metakb.services.search#

Provide search services.

exception metakb.services.search.EmptySearchError[source]#

Raise for invalid search parameters (e.g. no parameters given)

exception metakb.services.search.PaginationParamError[source]#

Raise for invalid pagination parameters.

async metakb.services.search.batch_search_statements(repository, normalizer, variations=None, start=0, limit=None)[source]#

Fetch all statements associated with any of the provided variation description strings.

Because this method could be expanded to include other kinds of search terms, variations is optionally nullable.

>>> from metakb.repository.neo4j_repository import get_driver, Neo4jRepository
>>> from metakb.normalizers import ViccNormalizers
>>> from metakb.services.search import batch_search_statements
>>> repo, normalizer = Neo4jRepository(get_driver()), ViccNormalizers()
>>> response = await batch_search_statements(repo, normalizer, ["EGFR L858R"])

All terms are normalized, so redundant terms don’t alter search results.

>>> redundant_response = await batch_search_statements(
...     repo, normalizer, ["EGFR L858R", "NP_005219.2:p.Leu858Arg"]
... )
>>> len(response.statement_ids) == len(redundant_response.statement_ids)
True
Parameters:

  • repository (AbstractRepository) –

  • normalizer (ViccNormalizers) –

  • variations (Optional[list[str]]) – a list of variation description strings, e.g. ["BRAF V600E"]

  • start (int) – Index of first result to fetch. Must be nonnegative.

  • limit (Optional[int]) – Max number of results to fetch. Must be nonnegative. Revert to default defined at class initialization if not given.

Return type:

SearchResult

Returns:

response object including all matching statements

Raises:
async metakb.services.search.search_statements(repository, normalizer, variation=None, disease=None, therapy=None, gene=None, statement_id=None, start=0, limit=None)[source]#

Get nested statements from queried concepts that match all conditions provided. For example, if variation and therapy are provided, will return all statements that have both the provided variation and therapy.

>>> from metakb.repository.neo4j_repository import get_driver, Neo4jRepository
>>> from metakb.normalizers import ViccNormalizers
>>> from metakb.services.search import search_statements
>>> repo, normalizer = Neo4jRepository(get_driver()), ViccNormalizers()
>>> result = search_statements(repo, normalizer, variation="BRAF V600E")
>>> result.statements[0].reportedIn[0].urls[0]
'https://www.accessdata.fda.gov/drugsatfda_docs/label/2020/202429s019lbl.pdf'

Variation, disease, therapy, and gene terms are resolved via their respective concept normalization services.

Parameters:

  • repository (AbstractRepository) – data repository instance

  • normalizer (ViccNormalizers) – normalizers container instance

  • variation (Optional[str]) – Variation query. Free text variation description, e.g. "BRAF V600E", or GA4GH variation ID, e.g. "ga4gh:VA.4XBXAxSAk-WyAu5H0S1-plrk_SCTW1PO". Case-insensitive.

  • disease (Optional[str]) – Disease query. Full disease name, e.g. "glioblastoma", common shorthand name, e.g. "GBM", concept URI, e.g. "ncit:C3058". Case-insensitive.

  • therapy (Optional[str]) – Therapy query. Full name, e.g. "imatinib", trade name, e.g. "GLEEVEC", or concept URI, e.g. "chembl:CHEMBL941". Case-insensitive.

  • gene (Optional[str]) – Gene query. Common shorthand name, e.g. "NTRK1", or compact URI, e.g. "ensembl:ENSG00000198400".

  • statement_id (Optional[str]) – Statement ID query provided by source, e.g. "civic.eid:3017".

  • start (int) – Index of first result to fetch. Must be nonnegative.

  • limit (Optional[int]) – Max number of results to fetch. Must be nonnegative. Revert to default defined at class initialization if not given.

Return type:

SearchResult

Returns:

Results including terms with normalization, and all statements

Raises: