[Psidev-mod-vocab] PSI-MOD version 1.008 OBO and XML Files Available

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

Version 1.008 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 is also available for browsing at the Ontology
Lookup Service
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD

This version of PSI-MOD has 1602 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 500 terms have
apparently uncurated definitions. 664 of 696 terms from approved
UniMod entries, and 227 of 304 terms from DeltaMass have been
categorized.  558 terms are from the RESID Database, and 357
terms have been introduced by annotation.

As announced at Turku, the "FormalCharge" record is introduced
in this release, and some resulting differences in monoisotopic masses
are to be expected where published values have failed to take this
correction into account.

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

Thanks to Luisa Montecchi for her valuable assistance in producing
this release, and 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