psidev-ms-dev

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

[Gerhard M. <may...@ru...>]

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>

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

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

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...; 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...<mailto:ger...@ru...>

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

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

[Binz Pierre-A. <Pie...@ch...>]

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...]
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>

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...

*Web: *www.ruhr-uni-bochum.de/mpc

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...
>
> *Web: *www.ruhr-uni-bochum.de/mpc
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

Re: [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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