[BiO BB] Re: {List of Chemical Names}

J.W. Bizzaro jeff at bioinformatics.org
Mon Nov 25 19:15:15 EST 2002


Sasank,

If you search for every chemical mentioned in the PubMed databases, many of your
results will be chemical reagents used in the lab.  Are you looking for chemical
reagents?  Are you looking for chemicals of biological origin?  Are you looking
for synthetic toxins?

Once you have determined types of chemicals and/or the types of articles, you
may want to do some literature mining, as Joe suggested.  There is no easy way
of identifying chemicals in biological literature, so you may need to search
your set of articles (which of course can't be easily done because of copyright
restrictions--you get abstracts and titles only) against your set of chemicals.

But, then again, maybe you just want a general list of biological compounds,
regardless of what is mentioned in research articles.

Please be more specific.

Cheers.
Jeff

Pandu wrote:
> 
>         Thanks for the reply...
> 
>         Maybe I can put my query this way. I would like to identify the
> chemical names in a research paper. I have already used the suffixes like
> -ols and -ones to name a few and identified some of them. But there are
> still quite a few, to name Zaprinast and Microcystin, which have to
> identified.
> 
>         Is there a way in which I can do this. I was requesting the list
> of chemical names which generally occur for this purpose.
> 
>         I would be helpful if someone can come up with a helpful
> suggestion.
> 
> Thank You
> Sasank
> 
> On Mon, 25 Nov 2002, J.W. Bizzaro wrote:
> 
> > Sasank,
> >
> > I would be helpful if the type of article could be narrowed down some.  If
> > you're looking to get the names of EVERY chemical EVER mentioned in ALL research
> > articles, you might as well copy the Dictionary of Chemical Compounds, Beilstein
> > (sp?) or the Merck Index.  We're talking about thousands upon thousands of
> > compounds.  This is why John thinks you are kidding.
> >
> > Cheers.
> > Jeff
> >
> > Pandu wrote:
> > >
> > > not exactly kidding...
> > >
> > >         atleast a partial list would do but we need it quite badly, so
> > > just in case u have it or atleast a link to it... pls post it...
> > >
> > > thank you
> > > sasank
> > >
> > > On Mon, 25 Nov 2002, John Hoey wrote:
> > >
> > > >
> > > > Are you kidding.....that could be a very extensive list!
> > > >  Pandu <sasank at students.iiit.net> wrote:
> > > > Hi
> > > >
> > > > Our group is currently working on a bio informatics project and in
> > > > this regard, we need a ocmplete list of chemical names which generally
> > > > occur in the various papers that are being published.
> > > >
> > > > We would be very grateful if u can either provide a link on the
> > > > net or send the corresponding file to us.
> > > >
> > > > Thank You
> > > > Sasank

-- 
J.W. Bizzaro                                jeff at bioinformatics.org
Director, Bioinformatics.Org        http://bioinformatics.org/~jeff
"As we enjoy great advantages from the inventions of others, we
should be glad of an opportunity to serve others by any invention
of ours; and this we should do freely and generously."
                   -- Benjamin Franklin
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