We are at a critical stage in implementation of a biological
database and need your advice as programmers, developers and users
The Microbial Germplasm Database, initiated with startup funding
from USDA-CSRS, contains information characterizing culture collections
associated with research in plant sciences (phytopathology,
agricultural biotechnology, soil ecology). The collections
contain germplasm types ranging from satellite nucleic
acids to bacteria and fungi to nematodes.
The purpose of the database and network would be to link
scientists with common research interests, to promote
sharing of strains, isolates and genetic constructs and to
attempt to prevent loss of these collections as researchers
change interests, retire or die.
The database will be on a UNIX machine probably running a
relation database management system such as INFORMIX, and
available by telnet through internet.
As database developers and as potential users of this database,
do you have any suggestions or preferences regarding some of the
strategies in storage of info? Are you aware of existing
standards that we should know about?
1. How would you suggest storing special characters such
as italics, subscripts, superscripts, greek letters (would you
suggest TEX or SGML?)? Given limitations of terminal emulations
and the varieties of machines that are connected to the networks,
what would you suggest as far as transmitting these characters to
users? Would you suggest limitation to vt-100 and tek4014 terminal
types?
2. Do you have recommendations as to how we can maintain
maximum compatibility of data storage and access. Are there
standards for an application program interface such that users
can develop their own front end? From your experiences do you have
any recommendations or advice regarding
development of a user interface.
3. We (in the future) are planning to store image data
objects, as well, to record pathological, morphological and
diagnostic information. What are your thoughts or suggestions?
3. Any thoughts or advice would be appreciated. We have a
prototype running now and are preparing to get in to full
development (pending continued funding) and any suggestions to
avoid reinventing wheels could make our work more efficient.
Also any suggestions of others scientists/database managers
with whom we could talk would be a help.
Thanks in advance for taking the time to read this. Please feel
free to be as candid and critical as you choose (within socially
acceptable bounds) as we are very receptive to
advice at this stage.
Also, if you are interested in getting on the mailing list
for the newsletter, either e-mail or hardcopy, send a reply to
that effect.
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Joe Hanus | E-MAIL hanusj at bionette.cgrb.orst.edu
Microbial Germplasm Database | hanusj at orstvm (bitnet)
Dept. of Botany and Plant Pathology | Phone (503)-737-5300
Oregon State University | FAX (503)-737-3045
Corvallis, OR 97331-2902 |
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