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

[Nuno B. <ban...@uc...>]

+1 makes sense to me too.

Best,

Nuno

On Fri, Jun 7, 2019, 6:57 AM Eric Deutsch <ede...@sy...>
wrote:

> 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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>
>
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