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x-atlas-consortia / hs-ontology-api

Ontology API built on top of the UBKG API and shared by HuBMAP and SenNet projects
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Enhancement: show encoding for assay modality #97

Closed AlanSimmons closed 2 weeks ago

AlanSimmons commented 3 months ago

FYI @bherr2

User story

As a consumer of the ubkg-api (actually, the hs-ontology-api deployment), I want to know how a dataset can be associated with a code in a standard biomedical ontology, such as OBI or EFO.

Solution

Encoded assay modality is already available in the UBKG. Endpoints related to datasets (datasets,assayname,and assaytypes) simply need to include existing information.

Details

The UBKG models the existing assay classification, in which an "assaytype" has a "dataset type". The UBKG model expands on the assay classification with entities of type "measurement assay". A measurement assay is a generic "assay modality" or experimental method that can be the basis of a number of downstream processes: for example, the _scRNAABC and _scRNADEF assay classications may both start with a scRNAseq experiment.

The following illustration illustrates the UBKG model related to assay classifications. Synonyms from the newer rules chain are in red.

image

A measurement assay node in UBKG can be cross-referenced to codes in standard ontologies that are also in UBKG, including OBI and EFO. For example, the Autofluorescence Microscopy measurment assay (HUBMAP:C006002) is cross-referenced to OBI:0003088.

The current mappings were performed with consultation from PSC and CEDAR. Not all of the measurement assays are mapped, and some may be out of date. This is especially the case with some of the assays proposed for SenNet--e.g., DBiT-seq.

AlanSimmons commented 1 month ago

This will be part of the new endpoints described in #102