Re: [Fis] Chemical information: a field of fuzzy contours ?
Dear Michel and FIS Colleagues, This will be an interesting discussion, since the core nature and role of information will be involved. Here is just one first point: to me, as a chemist, chemical information is only secondarily an object capable of being formalized, archived, etc. A formula has meaning for me in terms of the potential reactions the molecule to which it refers can undergo, what it looked like when crystallized for the first time and so on. Cheminformatics seems not to deal with such aspects of chemical information as part of a process of doing chemistry. Can this be captured by another system? Best wishes, Joseph Ursprüngliche Nachricht Von: petitjean.chi...@gmail.com Datum: 16.09.2011 09:44 An: fis@listas.unizar.es Betreff: [Fis] Chemical information: a field of fuzzy contours ? Chemical information: a field of fuzzy contours ? - Before turning to chemistry, I would recall some facts that I noticed on the FIS forum: although many people consider that a unifying definition of information science is possible (to be constructed), a number of other people consider that there are many concepts of information which are not necessarily the facets of an unique concept, so that it could be better to speak about information scienceS, and not about information science. I can read on http://en.wikipedia.org/wiki/Information_science Information science is an interdisciplinary science primarily concerned with the analysis, collection, classification, manipulation, storage, retrieval and dissemination of information. and some fewer lines above: Information Science consists of having the knowledge and understanding on how to collect, classify, manipulate, store, retrieve and disseminate any type of information. Clearly, collecting, storing, and retrieving information let us think that we must deal with databases. The question where is information is neglected, although answering it is enlighting: no doubt that much information is stored in data banks. There are strong connections of Information Science(s) with Data Mining (DM) and Knowledge Discovery in Databases (KDD). Is the situation clearer in chemistry ? Undoubtly there is a field of chemical information. The ACS (American Chemical Society) has a Division of Chemical Information (CINF), named as such in 1975, but which in fact goes back to 1943 (http://www.acscinf.org/). CINF is active and organizes various meetings which can be retrieved on the web. Visit also http://www.libsci.sc.edu/bob/chemnet/chchron.htm, an informative website. The ACS publishes the Journal of Chemical Information and Modeling renamed so in 2005 after having been named Journal of Chemical Information and Computer Sciences from 1975 to 2004, itself being the continuation of the Journal of Chemical Documentation from 1961 to 1974. In fact, it is the same journal (one volume per year), which turned to chemical information the same year that CINF received his actual name. Interestingly, still in 1975, the main cheminformatics lab in France (in fact the only one in France at this time) was renamed. The old name was LCOP (Laboratoire de Chimie Organique Physique), and the new name was ITODYS, still in vigor, meaning until 2001: Institut de TOpologie et de DYnamique des Systemes. This name, which can be understood in English due to the close similarity between the French and the English words, was partly due to the existence of a distance in the molecular graphs (this distance is the smaller number of chemical bonds separating two atoms), and as known, a distance induces a topology: it clearly acknowledged the cheminformatics aspects of the research performed in the lab. Chemical Information Science, which is sometimes named Chemical Informatics (http://www.indiana.edu/~cheminfo/acs800/soced_wash.html) can be reasonably considered to be a part of the Cheminformatics field. This latter is defined on Wikipedia (http://en.wikipedia.org/wiki/Cheminformatics): Chemoinformatics is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization. This definition, dated from 1998, clearly acknowledges the extraction of information from data, but it is restrictive since it discards all pioneering works about computerization of chemical databases, including structural formulas coding and structural motifs retrieval, which historically cannot be denied to be the core of the cheminformatics field. Now let me write more lines about the story of cheminformatics in France, which is a bit funny but enlights the debate on the definition on the field of chemical information. The French pioneer was Jacques-Emile Dubois (1920-2005), founder of the LCOP and of the ITODYS, who published his first cheminformatics paper in 1966. One of his main ideas was to use
Re: [Fis] Chemical information: a field of fuzzy contours ?
Dear Joe, dear FISErs, An organic chemist is able to predict a number of properties from the structural formula, including much about reactivity of the compound. But as you know, doing that properly is extremely difficult in a number of cases, because the rules governing reactivity are much more complicated that the ones which are taught at Universities, and the number of rules expands rapidly each year. In fact, an experienced Organic Chemist has in his head a so extraordinary rich collection of rules and a so enormous knowledge that even many chemists which are not Organicians cannot imagine the extent of this knowledge. It is clear that the doing chemistry process derives from these rules (these rules are chemical information), not only from the formulas. Since the 70's, some cheminformaticians tried to store that in databases: reactions databases plus databases of reactivity rules for computer sssisted synthesis or retrosynthesis, etc., then built programmes intended to output proposals supposed to help the chemist. As far as I know, the brain of the Organician is still by far much more efficient than the best softwares which were produced. So, I may tell that the information available in the brain of the Organician is extremely difficult to store on computer, and it is even very difficult to teach it, apart the very beginning. There are examples other than reactivity. A huge of QSAR studies were done in order to predict various physico-chemical properties of simple chemical compounds, e.g., predicting from the structural formulas the boiling temperatures of monofunctional compounds such as alcohols, cetones, etc. at 20 C under 1 atm. But even in these apparently simple cases, the chemical information we need to do that with an acceptable accuracy is difficult to extract: the conclusions of such QSAR studies cannot be applied to any alcohol or cetone (still assumed to be monofunctional compounds), and it is even difficult to know the extent of validity of the published empirical rules, concretely often summarized by some regression coefficients. The example of spectroscopic databases is also of interest. How simulate spectras (infrared, NMR, mass spectras, etc.) of chemical compounds ? Starting from the structural formula, it is really hard to simulate, e.g. a low resolution mass spectra. Most time, it was attempted to extract rules from spectroscopic databases, then try to predict the spectra of a compound absent from the database, or conversely, retrieving the structural formula of a compound from its spectra(s). Many such softwares were developped since the 70's (one of the oldest ones is STIRS), but really the chemical information needed to do that properly is very difficult to extract. To conclude, I retain your example of crystallization: for sure when we will able to retrieve from the structural formula H-O-H that water under 1 atm should crystallize at 0 C, then for sure we will be ready to predict more about crystallization of chemicals. Best regards, Michel. 2011/9/17 joe.bren...@bluewin.ch joe.bren...@bluewin.ch: Dear Michel and FIS Colleagues, This will be an interesting discussion, since the core nature and role of information will be involved. Here is just one first point: to me, as a chemist, chemical information is only secondarily an object capable of being formalized, archived, etc. A formula has meaning for me in terms of the potential reactions the molecule to which it refers can undergo, what it looked like when crystallized for the first time and so on. Cheminformatics seems not to deal with such aspects of chemical information as part of a process of doing chemistry. Can this be captured by another system? Best wishes, Joseph ___ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
Re: [Fis] Chemical information: a field of fuzzy contours ?
Michel -- Organic chemistry was known to be the most difficult course in
Columbia University. But I got interested in it, worked very hard
constantly, and I achieved an 'A'. But what you say here indicates several
orders of magnitude more difficulty than what I played with in university.
For me this raises a question about the 'realms of nature', as in the
subsumptive hierarchy: {physical realm {chemical realm {biological realm}}.
Do you think one should place an 'organic realm' between chemical and
biological? Or, otherwise, do you think it possible that there might be
organic realms out in the universe not entrained into biology?
STAN
On Sat, Sep 17, 2011 at 1:53 PM, Michel Petitjean
petitjean.chi...@gmail.com wrote:
Dear Joe, dear FISErs,
An organic chemist is able to predict a number of properties from the
structural formula, including much about reactivity of the compound.
But as you know, doing that properly is extremely difficult in a
number of cases, because the rules governing reactivity are much more
complicated that the ones which are taught at Universities, and the
number of rules expands rapidly each year. In fact, an experienced
Organic Chemist has in his head a so extraordinary rich collection of
rules and a so enormous knowledge that even many chemists which are
not Organicians cannot imagine the extent of this knowledge.
It is clear that the doing chemistry process derives from these
rules (these rules are chemical information), not only from the
formulas.
Since the 70's, some cheminformaticians tried to store that in
databases: reactions databases plus databases of reactivity rules for
computer sssisted synthesis or retrosynthesis, etc., then built
programmes intended to output proposals supposed to help the chemist.
As far as I know, the brain of the Organician is still by far much
more efficient than the best softwares which were produced.
So, I may tell that the information available in the brain of the
Organician is extremely difficult to store on computer, and it is even
very difficult to teach it, apart the very beginning.
There are examples other than reactivity. A huge of QSAR studies were
done in order to predict various physico-chemical properties of simple
chemical compounds, e.g., predicting from the structural formulas the
boiling temperatures of monofunctional compounds such as alcohols,
cetones, etc. at 20 C under 1 atm. But even in these apparently simple
cases, the chemical information we need to do that with an acceptable
accuracy is difficult to extract: the conclusions of such QSAR studies
cannot be applied to any alcohol or cetone (still assumed to be
monofunctional compounds), and it is even difficult to know the extent
of validity of the published empirical rules, concretely often
summarized by some regression coefficients.
The example of spectroscopic databases is also of interest. How
simulate spectras (infrared, NMR, mass spectras, etc.) of chemical
compounds ? Starting from the structural formula, it is really hard to
simulate, e.g. a low resolution mass spectra. Most time, it was
attempted to extract rules from spectroscopic databases, then try to
predict the spectra of a compound absent from the database, or
conversely, retrieving the structural formula of a compound from its
spectra(s). Many such softwares were developped since the 70's (one of
the oldest ones is STIRS), but really the chemical information needed
to do that properly is very difficult to extract.
To conclude, I retain your example of crystallization: for sure when
we will able to retrieve from the structural formula H-O-H that water
under 1 atm should crystallize at 0 C, then for sure we will be ready
to predict more about crystallization of chemicals.
Best regards,
Michel.
2011/9/17 joe.bren...@bluewin.ch joe.bren...@bluewin.ch:
Dear Michel and FIS Colleagues,
This will be an interesting discussion, since the core nature and role of
information will be involved. Here is just one first point: to me, as a
chemist, chemical information is only secondarily an object capable of
being formalized, archived, etc. A formula has meaning for me in terms
of the potential reactions the molecule to which it refers can undergo,
what
it looked like when crystallized for the first time and so on.
Cheminformatics seems not to deal with such aspects of chemical
information
as part of a process of doing chemistry. Can this be captured by
another system?
Best wishes,
Joseph
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