Menu
▾
▴
[Psidev-mod-vocab] Version 1.012.0 of the PSI-MOD
|
From: John S. G. <jsg...@ud...> - 2013-10-25 18:01:19
|
Version 1.012.0 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 4.00 files for AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass differences. Please take note that the IUPAC Standard Atom Weights have been further revised in Standard Atom Weights Revised v2 2013, http://www.iupac.org/news/news-detail/article/standard-atomic-weights-revised-v2.html The revised version 4.00 AtomTabl.XML (AtomTabl-04.00.XML) wa used in the construction of the new releases of RESID and PSI-MOD. 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 1982 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 300 terms have apparently uncurated definitions. 737 of 766 terms from approved UniMod entries, 246 of 308 terms from DeltaMass, and 139 terms from OMSSA have been categorized. 714 terms are from the RESID Database, and 504 terms have been introduced by ontology annotation and by user request. Note that in the last 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. If you are not subscribed to Psidev-mod-vocab and want to be (or if you are and wish you were not), you should visit https://lists.sourceforge.net/lists/listinfo/psidev-mod-vocab 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... |
