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Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 1.1.0_rc1 of XLMOD.obo
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From: Jones, A. <And...@li...> - 2017-06-27 09:58:42
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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 DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- 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 |
