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

[Jones, A. <And...@li...>]

Yes that seems okay to me. I’m sure ontology purists would hate this approach, but it seems pragmatically useful for what we need to achieve.
Best wishes
Andy

From: Nuno Bandeira [mailto:ban...@uc...]
Sent: 07 June 2019 16:14
To: Mass spectrometry standard development <psi...@li...>
Cc: Jones, Andy <jo...@li...>; psi...@li...; psi...@li...; Eric Deutsch <ede...@sy...>; Gerhard Mayer <may...@ru...>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

+1 makes sense to me too.

Best,

Nuno

On Fri, Jun 7, 2019, 6:57 AM Eric Deutsch <ede...@sy...<mailto: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...<mailto:Pie...@ch...>>
Sent: Thursday, June 6, 2019 11:42 PM
To: Jones, Andy <And...@li...<mailto:And...@li...>>; 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto: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...<mailto:And...@li...>>
Envoyé : mercredi 5 juin 2019 16:43
À : 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc : Gerhard Mayer <may...@ru...<mailto: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...]
Sent: 05 June 2019 15:40
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto: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...<mailto:ger...@ru...>

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

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