[Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI

[Colin Batchelor]

Hello,

(Apologies for top-posting; using webmail as at conference between talks.)

If the amino acid metabolism terms deal with amino acid residues within proteins as well as the free amino acid molecules, then the parent should be organic amino compound because all of them have amino nitrogens but only the C-terminal ones are carboxylic acids.  Can't tell from a really cursory inspection how the GO term is used, though.

Best wishes,
Colin.
________________________________________
From: Midori Harris [midori at ebi.ac.uk]
Sent: 29 June 2009 09:57
To: Chris Mungall
Cc: chebi-ontology at lists.sourceforge.net; Ontology Editors
Subject: Re: [Chebi-ontology] [Ontology-editors] Inference of GO BP relationships from CHEBI

On Fri, 26 Jun 2009, Chris Mungall wrote:

>
> On Jun 26, 2009, at 5:15 AM, Midori Harris wrote:
>
>> For the amine/amino/etc. terms, I wonder if the best fit between ChEBI and
>> GO might be:
>>
>> GO:amine_metabolism =def GO:metabolism that has_participant
>> ChEBI:organic_amino_compound
>>
>> ... even though the names don't quite match (we can edit the GO name and
>> def). At a quick glance, the children of the ChEBI term cover everything
>> currently grouped under amine metabolism in GO, and I didn't spot any
>> children in GO that obviously wouldn't work with this.
>
> OK, that looks like it will work nicely.
>
> I'm not sure which of the is_a parents of amino acid in CHEBI would be
> primary, organic amino compound or carboxylic acid.

urgh, it feels like a coin flip, but I'm leaning a bit towards organic
amino compound. I'd feel better if I could pin down reasons why I think
that ...

m


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