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OHDSI / Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
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why there's no replacement / Maps to links for OMOP Genomics? #967

Open dimshitc opened 6 months ago

dimshitc commented 6 months ago

why there's no replacement / Maps to links in the OMOP Genomics?

35986591 OMOP5074729 EGFR protein: Substitution in position 790 Thr replaced by Met measurement should be Mapped to 19576591 OMOP5488769 EGFR protein: Substitution in position 790 of T replaced by M measurement

35,984,352 OMOP5061945 BRAF protein: Substitution in position 600 Val replaced by Lys measurement should be Mapped to 19583251 OMOP5495633 BRAF protein: Substitution in position 600 of V replaced by L measurement

<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

35,986,591 | OMOP5074729 | EGFR protein: Substitution in position 790 Thr replaced by Met measurement -- | -- | --

cgreich commented 6 months ago

Yeah. Looks like it, right?

The problem is that "EGFR protein" is not a unique identifier. If there are splice or other types of variants, the coordinates could point to different parts of the protein. Whether or not it is truly the same depends on identifying the sequence either identified in the synonym or in the originating genomic vocabulary (CIViC etc.). That is not trivial. We are planning on doing that till the August release.