[Psidev-mod-vocab] Version 1.011.0 of the PSI-MOD

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

Version 1.011.0 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 3.00 files for
AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass
differences.  Please take note that the IUPAC Standard Atom Weights
Revised 2011 which was made available on 29 April 2013 at
http://iupac.org/publications/pac/asap/PAC-REP-13-03-02/ ,
defines a standard average atomic mass for 12 elements that have values
strongly dependent on environmental sampling, defines a range of values
for the average atomic mass. Those elements are hydrogen, lithium, boron,
carbon, nitrogen, oxygen, magnesium, silicon, sulfur, chlorine, bromine,
and thallium. 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.

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 1966 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 321 terms have apparently uncurated
definitions. 736 of 765 terms from approved UniMod entries, 246 of 308
terms from DeltaMass, and 139 terms from OMSSA have been categorized.
700 terms are from the RESID Database, and 504 terms have been
introduced by ontology annotation and by user request.

Note that in this release a significant change had to be made in the format
of the definition cross-references to the RESID and UniMod databases. 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"). We regret that we 
were
not able to announce this change in advance.

Because we have experienced on-going problems 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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Thanks to Simon Jupp at EBI for logistic support.

-- 
                          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...