Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] term proposal

[Juan A. V. <ju...@eb...>]

Hi Salva,

On 11 Nov 2012, at 15:38, Salvador Martínez de Bartolomé wrote:

> Hi Juanan,
> I know that PRIDE XML will "disappear" when you adopt the mzIdentML, but
> currently there are several tools generating PRIDE XML files that may want
> to clarify that.
> However, if the guideline is to include only the "correct" identifications,
> that's all.
> One question, what are your plans to substitute PRIDE XML by mzIdentML?

We will not 'substitute' but keep both formats as submission formats. The idea is to have mzIdentML 1.1 files supported at (around) March next year.


> Until when are you going to accept PRIDE XML files?

PRIDE XML will be supported for quite some years still. 

Cheers,

Juanan



> Thanks!
> 
> Salvador Martínez de Bartolomé Izquierdo 
> Bioinformatics Support - ProteoRed
> Lab- B1, National Center for Biotechnology 
> C/ Darwin, 3 Universidad Autónoma de Madrid Cantoblanco, 
> 28049 Madrid Spain
> Phone: +34 91 585 4613
> Fax: +34 91 585 4506
> 
> http://www.proteored.org
> http://proteo.cnb.csic.es/trac
> https://sites.google.com/site/bioinformaticaproteomica/
> 
> 
> -----Mensaje original-----
> De: Juan Antonio Vizcaino [mailto:ju...@eb...] 
> Enviado el: 09 November 2012 16:48
> Para: psi...@li...
> CC: psi...@li...; 'Gerhard Mayer'; 'Mass spectrometry
> standard development'
> Asunto: Re: [Psidev-pi-dev] [Psidev-ms-vocab] term proposal
> 
> Hi Salva,
> 
> I don't think a CV term is actually needed for this case. PRIDE XML will be
> slowly phased out and mzIdentML should be the substitute.
> 
> The guideline would be to include in the PRIDE XML file only the
> identifications that you consider to be reliable. 
> 
> Cheers,
> 
> Juan Antonio
> 
> 
> 
> On 7 Nov 2012, at 08:51, Salvador Martínez de Bartolomé wrote:
> 
>> Well, maybe is more suitable for a PRIDE XML file. What does the PRIDE 
>> team think?
>> 
>> Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support - 
>> ProteoRed
>> Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad 
>> Autónoma de Madrid Cantoblanco,
>> 28049 Madrid Spain
>> Phone: +34 91 585 4613
>> Fax: +34 91 585 4506
>> 
>> http://www.proteored.org
>> http://proteo.cnb.csic.es/trac
>> https://sites.google.com/site/bioinformaticaproteomica/
>> 
>> 
>> 
>> -----Mensaje original-----
>> De: Gerhard Mayer [mailto:Ger...@ru...]
>> Enviado el: 07 November 2012 09:49
>> Para: Salvador Martínez de Bartolomé; 
>> psi...@li...;
>> psi...@li...; Mass spectrometry standard 
>> development
>> Asunto: Re: term proposal
>> 
>> Hi Salvador, hi all,
>> 
>> I think you mean the attribute passThreshold of the elements 
>> SpectrumIdentificationItem and ProteindetectionHypothesis of mzIdentML.
>> 
>> In general we decided to avoid CV terms for informations which we can 
>> describe by attributes of our standard file formats.
>> In which ParamGroup do you want to state such a CV term?
>> 
>> Does anyone of the PRIDE team sees a need for such a CV term?
>> 
>> Best,
>> Gerhard
>> 
>> 
>> Am 07.11.2012 09:30, schrieb Salvador Martínez de Bartolomé:
>>> Hi Gerhard:
>>> Just a proposal for a new term:
>>> A term like "pass threshold" that takes boolean values.
>>> In the mzIdentML file there is already an attribute that means 
>>> exactly that, but maybe it would be useful to have the possibility of 
>>> having this term to state it in some ParamGroup... or to use it in 
>>> the a PRIDE XML file using the PSI-MS ontology.
>>> It just my opinion...
>>> Thanks!
>>> 
>>> Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support - 
>>> ProteoRed
>>> Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad 
>>> Autónoma de Madrid Cantoblanco,
>>> 28049 Madrid Spain
>>> Phone: +34 91 585 4613
>>> Fax: +34 91 585 4506
>>> 
>>> http://www.proteored.org
>>> http://proteo.cnb.csic.es/trac
>>> https://sites.google.com/site/bioinformaticaproteomica/
>>> 
>>> 
>> 
>> --
>> ---
>> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik 
>> Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für 
>> klinische Forschung I (ZKF I)
>> E.042
>> Universitätsstrasse 150
>> D-44801 Bochum
>> 
>> Phone:	+49(0)234/32-29836
>> Fax:	+49(0)234/32-14554
>> Email:	Ger...@ru...
>> Web:	http://www.medizinisches-proteom-center.de
>> 
>> 
>> 
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> 
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