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

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

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
>
> -- 
>
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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