[Psidev-mod-vocab] Interim Version 1.013.1 of the PSI-MOD

[John S. G. <jsg...@gm...>]

Interim Version 1.013.1 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 4.00 files for
AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass
differences.  The IUPAC Standard Atom Weights Revised v2 2013 are 
available at,
http://www.iupac.org/news/news-detail/article/standard-atomic-weights-revised-v2.html

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

This version of PSI-MOD has 1996 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. 299 terms have apparently uncurated definitions.
738 of 767 terms from approved UniMod entries, 245 of 307 terms from
DeltaMass, and 139 terms from OMSSA have been categorized.
721 terms are from the RESID Database, and 507 terms have been
introduced by ontology annotation and by user request.

Note that when an entry in the RESID Database is annotated with different
sources because the same modification can arise from different encoded
amino acids, then the PSI-MOD definition for each different source instance
carries the RESID cross-reference followed by a hash symbol "#" and a 3 
or 4
character label, such as RESID:AA0181#SER. (This was formerly indicated 
by a
cross-reference note "results".)  When an entry in the RESID Database is
annotated as a general modification with the same enzymatic activity 
producing
different chemical structures depending on natural variation in the
nonproteinaceous substrate, on secondary modifications that do not 
change the
nature of the primary modification, or on a combination of a primary and 
one
or more secondary modifications on the same residue, then the PSI-MOD 
definition
for each different instance carries the RESID cross-reference followed 
by the
special tag "#var", such as RESID:AA0146#var. (This was formerly indicated
by a cross-reference note "var".) When an entry in the UniMod database is
annotated as a general modification, and one or more instance sites are
listed, then the PSI-MOD definition for each different site instance 
carries
the UniMod cross-reference followed by a hash symbol and an amino acid 
code,
"N-term" or "C-term", such as UniMod:385#S and UniMod:41#N-term. (This was
formerly indicated by a cross-reference note "site").

Because we have experienced difficulties in maintaining PSI-MOD in the
OBO format, we are planning to introduce an OWL format version.

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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-- 
                          John S. Garavelli
                          Center for Bioinformatics &
                             Computational Biology
                          Delaware Biotechnology Institute
                          University of Delaware
                          15 Innovation Way, Suite 205
                          Newark, DE  19711-5449
                          302-831-6922
                          jsg...@ud...