BERLYN@yalemed.bitnet (04/19/91)
From: BIOMED::BERLYN 18-APR-1991 14:53:50.82 To: IN%"chualab@rockvax.rockefeller.edu" CC: BERLYN Subj: RE: Database for Arabidopsis. Andrew, We have a relational database for the E. coli Genetic Stock Center that describes Strains, Genes, Mutations, Pedigrees, Map, Gene Products, Chromosome Segments, etc., etc., with References and Persons of course associated with objects of virtually any type, and we are examining the possibility of adapting the design to plants, in conjunction with the USDA Plant Genome Project, and somewhat more specifically the Maize DB Project. It is in the Sybase Relational Database Management System and we have used their AptForms system and their version of SQL to develop and use a form for each major object type that serves to enter, query, and update information in the database. We query for combinations of alleles or any combination of traits or descriptors of the strain or other object, or by position (e.g., deletions or insertions or genes or whatever within a given region), or by ancestry (e.g., isogenic lines or all strains descendent from X). We have heavily used,and developed, i.e., expanded on, a concept of extensible controlled vocabulary for describing such things as mutation type (deletion, inversion, base pair substitution, insertions, etc.), mutation property (temperature sensitive, amber, ochre, etc.) , SiteType (gene, operon, chromosomal fragment, sequenced region....) and there would be a real advantage to standardizing this vocabulary across species. So I'm very interested in talking to others with databases in mind. Plant Genome Office has given funds to NSF for Arabidopsis database work, and it would certainly be good to coordinate all the efforts at some level. I'll be glad to provide you or others with a description of our fields, tables, forms (and advanced query capability and analytic tools, if you're interested), but not on this wire, since there are over a hundred tables with 2-12 fields per table. Mary Berlyn