From: kab@WELCHGATE.WELCH.JHU.EDU (Kerryn Brandt)
Newsgroups: bionet.molbio.gdb
Subject: GDB Version 5.0 Highlights
Date: 6 Jan 93 14:02:25 GMT
Distribution: bionet

AU$  GDB staff
LT$  NEWSLETTER
SO$  Human Genome News, November 1992; 4(4):10
TI$  GDB Version 5.0 Highlights
YR$  1992
AB$
     Genome Data Base (GDB) Version 5.0 contains major new
   features enhancing database content, data relationships, and software
   for data retrieval and display. Highlights are summarized below, and 
   a detailed description will be available online in the Release Notes 
   under News.
               Database Content and Organization
        Information in GDB is organized into ten data managers: Map,
   Locus, Probe, Polymorphism, Mutation, Population, Library, Cell
   Line, Citation (previously named Source), and Contact. Five of them
   are newly added to increase the searchability and types of data that
   can be retrieved and displayed:
        -Polymorphism - Data previously available for display only is
   now directly searchable and has been reorganized to show on one
   screen all polymorphism information (location, detection method,
   alleles, frequencies, and population).
        -Population - Population definitions, also previously available
   for display only, have been broken down into component elements such
   as race, geographical region, or ethnic group and reconstituted to
   facilitate creation of new population definitions. Mutations and
   polymorphisms specific to particular populations can now be
   retrieved.
        -Mutation - Mutation data will include location, sublocalization
   within the genes, and comparison of wildtype and mutant nucleotide
   and amino acid sequences.
        -Cell Line - Definitions can be retrieved independently from
   their breakpoints.
        -Library - DNA library descriptions will aid researchers in
   obtaining clones from the GDB contacts.
        Significant amounts of new data have also been added to three
   existing managers:
        -Map - Distance information (including degree of overlap)
   between two map objects is now included. Confidence limits for
   localization data are also available.
        -Probe - Amplification conditions for PCR primer sets include
   buffer concentrations, time/temperature cycles, and the name of the
   thermal cycler used. These conditions are linked to citations, and 
   multiple sets of amplification conditions can be linked to a single set
   of primers. Probe-to-probe interactions will make available such
   data as sequence tagged site screening of yeast artificial
   chromosomes.
        -Citation - Citations are ranked (important, supportive,
   background) with respect to all linked entries. MEDLINE citations
   include cross references to other databases including GenBank, EC
   (Enzyme Commission) number, RN (CAS Registry) number, and
   symbols or abbreviated forms of gene names as they appear in the
   published citation.
   Flexibility has been increased for retrieving linkage relationships
   among entries in different managers:
        -Multiple entries can be selected before another manager is
   called to retrieve linked entries.
        -A list of all linked data for a selected entry is available from
   the View menu.
                  Retrieving and Displaying Data
        A query can retrieve any number of entries. If more than 500
   entries are retrieved, data are grouped in sets and the user can
   move between sets. To provide a variety of ways to search for data,
   a basic set of fields (Cytogenetic Location, Locus Symbol, Locus
   Name, Probe Symbol) is included on the retrieve screens for loci,
   probes, polymorphisms, mutations, and populations. The detail view
   screens in each of these managers also include these basic fields.
        To make information available as quickly as possible, new
   entries that are complete in fields and citations but subject to
   modifications during review will be viewable by general users as
   PROPOSED DATA. However, unpublished material may be withheld from
   view for up to 6 months if requested by the submitter.
              Formats Available for Data Output
        Output functions now include additional types and formats of
   GDB data that can be sent via e-mail. In addition to personal
   search results, standard reports (see announcement at bottom of
   page) are also available in ASCII, Tab-delimited, and PostScript
   formats.
                    Using GDB
        An online system provides help with individual screens and
   fields and general topics. Help is now included in Citation and
   Locus managers and will be added to other managers on an ongoing
   basis.
       Menu choices are selected through <control> R followed by
   unique menu letters that are consistent across all screens and
   managers. A set of function keys is available for the most commonly
   used menu and submenu options.