[Psidev-mod-vocab] Version 1.013.0 of the PSI-MOD

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

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"