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Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 1.1.0_rc1 of XLMOD.obo
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From: Yasset Perez-R. <yp...@eb...> - 2017-06-27 10:11:06
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For example the current pride-mod library in PRIDE needs to handle three different providers: UNIMOD, PSI-MS and PSI-MOD. On 27/06/2017 11:08, Yasset Perez-Riverol wrote: > > 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* >> >> *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 >> >> >> ------------------------------------------------------------------------------ >> 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... >> 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 > > > ------------------------------------------------------------------------------ > 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... > 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 |
