Re: [Psidev-ms-dev] Associating CV / ontology annotations

[Kent L. <knl...@in...>]

Hi Phil,

Have a closer look at the ParamGoup and ParamGroupList types.  They were
designed with this sort of flexibility and aggregability in mind.

Regards,

Kent=20

> -----Original Message-----
> From: psi...@li...=20
> [mailto:psi...@li...] On=20
> Behalf Of Philip Jones
> Sent: Tuesday, February 27, 2007 1:18 PM
> To: psi...@li...
> Subject: [Psidev-ms-dev] Associating CV / ontology annotations
>=20
> Hi,
>=20
> I would like to suggest that it may be useful to include a=20
> mechanism to associate cvParam elements together to allow=20
> more complex annotation of entities in dataXML.  Here is an=20
> artificial example to illustrate the
> problem:
>=20
> <activation>
>     <cvParam cvLabel=3D"PSI" accession=3D"PSI:1000044" name=3D"Method" =

> value=3D"CID"/>
>     <cvParam cvLabel=3D"PSI" accession=3D"PSI:1000045"=20
> name=3D"CollisionEnergy" value=3D"35.00"/>
>     <cvParam cvLabel=3D"UO" accession=3D"UO:0000112"=20
> name=3D"Joule"/> </activation>
>=20
> In this example, the third CV parameter is an annotation of=20
> the second, indicating the units of the value of collision=20
> energy from the OBO unit ontology. (I know that collision=20
> energy is normally measured in eV, but eV is not in the UO=20
> ontology ! .... Just an example.)
>=20
> So the question is, do we need this mechanism and if so, how=20
> do we implement it?
>=20
>  From my point of view, I think it is needed.  I have wanted=20
> to be able to do this on numerous occasions when creating=20
> PRIDE entries for submissions - PRIDE uses the existing=20
> mzData schema cvParam mechanism for annotation.
>=20
> I think this could / should be kept simple.  It would be easy=20
> to allow an arbitrarily complex hierarchy of terms to be=20
> created, but I think that might result in chaos.=20
>=20
> Two possible solutions:
>=20
> 1. Perhaps just add an optional attribute to allow associated=20
> cvParams to be linked, e.g. with a number or perhaps=20
> something more guaranteed to be unique, like an LSID?
>=20
> 2. Perhaps add a single additional layer to the hierarchy,=20
> something like this:
>=20
> <activation>
>     <annotation>
>         <cvParam cvLabel=3D"PSI" accession=3D"PSI:1000044" =
name=3D"Method"=20
> value=3D"CID"/>
>     </annotation>
>     <annotation>
>         <cvParam cvLabel=3D"PSI" accession=3D"PSI:1000045"=20
> name=3D"CollisionEnergy" value=3D"35.00"/>
>         <cvParam cvLabel=3D"UO" accession=3D"UO:0000112" =
name=3D"Joule"/>
>     </annotation>
> </activation>
>=20
> Best regards,
>=20
> Phil.
>=20
> --
> _______________________________________
> Phil Jones
> Software Engineer
> PRIDE Project Team
> Sequence Database Group
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK
>=20
> Tel +44 (0)1223 492 610 (Direct Line)
> mailto:pj...@eb...
>=20
>=20
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>=20