Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

[Eric D. <ede...@sy...>]

I think this will be needed for the spectral library format at least since
we will be needed a substantial number of concepts that are elements in
mzIdentML. Pierre-Alain’s proposal seems pretty good to me. Anyone else
have comments about doing it that way or refine the idea?



Thanks,

Eric





*From:* Binz Pierre-Alain <Pie...@ch...>
*Sent:* Thursday, June 6, 2019 11:42 PM
*To:* Jones, Andy <And...@li...>; '
psi...@li...' <
psi...@li...>; psi...@li...;
psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
4.1.27_rc1 of psi-ms.obo



Good point Andy.

If one need them for another format (these or others), should one
systematically create all elements also as CV terms, have them annotated
with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in
order to make sure we have consistency of definition across formats?



Pierre-Alain





*De :* Jones, Andy <And...@li...>
*Envoyé :* mercredi 5 juin 2019 16:43
*À :* 'psi...@li...' <
psi...@li...>; psi...@li...;
psi...@li...
*Cc :* Gerhard Mayer <may...@ru...>
*Objet :* Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
4.1.27_rc1 of psi-ms.obo



Hi Gerhard,



Apologies for joining this conversation presumably late – these are encoded
in mzIdentML via named elements. Are these CV terms needed for a different
format?

Best wishes

Andy



*From:* Gerhard Mayer via Psidev-ms-vocab [
mailto:psi...@li...
<psi...@li...>]
*Sent:* 05 June 2019 15:40
*To:* psi...@li...;
psi...@li...; psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo



Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a
residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type."
[PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554

*E-Mail: *ger...@ru...

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