search

Search for entities by label, with optional filters

Args: q (str, optional): Query string. Defaults to ":". category (str, optional): Filter by biolink model category. Defaults to None. in_taxon (str, optional): Filter by taxon CURIE. Defaults to None. in_taxon_label (str, optional): Filter by taxon label. Defaults to None. namespace (str, optional): Restrict to these CURIE namespaces. Defaults to None. exclude_namespace (str, optional): Drop these CURIE namespaces. Defaults to None. subset (str, optional): Restrict to entities in these ontology subsets. Defaults to None. exclude_subset (str, optional): Drop entities in these ontology subsets. Defaults to None. scope (SearchScope, optional): A named filter bundle. Supplies category, namespace, subset, exclude_subset and in_taxon where they were not passed explicitly; an explicit value wins for that axis. The resolved filters are echoed on the response. Defaults to None. facets (bool, optional): True facets every filterable field with no cap on values, which is how a caller discovers what namespace and subsets accept. False disables faceting. Omitted keeps the historical category + in_taxon_label counts. Defaults to None. match_type (SearchMatchType, optional): relevance (default) or exact. In exact mode a result is returned only when q equals the entity's name or one of its exact synonyms as a whole string, case-insensitively; otherwise the result set is empty. Items carry matched_field and match_type so callers can apply their own precision policy. Defaults to relevance. include_phenotypes (bool, optional): Include phenotype annotations and closures. Defaults to False. include_descendants (bool, optional): Include ontology descendants. Defaults to False. offset (int, optional): Offset for pagination. Defaults to 0. limit (int, optional): Limit results. Defaults to 20.

Returns: EntityResults

get/v3/api/search

Request

  • Base URL
    https://monarchinitiative.org (the document declares no server; this is the origin it was published from)
  • URL
    https://monarchinitiative.org/v3/api/search
  • Auth
    none declared

Query parameters

qstring
categoryEntityCategory[] nullable
in_taxonstring[] nullable
in_taxon_labelstring[] nullable
namespacestring[] nullable
exclude_namespacestring[] nullable
subsetstring[] nullable
exclude_subsetstring[] nullable
scope'human_disease' | 'human_phenotype' | 'human_gene' | 'rare_disease'

The named filter bundles /search?scope= accepts.

facetsboolean nullable
match_type'relevance' | 'exact'

How strict /search should be about what counts as a hit.

relevance is the search contract: maximise recall and always return the best available hit. exact is the grounding contract: return an entity only when the query names it, and an empty result set otherwise.

include_phenotypesboolean

Include the entity's phenotype annotations and their closures. Large: these are most of the response when present.

include_descendantsboolean

Include the entity's ontology descendants. Large: these are most of the response when present.

limitinteger
offsetinteger

Response

Successful Response

limitinteger required

number of items to return in a response

offsetinteger required

offset into the total number of items

totalinteger required

total number of items matching a query

Changes

    • info

      added the new optional query request parameter exclude_namespace

    • info

      added the new optional query request parameter exclude_subset

    • info

      added the new optional query request parameter facets

    • info

      added the new optional query request parameter in_taxon

    • info

      added the new optional query request parameter include_descendants

    • info

      added the new optional query request parameter include_phenotypes

    • info

      added the new optional query request parameter match_type

    • info

      added the new optional query request parameter namespace

    • info

      added the new optional query request parameter scope

    • info

      added the new optional query request parameter subset

    • info

      added the enum value biolink:ClinicalMeasurement to the property anyOf[subschema #1]/items/ of the query request parameter category

    • info

      added the optional property // to the response with the status

    • info

      added the optional property // to the response with the status

    • info

      added the optional property to the response with the status