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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Make L-amino acid default #15087

Closed ValWood closed 4 months ago

ValWood commented 6 years ago

follow on from https://github.com/geneontology/go-ontology/issues/15022

Make L-amino acid the default (but exact synonym)

Only make a term if D-form only if required

pgaudet commented 6 years ago

https://en.wikipedia.org/wiki/Amino_acid

deustp01 commented 6 years ago

Works fine for mammals, but what about bacteria that use D-amino acids in their cell walls and L-amino acids in their proteins, and thus synthesize, transport both and distinguish between them?

pgaudet commented 6 years ago

Thanks @deustp01 Do they synthetize all amino acids as D-form ?

deustp01 commented 6 years ago

I don't know - @hdrabkin ? Or Jim Hu?

pgaudet commented 6 years ago

According to wikipedia (I know...) "These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics.[12]" https://en.wikipedia.org/wiki/Amino_acid

ValWood commented 4 months ago

Is this out of date?

pgaudet commented 4 months ago

Yes, we will deal with this with the CHEBI 7.3 ticket https://github.com/geneontology/go-ontology/issues/27059