Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 1.1.0_rc1 of XLMOD.obo

[Yasset Perez-R. <yp...@eb...>]

Why not adding this into PSI-MS as a section as you already did. It 
would be great to have this only in one place. We have already fragment 
neutral loss in the PSI-MS 
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001524 
. I recommend to extend only this concept and do not create another Obo 
file, for two main reasons:

   - Is not recommended in any of our file formats.

   - It is something will not growth more than a ~100 terms, then we 
need to mantain another file just for a few number of terms.

   - It will be in two files the same information in PSI-MS and XLMOD 
obo, we will need to take care of sync, etc.

Hope you understand my points.

Regards

Yasset


On 27/06/2017 10:58, Jones, Andy wrote:
>
> It is stand-alone for the moment – for encoding cross-linking reagents 
> that didn’t fit easily into other mod CVs (PSI-MOD or Unimod) for 
> different reasons
>
> *From:*Yasset Perez-Riverol [mailto:yp...@eb...]
> *Sent:* 27 June 2017 10:53
> *To:* mayerg97 <ger...@ru...>; 
> psi...@li...; 
> psi...@li...; Mass spectrometry standard 
> development <psi...@li...>; Lutz Fischer 
> <lfi...@st...>; le...@im...
> *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 
> 1.1.0_rc1 of XLMOD.obo
>
> Is this a new PTM ontology or this will be under PSI-MS?
>
> On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote:
>
>     Dear proteomics community,
>
>     attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file
>     for cross-linking reagents.
>
>     It contains many new terms for cross-linker reagents, PTM's
>     derived from
>     them and new "cross-linking attribute"'s describing their
>     properties, e.g.
>     property_value: spacerLength: "x.y" xsd:float
>     or information about their cleavability, labelling, handles used
>     for click chemistry or enrichment, ...
>
>     I used the following index ranges:
>     ===========================
>     reactive groups and attributes have ID's below XLMOD:01000
>     (mono-functional) cross-linker related PTM's have ID's above
>     XLMOD:01000
>     label transfer reagents have ID's above XLMOD:01800
>     analogues of amino acids have ID's above XLMOD:01900
>     bi-functional cross-linker have ID's above XLMOD:02000
>     tri-functional cross-linker have ID's above XLMOD:03000
>
>     Of course the ID's of our old version (releases/2016-07-13) were
>     not changed.
>
>     Where available I added also cross-references to databases
>     like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ...
>
>     I removed the chemical reaction-specificities from the
>     cross-linkers to the
>     reactive groups, which are now terms by their own, i.e. each
>     cross-linker has now a
>     relationship: has_reactive_group XLMOD:0xxxx ! ...
>
>     Therefore the specificities have to be specified only once for
>     each reactive group,
>     which avoids unnecessary redundancies.
>
>     I added also terms under the branch "label transfer reagents",
>     which are not yet contained in PSI-MOD.obo / unimod.obo
>
>     Best Regards,
>     Gerhard
>
>     -- 
>
>     *--------------------------------------------------------------------*
>
>     *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
>     *PhD student*
>
>     *Medizinisches Proteom-Center*
>
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>
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>     *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
>
>     *E-mail *ger...@ru... <mailto:ger...@ru...>
>
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>     <http://www.medizinisches-proteom-center.de/>
>
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> -- 
> Yasset Perez-Riverol PhD.
> Project Leader: PRIDE Resources
> Proteomics Services Team, PRIDE Group
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Twitter: @ypriverol
>
>
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-- 
Yasset Perez-Riverol PhD.
Project Leader: PRIDE Resources
Proteomics Services Team, PRIDE Group
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Twitter: @ypriverol