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Vocabulary community contribution: adding a concept class ID

Vocabulary Users
#1

@aostropolets, Thank you to you and the vocab team for all your work building a community contribution process.

I am preparing a submission containing improvements to OMOP Genomic on behalf of the Oncology WG. I would like to add a Concept Class ID of “Protein Expression” so that protein expression measurement concepts (N=131) are recognizable to cancer phenotypers. The current concept class of “Protein Variant” is biologically incorrect for that subset of concepts.

The community contribution templates all specify that only existing standard Concept Class IDs can be supplied. How do I request addition of a new standard Concept Class ID?

Thank you
John

#2

Hi John! Thanks to you and all the WG for working on oncology vocabularies! :slight_smile: Always great to see the community participation.

Adding standard concepts is usually handled through adding the pipeline of adding non-standard terms and then promoting them to standard. This case is more special through since I want to add a class and (I assume) change the class of existing concepts from Protein Expression to Protein Variant. In this way, it may be seen as two tasks:

a) add new class (don’t have template, will just need a short name and a full name)
b) change the attribute of existing concepts (~33k), template 5.

If that is the case and you want to change class for all current Protein Expression concepts, populating the template probably won’t make sense due to the size and uniformity of the task.

Therefore, we can proceed by a) gathering the feedback on such a change here and in the Vocab WG since it concerns modifying existing content and b) examining existing scripts to see if something breaks in OMOP Genomics if classes and changed.

Also tagging @Christian_Reich and @Vlad_Korsik

#3

It looks like the existing classes used in OMOP Genomic have their short and long names the same, so both the short and long name for the new class would be “Protein Expression”.

Not all of the members of the current Protein Variant class need their class changed. Only those that contain “protein expression” in their concept name. There are 131 of those.

I have prepared Template 5 for those 131 class changes, once the new class has been added.

I have also prepared a Template 1 for two new concepts that should be added in the Protein Express class to enable oncology phenotyping:

PD-L1 Protein Expression measurement
P16 Protein Expression measurement

I want the Oncology WG to review the templates before submitting, but if you could go ahead and create the new class that will pave the way.

Thank you!

t