[Psidev-mod-vocab] Version 1.009 of the PSI-MOD

[John S. G. <joh...@eb...>]

Version 1.009 of the PSI-MOD OBO and XML files are available at
http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/
Also available in that repository are the files AtomTabl.XML and
AtomTabl.DTD, used to calculate masses and mass differences.
This release should be available later today for browsing at the
Ontology Lookup Service
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD

This version of PSI-MOD has 1661 term entries organized in three
ontologies,
(1) categorized by amino acid modified,
(2) categorized by chemical process, and
(3) categorized by isobaric sets.
The ontology categorized by chemical process is organized into
31 major chemical categories. Fewer than 475 terms have
apparently uncurated definitions. 667 of 699 terms from approved
UniMod entries, and 229 of 306 terms from DeltaMass have been
categorized. 578 terms are from the RESID Database, and 393
terms have been introduced by ontology annotation and by user
request.

A subcategory "natural, standard, encoded residue removal" has
been introduced under "categorized by amino acid modified".
It is intended that entries in this subcategory, which have difference
formulas and difference masses only, can be combined with
entries in the subcategory "natural, standard, encoded residue"
to represent amino acid substitutions or single point mutations,
as required.  The combination of one or more difference formulas
and difference masses with the formula and mass of a standard or
modification entry to represent complex modifications should be
supported by data entry software.
Also at user requests, terms and ontology for modification by
Dabsyl chloride and Uniblue A, were added.  Terms for the
natural formation of pyruvoyl peptides from tyrosine were added
to PSI-MOD and to the RESID Database.
In the previous release, 1.008, terms for some of the iTRAQ
modifications and indicator ions, and for some SILAC labeled
modifications were added at user requests.

In the next release, 1.010, we hope to include cross-references,
synonyms and unmatched terms from OMSSA mods.

As always, we appreciate your comments, suggestions on the
format, names, improvements in the ontology, and requests for
terms accompanied by citations.

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Thanks to Richard Cote for logistic support.

-- 
                         John S. Garavelli
                         EMBL Outstation, European
                            Bioinformatics Institute
                         Wellcome Trust Genome Campus
                         Hinxton, Cambs  CB10 1SD
                         joh...@eb...
                         (044/0)-1223-492529