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obophenotype / bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)
https://obophenotype.github.io/bio-attribute-ontology
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Add lipid trait terms for GWAS/EFO #258

Closed rays22 closed 1 year ago

rays22 commented 1 year ago

Update some lipid trait term labels. Add new level of lipid in blood serum trait terms.

If applied, this is part of a series to fix #257.

Addresses https://github.com/EBISPOT/efo/issues/1905 Addresses https://github.com/EBISPOT/efo/issues/1924

rays22 commented 1 year ago

This error:

Level Rule Name Subject Property Value
ERROR biological-attribute-child-violation OBA:0003476 rdfs:subClassOf Not a subclass of biological attribute

is cause by the recent obsoletion of GO:0070265 necrotic cell death

The rest of the errors can be fixed by refreshing chebi-slim and the OBA imports.

matentzn commented 1 year ago

Move the cell death one into oba-edit.obo the way we did with some of the other ones?

matentzn commented 1 year ago

Looks great Ray, are these all the requested Lipid terms?

rays22 commented 1 year ago

Looks great Ray, are these all the requested Lipid terms?

I have found 24 ChEBI terms and 2 Swisslipid terms that are equivalent to the Lipid Maps terms. I could not find ChEBI/Swisslipid terms for 2 xenobiotics:

(5z7e)-(3s)-262626272727-hexafluoro-910-seco-5710(19)16-cholestatetraen-23-yne-325-diol measurement lipidmaps:LMST03020077  LM:LMST03020077 not found       This is a synthetic Vitamin D3 derivative, i.e. a xenobiotic.
cyanidin 35-diglucoside (66-malyl diester) measurement  lipidmaps:LMPK12010207  LM:LMPK12010207 not found       This is a plant flavonoid, i.e. xenobiotic.

LM:LMST03020077 (a synthetic vitamin D3 analog) and LM:LMPK12010207 (a flavonoid) could be added to OBA if desired (in a separate PR).