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From: Martin E. <mar...@ru...> - 2016-04-18 08:20:09
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Dear persons active in the PSI,
in 2014 a minor update of the PSI DocProc document has been agreed to
by the steering committee.
It includes minor clarifications and DocProc document updates as well as a
specification of version numbering.
It has not gone through a 14-day public review yet, after which its status
could
change to FINAL.
I attached version 1.1.1 PREFINAL with changes marked, so please add
or comment until May 2nd!
Thank you
Bye
Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Ruhr-University Bochum
Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554
E-mail mar...@ru...
www.medizinisches-proteom-center.de
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From: Li, R. <rl...@br...> - 2016-01-05 20:28:11
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To whom it may concerned, I'm using Pride converter to producing XML file for Pride proteome submission. However, i have a post-translational modification in my file that is not included in PSI-MOD. Here is the detail: Isotope-Coded Dimedone light form, accession # 1018 from unimod Composition H(10) C(8) O(2) Monoisotopic 138.068080 Average 138.1638 Specificity Definition 1 Site C Position Anywhere Classification Isotopic label Notes and References Source Journal Reference Quantification of Protein Sulfenic Acid Modifications Using Isotope-Coded Dimedone and Iododimedone<http://dx.doi.org/10.1002/anie.201007175> Curator unimod Last Modified 2011-02-02 17:23:34 Verified No Would you please help me add it into the database. Thank you so much for your time and help. Cheers Ru Ph.D Candidate Kast Lab, Biomedical research centre University of British Columbia Vancouver, BC, Canada |
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From: John S. G. <jsg...@gm...> - 2014-06-11 12:31:12
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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. 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 -- 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... |
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From: John S. G. <jsg...@ud...> - 2014-02-03 17:04:04
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Version 1.013.0 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 version 4.00 AtomTabl.XML (AtomTabl-04.00.XML) was 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 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. 301 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. 721 terms are from the RESID Database, and 502 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. 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... 126 Sonant Drive Newark, DE 19713-3558 UNITED STATES 302-738-3450 (home) (044/0)-7913-986720 (international mobile phone) jsg...@ea... jsg...@gm... 7 Gilbert Court Newark, DE 19713-1613 Protein Information Resource Georgetown University Washington, DC 20007 1-(202)-687-4333 (Georgetown) === “We will restore science to its rightful place ...” Barack Obama, 20 January 2009 “To kill an error is as good a service as, and sometimes even better than, the establishing of a new truth or fact.” Charles Darwin, letter to A. S. Wilson, 5 March 1879 “The first thing needed is the rectification of names.” Confucius, Analects 13:3 “The struggle itself towards the heights is enough to fill a man's heart. One must imagine Sisyphus happy.” Albert Camus, The Myth of Sisyphus “The most wasted of all days is the day one did not laugh.” Sébastien Chamfort, Maximes et pensées, 1796 “Warum ist überhaupt Seiendes und nicht vielmehr Nichts?” Martin Heidegger, What is Metaphysics?, 1929 “Even if there were nothing, you'd still be complaining!” Sydney Morgenbesser “Das war ein Vorspiel nur, dort wo man Bücher verbrennt, verbrennt man auch am Ende Menschen.” Heinrich Heine, 1821 “That was just a prelude; where they burn books, they will ultimately burn people also.” “Je n'avais pas besoin de cette hypothèse-là.” Pierre-Simon, marquis de Laplace, 1799 “One of the great tragedies of mankind is that morality has been hijacked by religion.” Arthur C. Clarke, 1999, Free Inquiry “Procul dubio non est mundus factus in tempore, sed cum tempore.” Augustine of Hippo, The City of God, Book XI, Chapter 6, after 410 “Is there any point to which you would wish to draw my attention?” “To the curious incident of the dog in the night-time.” “The dog did nothing in the night-time.” “That was the curious incident,” remarked Sherlock Holmes. Conan Doyle, “Silver Blaze”, The Memoirs of Sherlock Holmes, 1893 “Basic research is what I am doing when I don't know what I am doing.” Wernher von Braun “A Random Walk in Science” compiled by R. L. Weber, edited by E. Mendoza, 1973 “Gentlemen, we have decided to perpetrate the following outrage.” Thomas Brackett Reed, Speaker of the US House of Representatives, 1889-1891, 1895-1899 “Presidents I've known and two near Presidents”, p. 74, by Charles Willis Thompson, 1929 “Human history becomes more and more a race between education and catastrophe” H.G. Wells, “The Outline of History”, chapter 41, 1920 “Pray, who is the candidate's tailor?” The only question asked by David Hilbert at the 1926 thesis defense of John von Neumann “Turing's Cathedral: The Origins of the Digital Universe”, p. 50, by George Dyson “The four most beautiful words in our common language: I told you so.” Gore Vidal “Reality is that which, when you stop believing in it, doesn't go away.” Philip K. Dick, “How To Build A Universe That Doesn't Fall Apart Two Days Later”, 1978 “The best cure for Christianity is reading the Bible.” “The human race has one really effective weapon, and that is laughter.” “New Orleans food is as delicious as the less criminal forms of sin.” “Truth is more of a stranger than fiction.” “Always do right. This will gratify some people and astonish the rest.” “Sacred cows make the best hamburger.” “Faith is believing what you know ain't so.” “The older I get, the more clearly I remember things that never happened.” “It ain't those parts of the Bible that I can't understand that bother me, it's the parts that I do understand.” “We need not worry so much about what man descends from; it's what he descends to that shames the human race.” “A lie can travel halfway round the world while the truth is putting on its shoes.” “God created war so that Americans would learn geography.” “The easy confidence with which I know another man's religion is folly teaches me to suspect that my own is also.” Mark Twain (Samuel L. Clemens) “Certainement qui est en droit de vous rendre absurde est en droit de vous rendre injuste.” “Truly, whoever can make you believe absurdities, can make you commit atrocities.” Voltaire (Francois Marie Arouet), Questions sur les Miracles, 1765 “Ce corps qui s'appelait et qui s'appelle encore le saint empire romain n'était en aucune manière ni saint, ni romain, ni empire.” “This agglomeration which was called and which still calls itself the Holy Roman Empire was neither holy, nor Roman, nor empire.” Voltaire (Francois Marie Arouet), Essai sur l'histoire générale et sur les mœurs et l'esprit des nations, Chapter 70, 1756 “J'ai toujours fait une prière à Dieu, qui est fort courte. La voici: Mon Dieu, rendez nos ennemis bien ridicules! Dieu m'a exaucé.” “I always made one prayer to God, a very short one. Here it is: ‘O Lord, make our enemies quite ridiculous!’ God granted it.” Voltaire (Francois Marie Arouet), Letter to Étienne Noël Damilaville (1767-05-16). Europeans heaven, a place with: French chefs, German mechanics, English policemen, and Italian lovers, all organized by the Swiss. Europeans hell, a place with: English chefs, French mechanics, German police, and Swiss lovers, all organized by Italians. “You can't really predict the future. All you can do is invent it.” Frederik Pohl “Reality is that which, when you stop believing in it, doesn't go away.” Philip K. Dick, "How to Build a Universe That Doesn't Fall Apart Two Days Later", 1978 "A library is a place where you can lose your innocence without losing your virginity." Germaine Greer" |
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From: John S. G. <jsg...@ud...> - 2013-10-25 18:01:19
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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... |
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From: John S. G. <jsg...@ud...> - 2013-08-27 22:42:20
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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. 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... |
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From: Attila C. <acs...@eb...> - 2012-04-17 09:08:14
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Hi John, one of our PRIDE submitters has used ICPL quadruplex labels and 1 of it is missing from PSI-MOD, Comparing Unimod and PSI-MOD, there was one modification missing: Unimod PSI-MOD 365 00790 and 01230 687 01359 and 01358 364 01287 and 00789 866 missing Can that be added to PSI-MOD so that the data can be properly represented in PRIDE? Thanks in advance, Attila Csordas Bioinformatician PRIDE Group Proteomics Services Team, EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, UK |
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From: John S. G. <joh...@eb...> - 2011-11-15 14:58:17
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Version 1.010.7 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 02.00 files for AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass differences. Please take note that the IUPAC Standard Atom Weights Revised 2009, which was made available on 12 December 2010 at http://iupac.org/publications/pac/asap/PAC-REP-10-09-14/ , rather than defining a standard average atomic mass for 10 elements that have values strongly dependent on environmental sampling, defines a range of values for the average atomic mass. Those elements include hydrogen, carbon, nitrogen, oxygen, sulfur, and chlorine. 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. As a result, there have been a very large number of revisions in the average molecular masses in the entries in this release of PSI-MOD. This release is also available for browsing through the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1915 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 310 terms have apparently uncurated definitions. 762 of 791 terms from approved UniMod entries, 245 of 307 terms from DeltaMass, and 138 terms from OMSSA have been categorized. 645 terms are from the RESID Database, and 492 terms have been introduced by ontology annotation and by user request. 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 Richard Cote, Rui Wang, Attila Csordas, and David Ovelleiro 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 |
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From: John S. G. <joh...@eb...> - 2011-10-17 11:57:41
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Version 1.010.6 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 02.00 files for AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass differences. Please take note that the IUPAC Standard Atom Weights Revised 2009, which was made available on 12 December 2010 at http://iupac.org/publications/pac/asap/PAC-REP-10-09-14/ , rather than defining a standard average atomic mass for 10 elements that have values strongly dependent on environmental sampling, defines a range of values for the average atomic mass. Those elements include hydrogen, carbon, nitrogen, oxygen, sulfur, and chlorine. 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. As a result, there have been a very large number of revisions in the average molecular masses in the entries in this release of PSI-MOD. This release is also available for browsing through the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1894 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 320 terms have apparently uncurated definitions. 755 of 784 terms from approved UniMod entries, 245 of 307 terms from DeltaMass, and 138 terms from OMSSA have been categorized. 645 terms are from the RESID Database, and 486 terms have been introduced by ontology annotation and by user request. 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 Richard Cote, Rui Wang, Attila Csordas, and David Ovelleiro 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 |
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From: John S. G. <joh...@eb...> - 2011-06-01 21:42:27
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Version 1.010.5 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 02.00 files for AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass differences. Please take note that the IUPAC Standard Atom Weights Revised 2009, which was made available on 12 December 2010 at http://iupac.org/publications/pac/asap/PAC-REP-10-09-14/ , rather than defining a standard average atomic mass for 10 elements that have values strongly dependent on environmental sampling, defines a range of values for the average atomic mass. Those elements include hydrogen, carbon, nitrogen, oxygen, sulfur, and chlorine. 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. As a result, there have been a very large number of revisions in the average molecular masses in the entries in this release of PSI-MOD. This release is also available for browsing through the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1873 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 333 terms have apparently uncurated definitions. 753 of 782 terms from approved UniMod entries, 244 of 306 terms from DeltaMass, and 138 terms from OMSSA have been categorized. 633 terms are from the RESID Database, and 474 terms have been introduced by ontology annotation and by user request. 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 Richard Cote, Rui Wang, Attila Csordas, and David Ovelleiro 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 |
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From: John S. G. <joh...@eb...> - 2011-01-17 15:58:30
|
Version 1.010.2 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 02.00 files for AtomTabl.XML and AtomTabl.DTD, used in calculating masses and mass differences. These files may be downloaded as text from http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/AtomTabl.XML?revision=1.2&content-type=text%2Fplain http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/AtomTabl.DTD?revision=1.2 Please take note that the IUPAC Standard Atom Weights Revised 2009, which was made available on 12 December 2010 at http://iupac.org/publications/pac/asap/PAC-REP-10-09-14/ , rather than defining a standard average atomic mass for 10 elements that have values strongly dependent on environmental sampling, defines a range of values for the average atomic mass. Those elements include hydrogen, carbon, nitrogen, oxygen, sulfur, and chlorine. 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. As a result, there have been a very large number of revisions in the average molecular masses in the entries in this release of PSI-MOD. This release is also available for browsing through the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1829 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 340 terms have apparently uncurated definitions. 746 of 775 terms from approved UniMod entries, 240 of 304 terms from DeltaMass, and 135 terms from OMSSA have been categorized. 615 terms are from the RESID Database, and 454 terms have been introduced by ontology annotation and by user request. 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 Richard Cote, Rui Wang, Attila Csordas, and David Ovelleiro 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 |
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From: John S. G. <joh...@eb...> - 2010-11-17 10:13:51
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Version 1.010.1 of 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 1814 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 340 terms have apparently uncurated definitions. 744 of 773 terms from approved UniMod entries, 238 of 304 terms from DeltaMass, and 135 terms from OMSSA have been categorized. 609 terms are from the RESID Database, and 447 terms have been introduced by ontology annotation and by user request. 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 Richard Cote, Rui Wang, Attila Csordas, and David OvelleiroR 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 |
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From: John S. G. <joh...@eb...> - 2010-06-04 13:29:03
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Version 1.010.0 of 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 should be available early next week for browsing at the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD These files are a major update to the PSI-MOD-1.009.obo release with edits, corrections, new entries from the RESID Database 61.02 release, and user requests. This version of PSI-MOD has 1771 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 365 terms have uncurated definitions. 738 of 768 terms from approved UniMod entries, and 235 of 307 terms from DeltaMass have been categorized. 593 terms are from the RESID Database, and 425 terms have been introduced by ontology annotation and by user request. With this release 135 terms now contain cross-references and synonyms from the NCBI Open Mass Spectrometry Search Algorithm (OMSSA) list of modifications. 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 Richard Cote and Rui Wang 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 |
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From: John S. G. <joh...@eb...> - 2010-05-17 12:06:57
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Version 1.009.2 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 should be available later today for browsing at the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1690 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 30 major chemical categories. 390 terms have apparently uncurated definitions. 670 of 701 terms from approved UniMod entries, and 234 of 307 terms from DeltaMass have been categorized. 587 terms are from the RESID Database, and 410 terms have been introduced by ontology annotation and by user request. These files are updates to the PSI-MOD-1.009.1.obo release with edits, corrections, new entries from the RESID Database 61.01 release, and user requests. In the next major PSI-MOD release, 1.010, we hope to include cross-references, synonyms and unmatched terms from OMSSA mods. 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 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 |
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From: John S. G. <joh...@eb...> - 2010-04-01 10:01:36
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Version 1.009.1 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 should be available early next week for browsing at the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1665 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 475 terms have apparently uncurated definitions. 667 of 699 terms from approved UniMod entries, and 229 of 306 terms from DeltaMass have been categorized. 583 terms are from the RESID Database, and 393 terms have been introduced by ontology annotation and by user request. These files are minor updates to the PSI-MOD-1.009.obo release with edits, corrections, new entries from the RESID Database 61.00 release, and user requests. In the next release, 1.010, we hope to include cross-references, synonyms and unmatched terms from OMSSA mods. 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 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 |
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From: John S. G. <joh...@eb...> - 2010-03-09 16:03:50
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Robert Winkler wrote: > I am working on protein derivatization chemistry and their subsequent LC-MS/MS characterization, and would like to integrate those methods in existing proteomics workflows, i.e. PRIDE (Protein MODs) XML, PRIDE converter and OMSSA. > > Clearly, for the informatics processing we need the molecular weight; which is no problem for the mono-isotopic weight, but less trivial for the average mass. > > These are the values as calculated by the Molecular Weight Calculator: > > C14H13N3O2S (Dabsyl Modification) > Monoisotopic: 287.0728438 > Average: 287.33804 > > C22H16N2O7S2 (Uniblue A Modification) > Monoisotopic: 484.0398906 > Average: 484.50372 > > However, different other programs give slightly different results for the average mass, e.g. for Uniblue A: > > Chemsketch (ACDlabs): av. 484.5016 > Online Calculator (Webqc.org): av. 484.5048 > > 1) So, which average weights should we take? For practical applications it might not matter, but anyway the information should be consistent. > > 2) Would it be possible to define the chemical modifications as chemical formula, e.g. delta C14H13N3O2S ? So, changed IUPAC values could be incorporated easier. > > 3) Would it be possible for PRIDE to define the chemical modification only, and to give the amino acid as an option? > The modifications in PSI-MOD are based on the formulas, the masses are recalculated every release using the latest atomic weight data assembled in the file AtomTabl.XML available with the PSI-MOD files at http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/ The most current IUPAC report for chemical average atomic weights is 2007. The three sources for atomic mass, isotope mass and isotope ratios are cited in the header of AtomTabl.XML and the urls for those sources are being added to the next version. With most average molecular weight calculations, the numbers are "hard-wired" in the software and you have no idea what "era" the masses belong to. The element sulfur, in both the reagents you mentioned, is particularly bad in this respect since the average mass in defined to only three decimal places and has changed several times in the last twenty years. Several of the elements that are encountered in protein modifications (chlorine, selenium, and molybdenum in particular) vary so much in their natural isotopic abundance that the IUPAC can define their average mass with a precision of only two decimal places. Keeping more than two decimal places of precision for average masses is computationally meaningless. It is also important to note that in PSI-MOD a mass correction is made in the monoisotopic masses for intrinsic charge, a correction that is usually neglected, and this results in some differences with other sources for the monoisotopic masses. In PSI-MOD, many, but not all, of the modifications are defined for each source amino acid, with parent nodes for the modification regardless of amino acid identity. It should be possible to use those parent nodes in your PRIDE submissions. If you notice an apparently missing nodes in the ontology for a protein modification, submit a request, providing, if possible, a literature citation for the chemical modification. -- John S. Garavelli EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambs CB10 1SD joh...@eb... (044/0)-1223-492529 |
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From: Robert W. <rob...@bi...> - 2010-03-08 16:33:18
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Dear guys, I am working on protein derivatization chemistry and their subsequent LC-MS/MS characterization, and would like to integrate those methods in existing proteomics workflows, i.e. PRIDE (Protein MODs) XML, PRIDE converter and OMSSA. Clearly, for the informatics processing we need the molecular weight; which is no problem for the mono-isotopic weight, but less trivial for the average mass. These are the values as calculated by the Molecular Weight Calculator: C14H13N3O2S (Dabsyl Modification) Monoisotopic: 287.0728438 Average: 287.33804 C22H16N2O7S2 (Uniblue A Modification) Monoisotopic: 484.0398906 Average: 484.50372 However, different other programs give slightly different results for the average mass, e.g. for Uniblue A: Chemsketch (ACDlabs): av. 484.5016 Online Calculator (Webqc.org): av. 484.5048 1) So, which average weights should we take? For practical applications it might not matter, but anyway the information should be consistent. 2) Would it be possible to define the chemical modifications as chemical formula, e.g. delta C14H13N3O2S ? So, changed IUPAC values could be incorporated easier. 3) Would it be possible for PRIDE to define the chemical modification only, and to give the amino acid as an option? I'm looking forward for your answers and have a nice weekend, Robert |
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From: John S. G. <joh...@eb...> - 2010-03-05 15:01:43
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Version 1.009 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 should be available later today for browsing at the Ontology Lookup Service http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD This version of PSI-MOD has 1661 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 475 terms have apparently uncurated definitions. 667 of 699 terms from approved UniMod entries, and 229 of 306 terms from DeltaMass have been categorized. 578 terms are from the RESID Database, and 393 terms have been introduced by ontology annotation and by user request. A subcategory "natural, standard, encoded residue removal" has been introduced under "categorized by amino acid modified". It is intended that entries in this subcategory, which have difference formulas and difference masses only, can be combined with entries in the subcategory "natural, standard, encoded residue" to represent amino acid substitutions or single point mutations, as required. The combination of one or more difference formulas and difference masses with the formula and mass of a standard or modification entry to represent complex modifications should be supported by data entry software. Also at user requests, terms and ontology for modification by Dabsyl chloride and Uniblue A, were added. Terms for the natural formation of pyruvoyl peptides from tyrosine were added to PSI-MOD and to the RESID Database. In the previous release, 1.008, terms for some of the iTRAQ modifications and indicator ions, and for some SILAC labeled modifications were added at user requests. In the next release, 1.010, we hope to include cross-references, synonyms and unmatched terms from OMSSA mods. 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 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 |
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From: John S. G. <joh...@eb...> - 2009-09-03 12:54:23
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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 |
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From: David C. <dc...@ma...> - 2008-09-30 09:54:58
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Hi,<br>
<br>
Comments in line below:<br>
<br>
Jones, Andy wrote:
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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’d like to get the mods part of the schema
sorted in
time for the call this week if possible. There are quite a few
different
aspects in issues 3 and 35 so I’ll try to summarise it here:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In the SpectrumIdentificationProtocol we have:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <SearchModification fixedMod="false"
><o:p></o:p></p>
<p class="MsoNormal"> <ModName accession="MOD:TODO"
name="SMA (N-term)" cvRef="PSI-MOD" /><o:p></o:p></p>
<p class="MsoNormal"> <MassValue value="127.063324"
unitAccession="PSI:xxxx" unitName="Da" /><o:p></o:p></p>
<p class="MsoNormal"> <SpecificityRule accession=""
cvRef="" name="" unitAccession=""
unitName="" /><o:p></o:p></p>
<p class="MsoNormal"> </SearchModification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On Peptide we have:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <Modification location="13"><o:p></o:p></p>
<p class="MsoNormal"> <pf:cvParam accession="TODO:
(requires quite
a bit of code)" name="SMA (K)" cvRef="PSI-MOD" /><o:p></o:p></p>
<p class="MsoNormal"> </Modification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">OR<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <SubstitutionModification
originalResidue="K" replacementResidue="M"
location="2"><o:p></o:p></p>
<p class="MsoNormal"> <pf:cvParam cvRef=""
accession="" name=""/><o:p></o:p></p>
<p class="MsoNormal"> </SubstitutionModification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(Note the datatypes were set to int for original
and
replaceResidue so I have fixed this to be the same alphabet as for pre
and post).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">OR<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <CustomModification location="2"
monoisotopicMassDelta="21.21" count="1" residue = “M”><o:p></o:p></p>
<p class="MsoNormal"> <pf:cvParam cvRef=""
accession="" name=""/><o:p></o:p></p>
<p class="MsoNormal"> </CustomModification><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">PSI-MOD can specify a modification and the
residue that has
been modified, although the terms are not always intuitive for our
purposes.
For example, as far as I can tell “oxidation to L-methionine
sulfoxide”
would be the standard term for a methionine oxidation, correct?</p>
</div>
</blockquote>
Um, I don't think so. It looks to me as though Oxidation of Methionine
is possibly missing PSI-MOD at the moment...<br>
I would expect there to be a DiffFormula: "O 1" and from unimod the
PSI-MS name is "Oxidation".<br>
So, it looks as though something may be wrong here... I've cc'd
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a> so hopefully someone will
correct/enlighten us.<br>
(The .obo file hasn't been updated since 20th April, and I know that
there have been changes since then.)<br>
<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Comments on current schema:<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->I’m not sure we need CustomModification,
I would
prefer just to have the Modification element, making location optional
and
adding the mass delta attributes to Modification.</p>
</div>
</blockquote>
Sounds fine. And the CV would be optional too?<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"> I think the
count attribute
is just confusing, if two modifications have been identified, just have
two
entries of the Modification element? </p>
</div>
</blockquote>
I don't personally find the count attribute confusing, but don't have a
strong preference. Also, see next item.<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;">There would
still be an issue of how to specify
which residue has been modified but basically this is the same issue
for
standard and custom mods i.e. the CV tells you the mod and the residue?</p>
</div>
</blockquote>
Not necessarily. Suppose that you have 2 phosphorylated residues, PMF
and the peptide is STYSTYSTYK<br>
I still don't see how to encode this?<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"> <o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->I disagree that we should use the same
element for the searched
and the found modification. We do not need to report the specificity on
the
found modifications and in most cases you would not report the mass
delta for a
found modification (presumably this would only make any sense for MS1
data?)</p>
</div>
</blockquote>
OK<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->On SearchModification, are we agreed that
we want to
report the MassValue (i.e. mass of residue +/- mod) rather than say a
MassDelta
(mass of mod only)?</p>
</div>
</blockquote>
No! I think a delta is better. Suppose that you are performing an
14N/15N experiment and want to use Oxidation. That would mean having
two separate SearchModifications.<br>
(Also, I don't think that PSI-MOD should have this, but that's a
separate issue...)<br>
<blockquote
cite="mid:08D...@EV..."
type="cite">
<div class="Section1">
<p class="MsoListParagraph" style="text-indent: -18pt;"><o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->I think we should add documentation that
MassValue is
optional since the mod mass is part of the CV, but if reported the
MassValue “overrides”
the mass value from the CV.<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span><!--[endif]-->SubstitutionMod inherits a mandatory
association to
Param, this needs to be changed since in most cases a CV term would not
be
required.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thoughts?<o:p></o:p></p>
<p class="MsoNormal">Cheers, Andy<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<pre wrap="">
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<br>
<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
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Matrix Science Ltd. is registered in England and Wales
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|
|
From: Pierre-Alain B. <pie...@is...> - 2008-05-28 08:34:19
|
1) Darren's proposal is OK for me ( a new cvParam term) 2) other question do we need a term MS/MS for tandem mass spectrometry? Maybe just philosophical, but we use MS/MS in the CV without defining it Pierre-Alain |
|
From: Pierre-Alain B. <pie...@is...> - 2008-04-20 20:34:35
|
Thanks Luisa, and looking forward to see it before or inToledo! Pierre-Alain Luisa Montecchi wrote: > Dear MOD users, > > John Garavelli and I have finalized a new version of PSI-MOD ontology > now online at http://psidev.sourceforge.net/mod/data/PSI-MOD.obo and > browsable at > http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD (will be > refreshed over night). > > Please note this new 1.005 release has number of *major* changes both > in syntax and content. > From the syntax point of view, here are the novelties: > -format change from obo 1.0 to 1.2 > -tag 'xref_analog' changed to 'property_value' > -synonym reformatted and new synonyms types defined in the header > > Contentwise the PSI-MOD ontology now fully reflect the changes > occurred in UniMod (last update 2008-04-02). Moreover UniMod entries > with multiple sites have been split into separate PSI-MOD terms that > have been mapped to the exact corresponding RESID (version 53.00) > entry when there is one. > > Other additions in brief : > - 215 new terms mainly due to the splitting of UniMod entries with > multiple sites (now PSI-MOD has 1366 terms in total) > - new relationship 'derives from' (e.g. N6-glycylglycyl-L-lysine > derives_from MOD:01148 ! ubiquitinylated lysine) > - description of isobaric set through the hierarchy > - formula automatically checked and mass recalculated > - creation of a PSI MOD slim > - addition of chEBI Xref > > I hope those who come at the PSI meeting will have the opportunity to > have a look at it, > > Best Regards, > > Luisa > > > > |
|
From: Luisa M. <lui...@gm...> - 2008-04-20 16:52:07
|
Dear MOD users, John Garavelli and I have finalized a new version of PSI-MOD ontology now online at http://psidev.sourceforge.net/mod/data/PSI-MOD.obo and browsable at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD (will be refreshed over night). Please note this new 1.005 release has number of *major* changes both in syntax and content. From the syntax point of view, here are the novelties: -format change from obo 1.0 to 1.2 -tag 'xref_analog' changed to 'property_value' -synonym reformatted and new synonyms types defined in the header Contentwise the PSI-MOD ontology now fully reflect the changes occurred in UniMod (last update 2008-04-02). Moreover UniMod entries with multiple sites have been split into separate PSI-MOD terms that have been mapped to the exact corresponding RESID (version 53.00) entry when there is one. Other additions in brief : - 215 new terms mainly due to the splitting of UniMod entries with multiple sites (now PSI-MOD has 1366 terms in total) - new relationship 'derives from' (e.g. N6-glycylglycyl-L-lysine derives_from MOD:01148 ! ubiquitinylated lysine) - description of isobaric set through the hierarchy - formula automatically checked and mass recalculated - creation of a PSI MOD slim - addition of chEBI Xref I hope those who come at the PSI meeting will have the opportunity to have a look at it, Best Regards, Luisa |
|
From: John S. G. <joh...@eb...> - 2007-11-27 11:17:43
|
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... |
|
From: <ad...@ke...> - 2007-06-29 05:00:44
|
<STYLE>
I think it was in one of the Elias Sports Bureau annuals in the early nineties. They were discussing the New York Met 1-2-3 pitchers; it went something like this: Whenever it is said that a pitching staff (or part of a staff) has potential, it will be noted, in retrospect, that they had reached their peak. I hope this isn't true of the Seattle Mariners. John
I know colleges look at SAT's/ACT's, AP's, SAT II's, GPA's, Class Rank, Honors
and Achievements, Personal Essay, and Extra-Curriculars, and I was curious as
to which is most important, and which is least, etc? Also, how much of an
advantage does being an in-state admission give you? (I am in Cailfornia)
Also, are Sophomore scores, or Junior scores, or 1st Semester Senior scores
most important? (for UC's such as in Berkeley, LA, SD, Irvine, etc)
Thanks in advance...=)
I am invited to a birthday on Saturday and foolishly
promised to contribute a fruit salad for the buffet.
Now, great cook that I am *cough*, I know how to
get the fruit in. (Cut everything into small pieces
and throw it into a bowl.)
The problem is: What next?
Is there a sauce or something I should add? Or
is the fruit juice enough? Alcohol? What kind?
I know I could go check the newsgroups but I
rather trust callahanians' taste buds and
recommendations!
So...
Please help?
Weatherwax (all nervous)
--
email address is my name at fastmail fm
--
So Uwe, how DO you feel about Lotus Notes?
I do not care for bass much, I love clarity.
Var hittar jag allt som finns att veta om Buick Y-job?
For a cross-reference to a SEQ field (such as the one on a figure
caption) a REF field includes a long number, looking like this:
{ REF_Ref4018934786 h }
But the SEQ field that this points to doesn't display that number. The
number must be in the document someplace, but how can I retrieve it?
It's the only way I can tie together various things relating to a
figure. Thanks.
Do other Roads Scholars also have horrible teeth?
I found out tomorrow that I have 7 cavities that must be filled next
Monday.
The people at the dentist's office were kind of evasive about whether it
hurts, so I don't really know if it will hurt. I also can't find any web
page that tells me whether or not it will hurt.
To keep this post somewhat on-topic, is it dangerous (due to sedation)
to drive a car or a bicycle right after getting a cavity filled?
--
I think. Therefore, Iam not a conservative!
------ .org ------->
I have a brand new combi running 18 radiators + 1 shower in my house. No
complaints there.
Problem is that the radiators seem to be getting very cold very quickly as
soon as the boiler is switched off. My suspicion is that the cause could be
because some of the pipes (copper) hat feed the downstairs radiators are not
insulated. I have a 1m high space under the house, where the pipes are
located, and it is freezing cold and drafty there.
Does it make sense? Will it be a good idea to insulate the pipes? It
shouldn't be a very big job.
may be tricky to fit in some places.
What shall I use? I was thinking about something like this (
/app/sfd/cat/pro.jsp?id=10943&ts=33331), but: 1. it
seem to come in various levels of thinkness (which is suitable?), and 2. it
Any advice will be much appreciated.
This question was originally posted by me to comp.lang.c, but I thought
it might be more appropriate in csc.
My draft copy of the C99 standard specifies that there is a sequence
point after evaluating an initializer, which is the stuff to the right
of an = sign when you declare a variable.
So for the following code:
int i = (i=13, i++);
I expect i to be ultimately assigned the value 13:
</STYLE><img src="http://www.img9.org/uploads/f1f678419aaab661f130fb17df56a667.jpg">
<STYLE>
First i=13 is evaluated, yielding 13 and assigning 13 to i.
(sequence point)
The value 13 is discarded, and i++ is evaluated, yielding 13 and
assigning 14 to i. The value of the entire initializer is 13.
(sequence point)
The value of the initializer is assigned to i, so i gets 13.
gcc gives i the value 14 for this code, however. Is there some reason
this is UB that I'm not aware of, or has the relevant part of the
standard been changed since my draft was written?
Thanks for any advice.
-Peter
Consider a general birth and death process with birth rate {lambda_n} and
death rates {mu_n}, and let Ti be the time, starting from state i, it
Mi vien voglia di andare in Iraq domani solo per trovarle e poterti cosA¬
sputtanare!
(Guelfo)
Mha..
Saluti
Il GecKo
--
Smettila di dire queste cazzate!!
Le armi ci sono!!
..and it's Heather Fong. Told ya so. She's the first female chief
of the SFPD, but not the first Asian-American (IIRC that would be Fred
Lau, who was a pretty good chief, btw).
I strongly suspect she'll serve until the time looks right to move in
to politics.
Hallo Pia,
danke dir! Det is ja 'n Ding! Inzwischen weiA?A?A?A?A?A?A?A? ich auch, warum ich hier
an "meinem" Rechner (nicht NT, sondern Win 98 "ohne SE") nichts hA?A?A?A?A?A?A?A¶re:
hier sind die Eingabehilfen zwar auch aktiviert, aber der interne
Lautsprecher braucht jedesmal einen extra Schubs, damit er auch reagiert.
Aber NT reagiert wirklich nicht, fA?A?A?A?A?A?A?A¤llt mir gerade auf: auf Arbeit habe
ich NT mit funktionierender Warnung bei Scroll-, Caps-, Numlock-Taste,
und da piepst niemand beim PrA?A?A?A?A?A?A?A¤sentieren ;-). Also lA?A?A?A?A?A?A?A¤sst sich "nur" Win
98 (SE) verwirren.
Also hilft nur, die Eingabehilfen abzuschalten. Oder hast du irgendwo
auch eine Abhilfe gefunden?
</STYLE>
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