Subject: Personal Structure/Bioassay/Inventory DB's

From: [email-masked] (M. Nicklaus)
Date: Thu, 4 May 95 12:18:45 -0400

Dear CCL'ers,

We'd like to ask everyone for their experiences and recommendations as
to what solutions/programs people have come up with for creation and
management of personal and project-oriented chemical databases.  This
means that the number of compounds in the database would typically be
up to a few hundred or maybe 1000.  Such a database (system) would ideally
- allow storage and search of 2D chemical structures, numerical data
  such as bioassay results and inventory data, textual data such as 
  comments and planned steps in a project, reference data such as 
  literature references etc.  A really *good* system would allow 
  intelligent handling of semi-quantitative data such as "IC50 > 100uM"
  for the purposes of queries, sorting etc.;
- allow "upward linking", i.e. to molecular modeling (programs).  It
  may, but need not, be a module of a molecular modeling package;
- allow "horizontal linking", i.e. to other, larger-scale database
  systems such as Oracle or INGRESS;
- allow "downward linking", i.e. to word processing, DTP and similar
  programs for the purpose of manuscript and presentation preparation.
  It should at least allow printing of publication-quality output such
  as tables containing 2D structures etc., but should ideally allow to
  create, e.g., PostScript files and/or export output to the common 
  word processor formats such as WordPerfect, Word etc. [this is a 
  very important requirement for what *our* group is looking for];
- be available on, and allow seamless data transfer between, the
  platforms/OS's Unix, PC's (DOS(?) / Windows / OS/2), Mac's;
- be easy to install, maintain, and use even for a non-database expert;
  in particular, the database definition (number, order, name of columns,
  type of data etc.) should be easily changeable as the project evolves;
- be as low-cost as possible, or even an outright public domain program.
We are of course aware of a number of programs that fulfill at least
some of the above requirements, a few of them having been around for
quite some time; but even if they are "just" a module in a chemical 
information of molecular modeling package, they tend to be quite, if not
very, expensive.
   A search in the CCL archives turned up a few summary postings on
similar questions about 1 1/2 years ago.  So we wondered whether people
have come up with anything new in the meantime.
   Answers from commercial companies are certainly welcome, but we are
especially interested to hear from individual researches or small groups
who might have implemented a solution (for example by basing a system
on "low-end", and low-cost, commercial programs for Windows or Mac's)
that might be easily duplicated by others.  Of course, if such a 
solution would be available in the public domain, even better....

   I will summarize for the Net if I get useful answers.

   Marc C. Nicklaus

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 Marc C. Nicklaus                        Lab. of Medicinal Chemistry
 e-mail: [email-masked]               National Cancer Institute, NIH
 Phone:  (301) 402-3111                  Bldg 37, Rm 5B29
 Fax:    (301) 496-5839                  BETHESDA, MD 20892-4255
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