[Fis] RE: FIS message (Fw)

Dear all,

I introduce myself since it is the first time I take part in the
conversation. My name is Ana Maldonado, I'm a PhD student on theoretical and
informatics chemistry in Paris 7 university. My research interest deals with
Similarity and Diversity Analysis for HTS and VS, structural descriptors,
chemical databases and markup languages in chemistry.

The last conversation keeps my attention because of the commentary of Michel
Petitjean and Giuseppina Gini about structural chemical standards.

Commonly in chemistry the "general feeling" when talking about standards is
not really optimistic. However, new efforts and applications have been made
the last years. Most of the times they are unknown or ignored, because of
the abstract computational nature of the solutions implemented. The markup
languages and the semantic web technologies enter in this group.

Markup languages and particularly XML are often considered to be the
universal format for structured documents on the web. But today this
meta-language is widely used for representing any structured data, and
particularly scientific and hence chemistry data.

The complex nature of chemical information and the size of chemical
databases today are well know reasons to search for standards that easy the
exchange and the treatment of chemical data, XML have proved to be a
powerful alternative to current approaches. I don't will expose here the
advantages and uses of XML in chemistry (for more details see:
http://www.mdpi.org/fis2005/F.42.paper.pdf) but I invite to take a look, of
some examples of what is being made today in this sense...

In academies:
* Chemical Markup Language (CML): the first implementation of XML in
chemistry. http://www.xml-cml.org The community counts with a discussion
list: https://lists.sourceforge.net/lists/listinfo/cml-discuss
* Computational CML (CMLComp): use of XML and CML in Computational Chemistry
and Physics Programs. http://www.allhands.org.uk/proceedings/papers/274.pdf

In the industry:
* Chemical Industry Data Exchange (CIDX): have developed the Chem
eStandards™ which are the uniform standards of data exchange developed for
the buying, selling and delivery of chemicals. More information in:
http://www.cidx.org/ChemeStandards/default.asp
* Is important to note that most pharmaceutical companies have developed
their own XML standards. Luckily DTDs allows translation between chemical
XML formats.

In organisations:
* The NIST XML Standards for Analytical Chemistry (SpectroML):
http://polymers.msel.nist.gov/combi/Presentation_Slides/NCMC-3_Presenations/
SpectroML%20-%20Kramer.pdf
* And of course the IUPAC InChI project already pointed by Giuseppina Gini:
http://inchi.sourceforge.net/ , http://www.iupac.org/inchi/

As chemists, we can choose to use and discuss these proposals. By
implementing and using them, we participate in the validation and improving
process. This will encourage their wide use in the future. I think it is one
of the ways to consolidate a chemical standard.

Cordially

Ana Maldonado

-- 
Ana Maldonado 
Universit� Paris 7 - Denis Diderot, Laboratoire ITODYS-CNRS UMR 7086 
1 rue Guy de la Brosse, 75005 Paris FRANCE
e-mail: ana.mald.troncy@gmail.com, maldonad@itodys.jussieu.fr
Tel: +33 1 44 27 79 49 | Fax: +33 1 44 27 68 14
> ................................................................
> From gini@elet.polimi.it Tue Nov 22 12:50:44 2005
> Date: Tue, 22 Nov 2005 12:53:07 +0100
> To: Michel Petitjean <ptitjean@itodys.jussieu.fr>, fis@listas.unizar.es
> From: Giuseppina Gini <gini@elet.polimi.it>
> Subject: Re: [Fis] molecular structures (was: ON MOLECULAR BIONETWORKS
>  (II))
> 
> Dear all
> 
> about the discussion on chemical structures, many interesting points
> have been raised. Referring to the post of Michel Petitjean:
> 
> >
> >An example here: there are various file formats used to store chemical
> >structures on computer (mol, mol2, pdb, cas, csd, etc..), and many
> >users are asking for an universal format. BABEL do conversions, but
> >developpers would like to programme themselves the input/output modules
> >reading/writing molecular structures. There are tasks groups working
> >on this topic, but I am not optimistic: as a consequence of the multiple
> >definitions of "structure", it is impossible to define a file format
> >handling all situations for all users: it would be an enormous dataset,
> >so much complicated that nobody would use it.
> >
> 
> 
> the point  he makes is important.
> But not enough people know yet the effort, in the definition of a
> unique text  format for chemical structures, taken by IUPAC, namely
> InChI, which uses an extended xml definition.
> You can get details from their official sites:
> http://inchi.sourceforge.net/, and  http://www.iupac.org/inchi/
> I think that this project is in the right direction to define a
> standard for chemical structures, valuable in many fields, first of
> all to develop databases exchangeable between any users .
> 
> 
> 
> Sincerely
> --
> - - - -
> Giuseppina C. Gini
>      DEI, Politecnico di Milano
>      piazza L. da Vinci 32, I-20133 MILANO
> fax:   (+39) 02-2399.3411
> phone: (+39) 02-2399.3626
> e-mail: gini@elet.polimi.it
> page: http://www.elet.polimi.it/upload/gini/
> my EU  projects: http://www.ion-project.net,
> http://www.demetra-tox.net, http://www.openmolgrid.org/,
> http://www.fateallchem.dk/,  http://airlab.elet.polimi.it/imagetox/,
> http://europa.eu.int/comm/research/endocrine/pdf/qlk4-ct2002-02286-y1-pr-
> rep_en.pdf,
> 
> Delegate  COST Action 282:
> http://www.MPA-Garching.MPG.DE/~opmolsrv/COST282/index.html
> Member AGENTLINK: http://www.AgentLink.org/
_______________________________________________
fis mailing list
fis@listas.unizar.es
http://webmail.unizar.es/mailman/listinfo/fis