SenNet Source schema

Overview:

This page describes the Source attributes available for querying via the SenNet parameterized search endpoint. Full Source schema information can be found at the SenNet Search API documentation page at the bottom of the page in the Schemas section under the Source section. This page describes the Source schema for SenNet data. Source data may be returned itself or a part of another entity. For example, this endpoint searches Sources :

GET https://search.api.sennetconsortium.org/param-search/sources?group_name=TMC%20-%20Johns%20Hopkins%20University

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 Source Schema attribute metadata.living_source_data has a type of Source Metadata Schema, and Source Metadata Schema has an attribute preferred_term supporting UMLS concepts. Querying Sources supports a term to search for living sources who are male, such as metadata.living_source_data.preferred_term=Male, and a query like:

GET https://search.api.sennetconsortium.org/param-search/sources?metadata.living_donor_data.preferred_term=Male

Dataset Attributes

Attribute Type Description
description string Free text description of the source
uuid string The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17
sennet_id string A SenNet Consortium wide unique identifier randomly generated in the format SNT###.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 SenNet data provider group which registered the sample. See the SenNet Data Provider Groups for a list of valid group names.
label string Lab provided, de-identified name for the source
metadata.living_source_data array of Source Metadata Schema Information about the source who’s tissue was used. The tissue was obtained during a procedure. Only living_source_data or organ_source_data, not both can be defined for a single source.
metadata.organ_source_data array of Source Metadata Schema Information about the source who’s organ(s) was/were used. The organ was obtained via an organ donation program from a deceaced source. Only living_source_data or organ_source_data, not both can be defined for a single source.

Source Metadata Schema

attributes as listed at entity-api Source schema drop-down, metadata drop-down, SourceMetadata drop-down:

Attribute Type Description
code string This is a Code from a source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS source vocabulary terms.
sab string This is the source vocabulary in the SenNet Knowledge Graph. Currently limited to UMLS source vocabularies.
concept_id string This is the Concept ID from the SenNet 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 SenNet 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 SenNet 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 SenNet Knowledge Graph, currently limited to UMLS source vocabularies.. This sab corresponds to the grouping_code.
graph_version string This is the version of the SenNet 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 source-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 source-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 SourceSchema is one of the values following enumerated values: