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x-atlas-consortia / ubkg-etl

A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)
MIT License
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Update assay classes to match PR #4 in dev-assay-class #166

Open AlanSimmons opened 1 week ago

AlanSimmons commented 1 week ago

Reference

https://github.com/x-atlas-consortia/dev-assay-class-api/pull/4#event-15300626646

AlanSimmons commented 1 week ago

Changes

  1. HUBMAP:C004022/SENNET:C004022 term changed from "json-based" to "json_based".
  2. All references to vitessce_hint of "json-based" changed to "json_based".
  3. Added assay classification C202010 (derived salmon_rnaseq_10x json-based).
  4. Added vitessce_hint C202023 (segmentation_mask), with term separate from assaytype of segmentation-mask.
  5. Added vitessce_hints to assay classification C200370 (derived pas_ftu_segmentation).
AlanSimmons commented 1 week ago

Bug fix

The description concept scRNAseq (10x Genomics v3) was missing a concept ID. This is why the description was null for at least 2 assay classifications.

AlanSimmons commented 1 week ago

Update

Local instance of UBKG neo4j appears to align with latest assayclasses.json.

AlanSimmons commented 1 week ago

Additional corrections to dir-schema to match changes made to assayclasses.json