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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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map Orphanet to ORDO #99

Closed AlanSimmons closed 3 months ago

AlanSimmons commented 10 months ago

Statement of problem

When ingesting Orphanet, the current generation framework maps Orphanet IRIs (e.g., http://www.orpha.net/ORDO/Orphanet_69028) to nodes with SAB of ORPHANET.

DOID, on the other hand, uses ordo as the SAB in the dbxref column. The result is that if a DOID node only has a cross-reference to a node in Orphanet, the cross-reference will not be set in UBKG.

Solution

Either map the Orphanet IRIs to the SAB ORDO or map ORDO to Oprhanet.

AlanSimmons commented 9 months ago

Corrected. Will close this after generating a new Data Distillery context.