Added new 'growth factor' terms #227
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ar-ibrahim
commented
Mar 9, 2023
ar-ibrahim
commented
- issue EFO-OBA mapping (growth factor measurements) #225
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QC checks for this PR repeatedly failed. There were several issues identified by QC which I've attempted to resolve. First, I removed a new OBA term which already exists. Then I removed duplicated terms. I then imported the Protein Ontology terms used to construct the new terms. The checks still failed. |
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There are more than 70 errors still, I think you will need a bit of Ray magic when he is back, but if you dare to fix yourself, you should learn how to run the test pipeline locally, and open this file: reports/oba.owl-obo-report.tsv Which has most of the errors in it. From what I can see, the main problem is that your biological attribute terms do not currently classify under "OBA:biological attribute" - is there a grouping class for you new terms that you can manually turn into a subclass of OBA:biological attribute? |
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These new terms (growth factors) can be a subclass of 'protein amount' OBA:VT0010120. |
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Are they all just a flat list under that class? you will have to open protege and manually make the top level classes of your newly added classes children of protein amount |
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In Protege the new terms are all children of 'amount'. It's more accurate that they should be subclasses of 'protein amount'. There are a total of 63 new terms. So in Protege in 'Subclass of', do I manually add 'protein amount' to all these terms? |
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If they are a flat list, then yes; but it would be better if you had a grouping class for your new terms, like "growth factor attribute" - then you can simply make that a subclass of protein amount, and the rest will automatically classify under "growth factor attribute". |
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Not exactly sure how to do that. |
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Ok, I fixed all but two errors (which required adding a bunch of PRO terms to our PRO slim). These two need fixing from your side:
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- fixed 2 errors: 1- OBA:2050131 and OBA:2050134 use the same PRO term 2 -OBA:2050145 and OBA:2050182 use the same PRO term - replaced entity term (PR:000032046) for (OBA:2050177 transforming growth factor beta receptor type 3 amount) with more accurate term (PR:Q03167)
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I think the QC fail this time is because after reviewing all the entity PRO terms, I replaced the entity term (PR:000032046) for (OBA:2050177 transforming growth factor beta receptor type 3 amount) with the more accurate term (PR:Q03167), so an updated import is needed. |
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Cool checking it. Thanks! |
@ar-ibrahim it seems like you didnt update (or maybe not commit?) the import file after all?
