[Psidev-pi-dev] New version 1.1.0 of XLMOD.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 1.1.0 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*

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