HuBMAP Donor schema
Overview:
This page describes the Donor attributes available for querying via the HuBMAP parameterized search endpoint. Full Donor schema information can be found at the HuBMAP Search API documentation page at the bottom of the page in the Schemas section under the Donor section.
This page describes the Donor schema for HuBMAP data. Donor data may be returned itself or a part of another entity. For example, this endpoint searches Donors :
GET https://search.api.hubmapconsortium.org/v3/param-search/donors?group_name=Stanford%20TMC
Description:
A query string is built by combining schema elements documented below with matching values. Each “term” of the query is combined using the & character, and the entire query is attached to the base URL after a ? character, per web standards.
Query terms may be composited from attributes deeper in the schema type of an attribute. For example, the Donor Schema attribute metadata.living_donor_data is has a type of Donor Metadata Schema, and Donor Metadata Schema has an attribute preferred_term supporting UMLS concepts. Querying Donors supports a term to search for living donors who are male, such as metadata.living_donor_data.preferred_term=Male, and a query like:
GET https://search.api.hubmapconsortium.org/v3/param-search/donors?metadata.living_donor_data.preferred_term=Male
Dataset Attributes
| Attribute | Type | Description |
|---|---|---|
| description | string | Free text description of the donor |
| uuid | string | The HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17 |
| hubmap_id | string | A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity. |
| data_access_level | string from data_access_level attribute values |
One of the values: public, consortium |
| group_name | string | The name of the HuBMAP data provider group which registered the sample. See the HuBMAP Data Provider Groups for a list of valid group names. |
| label | string | Lab provided, de-identified name for the donor |
| metadata.living_donor_data | array of Donor Metadata Schema |
Information about the donor who’s tissue was used. The tissue was obtained during a procedure. Only living_donor_data or organ_donor_data, not both can be defined for a single donor. |
| metadata.organ_donor_data | array of Donor Metadata Schema |
Information about the donor who’s organ(s) was/were used. The organ was obtained via an organ donation program from a deceaced donor. Only living_donor_data or organ_donor_data, not both can be defined for a single donor. |
Donor Metadata Schema
attributes as listed at entity-api Donor schema drop-down, metadata drop-down, DonorMetadata drop-down:
| Attribute | Type | Description |
|---|---|---|
| code | string | This is a Code from a source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS source vocabulary terms. |
| sab | string | This is the source vocabulary in the HuBMAP Knowledge Graph. Currently limited to UMLS source vocabularies. |
| concept_id | string | This is the Concept ID from the HuBMAP Knowledge Graph. Currently limited to UMLS concepts. |
| data_value | string | The data value of the record. |
| units | string | This are the units for the data value. |
| preferred_term | string | This is the preferred display term for the item. It may or may not correspond to a term in UMLS for this concept. |
| grouping_concept | string | This is the Concept ID from the HuBMAP Knowledge Graph, currently limited to UMLS concetps, that is to be used for grouping the record. |
| grouping_concept_preferred_term | string | This is the preferred display term for the facet in which this record should be counted for faceted search in the portal. It may or may not correspond to a term in UMLS for the grouping concept. |
| grouping_code | string | This is a Code from a source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS vocabulary codes. This code corresponds to the grouping_concept. |
| grouping_sab | string | This is a grouping for the source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS source vocabularies.. This sab corresponds to the grouping_code. |
| graph_version | string | This is the version of the HuBMAP Knowledge Graph that the Concept appears in, currently the version of UMLS that is used. |
| start_datetime | integer | This is the approximate time difference in seconds between the procurement and the start of this event (this is to construct time series records of clinical data for event-level data not donor-level data). An empty or zero value designates missing data or that this field is not applicable for the concept. |
| end_datetime | integer | This is the approximate time difference in seconds between the procurement and the end of this event (this is to construct time series records of clinical data for event-level data not donor-level data). An epty of zero value designates missing data or that this field is not applicable for the concept |
data_access_level attribute values
The data_access_level of the DonorSchema is one of the values following enumerated values:
publicconsortium