=None, molecule_chembl_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chembl_id`	string	None	ChEMBL molecule ID, e.g., 'CHEMBL25'
`format`	string	None	Response format
`molecule_chembl_id`	string	None	Alias for chembl_id. ChEMBL molecule ID, e.g., CHEMBL1229517.
`verbose`	bool	True	Progress flag.

Retrieve bioactivity measurements for a target¶

dnakit.databases.ch_embl_get_target_activities(*, target_chembl_id__exact=None, limit=None, offset=None, target_chembl_id=None, chembl_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`target_chembl_id__exact`	string	None	ChEMBL target ID (e.g., 'CHEMBL2074'). To find a target ID, use ChEMBL_search_targets with a target name or gene symbol.
`limit`	integer	None	Maximum results for the current request, not a database-wide total.
`offset`	integer	None	Pagination offset within the current query.
`target_chembl_id`	string	None	Alias for target_chembl_id__exact. ChEMBL target ID (e.g., CHEMBL213).
`chembl_id`	string	None	DNAKit optional alias for target_chembl_id
`verbose`	bool	True	Progress flag.

Provide exactly one of these parameter groups: target_chembl_id__exact; target_chembl_id.

Search drugs by name and development phase¶

dnakit.databases.ch_embl_search_drugs(*, query=None, max_phase=None, limit=None, offset=None, molecule_chembl_id=None, q=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	None	Drug name to search for (partial match, case-insensitive). E.g., "sotorasib", "olaparib", "imatinib".
`max_phase`	integer	None	Filter by maximum development phase (0-4)
`limit`	integer	None	Maximum results for the current request, not a database-wide total.
`offset`	integer	None	Pagination offset within the current query.
`molecule_chembl_id`	string	None	Filter by ChEMBL molecule ID (e.g., "CHEMBL1201580" for adalimumab).
`q`	string	None	DNAKit optional alias for query
`verbose`	bool	True	Progress flag.

Search drug targets by name, organism or type¶

dnakit.databases.ch_embl_search_targets(*, target_chembl_id=None, pref_name__contains=None, organism=None, target_type=None, fields=None, limit=None, offset=None, q=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`target_chembl_id`	string	None	Filter by target ChEMBL ID
`pref_name__contains`	string	None	Filter by target name (contains)
`organism`	string	None	Filter by organism (e.g., 'Homo sapiens')
`target_type`	string	None	Filter by target type (e.g., 'SINGLE PROTEIN', 'PROTEIN COMPLEX')
`fields`	array	None	Optional list of ChEMBL target fields to include in each returned target object (projection). ToolUniverse maps this to ChEMBL's `only` query parameter (comma-separated). Supported fields: target_chembl_id, pref_name, organism, target_type, target_components. {"uniqueItems": true, "items": {"type": "string", "enum": ["target_chembl_id", "pref_name", "organism", "target_type", "target_components"]}}
`limit`	integer	None	Maximum results for the current request, not a database-wide total.
`offset`	integer	None	Pagination offset within the current query.
`q`	string	None	DNAKit optional alias for pref_name__contains
`verbose`	bool	True	Progress flag.

Inspect the unavailable CTD chemical–gene interaction query¶

dnakit.databases.ctd_get_chemical_gene_interactions(*, input_terms, verbose=True)

Parameter	Type	Required / default	Description and constraints
`input_terms`	string	Required	Chemical name, CAS RN, or MeSH ID. Unused -- this tool always returns an error; see the tool description.
`verbose`	bool	True	Progress flag.

Retrieve drug–gene interaction evidence in batches¶

dnakit.databases.dgidb_get_drug_gene_interactions(*, genes=None, gene_name=None, gene=None, interaction_sources=None, interaction_types=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`genes`	array	None	List of gene symbols (e.g., ['EGFR', 'BRAF']). Also accepts a single gene as string. Aliases: gene_name, gene. {"items": {"type": "string"}}
`gene_name`	string	None	Alias for genes. Single gene symbol (e.g., 'EGFR').
`gene`	string	None	Alias for genes. Single gene symbol (e.g., 'EGFR').
`interaction_sources`	array	None	Optional filter by data sources (e.g., ['DrugBank', 'ChEMBL']). {"items": {"type": "string"}}
`interaction_types`	array	None	Optional filter by interaction types (e.g., ['inhibitor', 'antagonist']). {"items": {"type": "string"}}
`verbose`	bool	True	Progress flag.

Retrieve gene druggability categories¶

dnakit.databases.dgidb_get_gene_druggability(*, genes=None, gene_name=None, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`genes`	array	None	List of gene symbols to check druggability. Aliases: gene_name, gene. {"items": {"type": "string"}}
`gene_name`	string	None	Alias for genes. Single gene symbol (e.g., 'EGFR').
`gene`	string	None	Alias for genes. Single gene symbol (e.g., 'EGFR').
`verbose`	bool	True	Progress flag.

Retrieve basic drug information and approval status¶

dnakit.databases.drugbank_get_drug_basic_info_by_drug_name_or_id(*, query, case_sensitive=None, exact_match=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	Required	Drug name or DrugBank ID to search for
`case_sensitive`	boolean	None	Select True to perform a case-sensitive search
`exact_match`	boolean	None	Select True to require an exact match with the queried name or ID
`limit`	integer	None	Maximum number of results to return
`verbose`	bool	True	Progress flag.

Retrieve pharmacodynamics, mechanisms and pharmacokinetics¶

dnakit.databases.drugbank_get_pharmacology_by_drug_name_or_drugbank_id(*, query, case_sensitive=None, exact_match=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	Required	Drug name or Drugbank ID to search for
`case_sensitive`	boolean	None	Select True to perform a case-sensitive search
`exact_match`	boolean	None	Select True to require an exact match
`limit`	integer	None	Maximum number of results to return
`verbose`	bool	True	Progress flag.

Retrieve drug targets, enzymes, carriers and transporters¶

dnakit.databases.drugbank_get_targets_by_drug_name_or_drugbank_id(*, query, case_sensitive=None, exact_match=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	Required	Drug name or Drugbank ID to search for
`case_sensitive`	boolean	None	Select True to perform a case-sensitive search
`exact_match`	boolean	None	Select True to require an exact match
`limit`	integer	None	Maximum number of results to return
`verbose`	bool	True	Progress flag.

Search the DrugBank vocabulary by name or synonym¶

dnakit.databases.drugbank_vocab_search(*, query, search_fields=None, case_sensitive=None, exact_match=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	string	Required	Search query string. Can be drug name, synonym, DrugBank ID, or any text to search for.
`search_fields`	array	None	Fields to search in. Available fields: 'DrugBank ID', 'Accession Numbers', 'Common name', 'CAS', 'UNII', 'Synonyms', 'Standard InChI Key'. Defaults to ['Common name', 'Synonyms', 'DrugBank ID']. {"items": {"type": "string"}}
`case_sensitive`	boolean	None	Whether the search should be case sensitive.
`exact_match`	boolean	None	Whether to perform exact matching instead of substring matching.
`limit`	integer	None	Maximum number of results to return.
`verbose`	bool	True	Progress flag.

Retrieve literature-based disease–target association scores¶

dnakit.databases.europepmc_disease_target_score(*, efoId, pageSize=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO (Experimental Factor Ontology) ID of the disease, e.g., 'MONDO_0011996' for chronic myelogenous leukemia
`pageSize`	integer	None	Upstream fetch batch size (max 100), NOT a limit on results returned. The tool pages through all of the disease's associated targets regardless of this value -- 'pageSize': 10 on MONDO_0005011 (Crohn disease) still returns 390 scored targets. Lower it only to make each upstream request smaller.
`verbose`	bool	True	Progress flag.

Retrieve expression-based disease–target association scores¶

dnakit.databases.expression_atlas_disease_target_score(*, efoId, pageSize=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO (Experimental Factor Ontology) ID of the disease, e.g., 'MONDO_0011996' for chronic myelogenous leukemia
`pageSize`	integer	None	Number of results per page (default: 100, max: 100)
`verbose`	bool	True	Progress flag.

Retrieve active ingredients in a drug product¶

dnakit.databases.fda_get_active_ingredient_info_by_drug_name(*, drug_name, limit=None, skip=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drug_name`	string	Required	The name of the drug.
`limit`	integer	None	The number of records to return.
`skip`	integer	None	The number of records to skip.
`verbose`	bool	True	Progress flag.

Retrieve adverse reactions from drug labels¶

dnakit.databases.fda_get_adverse_reactions_by_drug_name(*, drug_name, limit=None, skip=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drug_name`	string	Required	The name of the drug.
`limit`	integer	None	The number of records to return.
`skip`	integer	None	The number of records to skip.
`verbose`	bool	True	Progress flag.

Retrieve drug boxed warnings and safety information¶

dnakit.databases.fda_get_boxed_warning_info_by_drug_name(*, drug_name, limit=None, skip=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drug_name`	string	Required	The name of the drug.
`limit`	integer	None	The number of records to return.
`skip`	integer	None	The number of records to skip.
`verbose`	bool	True	Progress flag.

Retrieve clinical study information from drug labels¶

dnakit.databases.fda_get_clinical_studies_info_by_drug_name(*, drug_name, limit=None, skip=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drug_name`	string	Required	The name of the drug.
`limit`	integer	None	The number of records to return.
`skip`	integer	None	The number of records to skip.
`verbose`	bool	True	Progress flag.

Retrieve drug indications and usage information¶

dnakit.databases.fda_get_indications_by_drug_name(*, drug_name, limit=None, skip=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drug_name`	string	Required	The name of the drug.
`limit`	integer	None	The number of records to return.
`skip`	integer	None	The number of records to skip.
`verbose`	bool	True	Progress flag.

Retrieve mechanisms of action from drug labels¶

dnakit.databases.fda_get_mechanism_of_action_by_drug_name(*, drug_name, limit=None, skip=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drug_name`	string	Required	The name of the drug.
`limit`	integer	None	The number of records to return.
`skip`	integer	None	The number of records to skip.
`verbose`	bool	True	Progress flag.

Retrieve metabolite–disease associations¶

dnakit.databases.hmdb_get_diseases(*, operation=None, hmdb_id=None, compound_name=None, pubchem_cid=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`operation`	string	None	Provider operation mode; see this row's default and allowed values.
`hmdb_id`	string	None	HMDB ID (e.g., HMDB0000122)
`compound_name`	string	None	Compound name (e.g., glucose)
`pubchem_cid`	string	None	PubChem CID as an alternative identifier to hmdb_id or compound_name.
`limit`	integer	None	Maximum number of disease associations to return (default 50).
`verbose`	bool	True	Progress flag.

Retrieve metabolite information by identifier or name¶

dnakit.databases.hmdb_get_metabolite(*, operation=None, hmdb_id=None, compound_name=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`operation`	string	None	Provider operation mode; see this row's default and allowed values.
`hmdb_id`	string	None	HMDB ID (e.g., HMDB0000122)
`compound_name`	string	None	Compound name (e.g., glucose)
`verbose`	bool	True	Progress flag.

Search metabolites by name or molecular formula¶

dnakit.databases.hmdb_search(*, operation=None, query, verbose=True)

Parameter	Type	Required / default	Description and constraints
`operation`	string	None	Provider operation mode; see this row's default and allowed values.
`query`	string	Required	Compound name or molecular formula to search
`verbose`	bool	True	Progress flag.

Retrieve known drugs associated with a disease¶

dnakit.databases.open_targets_get_associated_drugs_by_disease_efo_id(*, efoId, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`size`	integer	None	Limit for the returned page; does not automatically retrieve later pages.
`verbose`	bool	True	Progress flag.

Retrieve target-associated drugs and development phases¶

dnakit.databases.open_targets_get_associated_drugs_by_target_ensembl_id(*, ensemblId, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target.
`size`	integer	None	Limit for the returned page; does not automatically retrieve later pages.
`verbose`	bool	True	Progress flag.

Retrieve HPO phenotypes associated with a disease¶

dnakit.databases.open_targets_get_associated_phenotypes_by_disease_efo_id(*, efoId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The efoId of a disease or phenotype.
`verbose`	bool	True	Progress flag.

Retrieve disease-associated targets with pagination¶

dnakit.databases.open_targets_get_associated_targets_by_disease_efo_id(*, efoId, size=None, index=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The efoId of a disease or phenotype.
`size`	integer	None	Number of top-scored associated targets to return (default 50). A disease can have thousands of associated targets; raise this to retrieve more than the first page.
`index`	integer	None	Zero-based page index for paginating beyond the first `size` targets (default 0).
`verbose`	bool	True	Progress flag.

Retrieve GWAS credible set and locus-to-gene details¶

dnakit.databases.open_targets_get_credible_set_detail(*, studyLocusId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`studyLocusId`	string	Required	Credible set identifier (studyLocusId), a 32-character hash (e.g., 'b758d8fb10924f5338cbad8d27c7dee8'). Obtain from variant credible sets or study credible sets queries.
`verbose`	bool	True	Progress flag.

Retrieve disease ontology parents and ancestors¶

dnakit.databases.open_targets_get_disease_ancestors_parents_by_efo_id(*, efoId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`verbose`	bool	True	Progress flag.

Retrieve disease ontology children and descendants¶

dnakit.databases.open_targets_get_disease_descendants_children_by_efo_id(*, efoId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`verbose`	bool	True	Progress flag.

Retrieve disease descriptions and cross-references¶

dnakit.databases.open_targets_get_disease_description_by_efo_id(*, efoId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`verbose`	bool	True	Progress flag.

Resolve disease names to ontology identifiers¶

dnakit.databases.open_targets_get_disease_id_description_by_name(*, diseaseName=None, query=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`diseaseName`	string	None	The name of the disease to search for.
`query`	string	None	DNAKit optional alias for diseaseName
`verbose`	bool	True	Progress flag.

Retrieve disease synonyms¶

dnakit.databases.open_targets_get_disease_synonyms_by_efo_id(*, efoId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`verbose`	bool	True	Progress flag.

Retrieve therapeutic areas associated with a disease¶

dnakit.databases.open_targets_get_disease_therapeutic_areas_by_efo_id(*, efoId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`verbose`	bool	True	Progress flag.

Retrieve target-associated diseases and phenotypes with pagination¶

dnakit.databases.open_targets_get_diseases_phenotypes_by_target_ensembl(*, ensemblId, page=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The ensemblId of a target.
`page`	object	None	Pagination parameters. `count` in the response is the total across all pages; omit this to get the first page only. {"properties": {"index": {"type": "integer", "description": "The index of the page to retrieve (0-based)."}, "size": {"type": "integer", "description": "The number of associations per page."}}}
`verbose`	bool	True	Progress flag.

Retrieve significant drug adverse event records¶

dnakit.databases.open_targets_get_drug_adverse_events_by_chembl_id(*, chemblId, page=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chemblId`	string	Required	The ChEMBL ID of the drug.
`page`	object	None	Pagination settings. {"properties": {"index": {"type": "integer", "description": "Index of the page to fetch, starting from 0."}, "size": {"type": "integer", "description": "Number of entries per page."}}}
`verbose`	bool	True	Progress flag.

Resolve a generic drug name to a ChEMBL identifier¶

dnakit.databases.open_targets_get_drug_chemb_id_by_generic_name(*, drugName=None, query=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`drugName`	string	None	The generic name of the drug for which the ID is required.
`query`	string	None	DNAKit optional alias for drugName
`verbose`	bool	True	Progress flag.

Retrieve drug indications by ChEMBL identifier¶

dnakit.databases.open_targets_get_drug_indications_by_chembl_id(*, chemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chemblId`	string	Required	The chemblId of the drug for which to retrieve treatable phenotypes information.
`verbose`	bool	True	Progress flag.

Retrieve drug mechanisms by ChEMBL identifier¶

dnakit.databases.open_targets_get_drug_mechanisms_of_action_by_chembl_id(*, chemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chemblId`	string	Required	The ChEMBL ID of the drug.
`verbose`	bool	True	Progress flag.

Retrieve drug warnings by ChEMBL identifier¶

dnakit.databases.open_targets_get_drug_warnings_by_chembl_id(*, chemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`chemblId`	string	Required	The ChEMBL ID of the drug.
`verbose`	bool	True	Progress flag.

Filter target–disease evidence by data source¶

dnakit.databases.open_targets_get_evidence_by_datasource(*, efoId=None, ensemblId=None, gene_symbol=None, disease_name=None, datasourceIds=None, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	None	Disease EFO/MONDO ID (e.g., 'MONDO_0005011' for Crohn disease). Alternative to disease_name.
`ensemblId`	string	None	Target Ensembl gene ID (e.g., 'ENSG00000141510' for TP53). Alternative to gene_symbol.
`gene_symbol`	string	None	HGNC gene symbol (e.g., 'TP53', 'BRCA1'). Auto-resolved to ensemblId.
`disease_name`	string	None	Disease or phenotype name (e.g., 'Crohn disease'). Auto-resolved to efoId.
`datasourceIds`	array	None	List of datasource IDs to filter evidence. Examples: ['gwas_credible_sets', 'europepmc'], ['eva', 'clinical_precedence'], ['intogen', 'cancer_gene_census']. For genetic (GWAS) association evidence use 'gwas_credible_sets' — the retired 'ot_genetics_portal' name is remapped automatically. Omit or pass empty array for all sources. {"items": {"type": "string"}}
`size`	integer	None	Maximum evidence rows to return (default: 50)
`verbose`	bool	True	Progress flag.

Retrieve GWAS cohort and study metadata¶

dnakit.databases.open_targets_get_gwas_study(*, studyId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`studyId`	string	Required	GWAS study accession ID (e.g., 'GCST000392' for T1D Barrett et al., 'GCST90029024' for T2D Loh et al.)
`verbose`	bool	True	Progress flag.

Retrieve publications associated with a target¶

dnakit.databases.open_targets_get_publications_by_target_ensembl_id(*, entityId, additionalIds=None, startYear=None, startMonth=None, endYear=None, endMonth=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`entityId`	string	Required	The ID of the entity (ensemblID).
`additionalIds`	array	None	List of additional IDs to include in the search. {"items": {"type": "string"}}
`startYear`	integer	None	Year at the lower end of the filter.
`startMonth`	integer	None	Month at the lower end of the filter.
`endYear`	integer	None	Year at the higher end of the filter.
`endMonth`	integer	None	Month at the higher end of the filter.
`verbose`	bool	True	Progress flag.

Retrieve biomedical entities similar to a disease¶

dnakit.databases.open_targets_get_similar_entities_by_disease_efo_id(*, efoId, threshold, size, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO ID of the disease.
`threshold`	number	Required	Threshold similarity between 0 and 1. Only results above threshold are returned.
`size`	integer	Required	Number of similar entities to fetch.
`verbose`	bool	True	Progress flag.

Retrieve credible sets from a GWAS study¶

dnakit.databases.open_targets_get_study_credible_sets(*, studyIds, size=None, index=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`studyIds`	array	Required	GWAS study accession IDs (e.g., ['GCST000392']) {"items": {"type": "string"}}
`size`	integer	None	Number of credible sets to return (default 20)
`index`	integer	None	Page index for pagination (0-based, default 0)
`verbose`	bool	True	Progress flag.

Retrieve target functional classes¶

dnakit.databases.open_targets_get_target_classes_by_ensembl_id(*, ensemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target.
`verbose`	bool	True	Progress flag.

Retrieve GO annotations for a target¶

dnakit.databases.open_targets_get_target_gene_ontology_by_ensembl_id(*, ensemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target for which to retrieve Gene Ontology annotations.
`verbose`	bool	True	Progress flag.

Retrieve target genomic coordinates and strand¶

dnakit.databases.open_targets_get_target_genomic_location_by_ensembl_id(*, ensemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target for which to retrieve genomic location information.
`verbose`	bool	True	Progress flag.

Retrieve homologues of a target¶

dnakit.databases.open_targets_get_target_homologues_by_ensembl_id(*, ensemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target for which to retrieve homologues.
`verbose`	bool	True	Progress flag.

Resolve target names to identifiers and descriptions¶

dnakit.databases.open_targets_get_target_id_description_by_name(*, targetName, verbose=True)

Parameter	Type	Required / default	Description and constraints
`targetName`	string	Required	The name of the target for which the ID is required.
`verbose`	bool	True	Progress flag.

Retrieve target interaction partners and evidence with pagination¶

dnakit.databases.open_targets_get_target_interactions_by_ensembl_id(*, ensemblId, page=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target.
`page`	object	None	Pagination parameters. {"properties": {"index": {"type": "integer", "description": "The index of the page to retrieve."}, "size": {"type": "integer", "description": "The number of items per page."}}}
`verbose`	bool	True	Progress flag.

Retrieve known target safety liabilities¶

dnakit.databases.open_targets_get_target_safety_profile_by_ensembl_id(*, ensemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target for which to retrieve safety liabilities.
`verbose`	bool	True	Progress flag.

Retrieve target tractability across treatment modalities¶

dnakit.databases.open_targets_get_target_tractability_by_ensembl_id(*, ensemblId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`ensemblId`	string	Required	The Ensembl ID of the target.
`verbose`	bool	True	Progress flag.

Retrieve GWAS credible sets containing a variant¶

dnakit.databases.open_targets_get_variant_credible_sets(*, variantId=None, size=None, variant_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variantId`	string	None	Open Targets variant ID in format chr_position_ref_alt (e.g., '10_112998590_C_T' for rs7903146)
`size`	integer	None	Number of credible sets to return (default 10)
`variant_id`	string	None	DNAKit optional alias for variantId
`verbose`	bool	True	Progress flag.

Retrieve variant coordinates, frequencies and consequences¶

dnakit.databases.open_targets_get_variant_info(*, variantId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`variantId`	string	Required	Open Targets variant ID in format chr_position_ref_alt (e.g., '10_112998590_C_T' for rs7903146, '19_44908684_T_C' for rs429358). Use the search tool to find variant IDs from rsIDs.
`verbose`	bool	True	Progress flag.

Map disease and phenotype identifiers across databases¶

dnakit.databases.open_targets_map_any_disease_id_to_all_other_ids(*, inputId, verbose=True)

Parameter	Type	Required / default	Description and constraints
`inputId`	string	Required	Any known disease ID (e.g. OMIM:604302, UMLS:C0003873, ICD10:M05, MONDO_0008383, etc.)
`verbose`	bool	True	Progress flag.

Search disease, target and drug entities together¶

dnakit.databases.open_targets_multi_entity_search_by_query_string(*, queryString, entityNames=None, page=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`queryString`	string	Required	The search string for querying information.
`entityNames`	array	None	List of entity names to search for (e.g., target, disease, drug). {"items": {"type": "string"}}
`page`	object	None	Pagination settings with index and size. {"properties": {"index": {"type": "integer", "description": "Pagination index."}, "size": {"type": "integer", "description": "Pagination size."}}}
`verbose`	bool	True	Progress flag.

Find GWAS studies by disease or trait¶

dnakit.databases.open_targets_search_gwas_studies_by_disease(*, diseaseIds=None, enableIndirect=None, disease_name=None, disease=None, trait=None, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`diseaseIds`	array	None	Disease ontology IDs (e.g., ['MONDO_0005148'] for type 2 diabetes, ['MONDO_0004975'] for Alzheimer disease) {"items": {"type": "string"}}
`enableIndirect`	boolean	None	Include studies for child disease terms (default true)
`disease_name`	string	None	Disease or trait name for auto-resolution (e.g., 'type 2 diabetes'). Resolved to diseaseIds automatically.
`disease`	string	None	Alias for disease_name.
`trait`	string	None	Alias for disease_name.
`size`	integer	None	Limit for the returned page; does not automatically retrieve later pages.
`verbose`	bool	True	Progress flag.

Retrieve IntOGen cancer driver association evidence¶

dnakit.databases.open_targets_target_disease_evidence(*, efoId=None, ensemblId=None, gene_symbol=None, disease_name=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	None	EFO/MONDO disease ID (e.g., MONDO_0005011). Alternative to disease_name.
`ensemblId`	string	None	Ensembl gene ID (e.g., ENSG00000141510). Alternative to gene_symbol.
`gene_symbol`	string	None	HGNC gene symbol (e.g., 'TP53', 'BRCA1'). Auto-resolved to ensemblId.
`disease_name`	string	None	Disease or phenotype name (e.g., 'Crohn disease', 'breast carcinoma'). Auto-resolved to efoId.
`verbose`	bool	True	Progress flag.

Resolve compound names to PubChem CIDs¶

dnakit.databases.pub_chem_get_cid_by_compound_name(*, name=None, compound_name=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`name`	string	None	Chemical compound name (e.g., "Aspirin", "Acetaminophen") or IUPAC name. Do not use disease names or medical conditions.
`compound_name`	string	None	Alias for name. The compound name to look up.
`verbose`	bool	True	Progress flag.

Retrieve molecular properties by PubChem CID¶

dnakit.databases.pub_chem_get_compound_properties_by_cid(*, cid, properties=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`cid`	integer	Required	PubChem compound ID to query, e.g., 2244 (Aspirin).
`properties`	array \| string \| null	None	Optional list of PubChem property names to retrieve (e.g. ['MolecularFormula','InChIKey','XLogP','IUPACName','MolecularWeight']). If omitted, returns a default set (MolecularWeight, IUPACName, ConnectivitySMILES). For SMILES use the current names 'ConnectivitySMILES' (was 'CanonicalSMILES') or 'SMILES' (was 'IsomericSMILES') — a legacy name still returns data, but under the current key, not the one requested. See PubChem PUG-REST property tables for valid names. Accepts a list or a comma-separated string. {"items": {"type": "string"}}
`verbose`	bool	True	Progress flag.

Retrieve pathway-based disease–target association scores¶

dnakit.databases.reactome_disease_target_score(*, efoId, pageSize=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`efoId`	string	Required	The EFO (Experimental Factor Ontology) ID of the disease, e.g., 'MONDO_0011996' for chronic myelogenous leukemia
`pageSize`	integer	None	Number of results per page (default: 100, max: 100)
`verbose`	bool	True	Progress flag.