[Psidev-mod-vocab] Version 1.010.7 of the PSI-MOD

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

Version 1.010.7 of PSI-MOD OBO and XML files are available at
http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/

http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo
http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo.xml

Also available in that repository are the Version 02.00 files for
AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass
differences.
Please take note that the IUPAC Standard Atom Weights Revised 2009,
which was made available on 12 December 2010 at
http://iupac.org/publications/pac/asap/PAC-REP-10-09-14/ , rather than
defining a standard average atomic mass for 10 elements that have values
strongly dependent on environmental sampling, defines a range of values
for the average atomic mass. Those elements include hydrogen, carbon,
nitrogen, oxygen, sulfur, and chlorine. The report does provide
"conventional atomic weights" with 4 significant digits for hydrogen,
sulfur, and chlorine, and 5 significant digits for carbon, nitrogen, and
oxygen.  As a result, there have been a very large number of revisions in
the average molecular masses in the entries in this release of PSI-MOD.

This release is also available for browsing through the Ontology Lookup
Service
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD

This version of PSI-MOD has 1915 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 33 major
chemical categories. Fewer than 310 terms have apparently uncurated
definitions. 762 of 791 terms from approved UniMod entries, 245 of 307
terms from DeltaMass, and 138 terms from OMSSA have been categorized.
645 terms are from the RESID Database, and 492 terms have been
introduced by ontology annotation and by user request.

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, Rui Wang, Attila Csordas, and David Ovelleiro
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