[Psidev-mod-vocab] PSI-MOD version 1.004 OBO and XML files Available

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

Version 1.004 of the PSI-MOD OBO and XML files are available at
http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/
The OBO format file, referred to as "Revision 1.8" in CVS,
can be downloaded at
http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo?view=log
and the XML format file, referred to as "Revision 1.9" in CVS,
can be downloaded at
http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo.xml?view=log

This version has 1128 term entries organized in three ontologies,
(1) categorized by amino acid modified,
(2) categorized by chemical process, and
(3) categorized by isobaric sets.
The isobaric set categorization is introduced in preliminary form
in this release.  It is designed to provide a means of browsing
sets of modified amino acid residues that are isobaric at
predetermined levels of resolution; in this release the levels
are 0.1 Da, 0.01 Da, and 0.000001 Da.  The latter set is composed
essentially of subsets of structural isomers.

The ontology categorized by amino acid modified is now based on
22 encoded amino acids, with selenocysteine and pyrrolysine
included as both encoded residues and as hypothetical modifications
of cysteine and lysine, respectively.  It also includes a category
of unnatural amino acids not regarded as derivatives of encoded
residues.

The ontology categorized by chemical process is organized into
28 major chemical categories.  More of the categorized terms
now have "short names" and full definitions.  The chemical
formulas and the mass precisions have a standard presentation.
The description of modifications as features in the UniProt
Knowlegebase are presented as synonyms when they differ from
the names of the corresponding entries in the RESID Database.
The names of the leaf nodes have been revised to standard
chemical names, while the process related "-ated" suffix names
are retained for the parent level names.  Entries with UniMod
accessions now reflect any merges that have been performed
within UniMod, and where necessary terms were made obsolete.

As always, we appreciate your comments and suggestions on the
format and choices for the short names, for improvements in
the ontology, and for any changes in the XML.

Thanks to Luisa Montecchi for her valuable assistance in
producing this release.
-- 
                              John S. Garavelli
                              EMBL Outstation - EBI
                              Wellcome Trust Genome Campus
                              Hinxton, Cambridge CB10 1SD
                              UNITED KINGDOM
                              (44)-01223-492529
                              joh...@eb...