Published in Probe Volume 4(1-2): July 1993-July 1994
Stephen M. Beckstrom-Sternberg
Plant Genome Data and Information Center
National Agricultural Library, USDA
Beltsville, MD 20705-2351
The Plant Genome Database has been considerably augmented in the past few months. A number of new connections and capabilities have been added to the World Wide Web (WWW) and gopher interfaces, and a text-based Lynx client has been added to provide access to those with slower Internet connections and/or low resolution graphics. The following is a summary list of recent changes to the Plant Genome Database:
1). WWW Interface to ACEDB Databases; 2). New Query Capabilities for Plant Genome Data; 3). Links to external data (Agricola, GenBank, Swiss-Prot, Images); 4). New Gopher Services; 5). Telnet access to WWW Lynx Client; 6). Collaborator's Page summarizes Collaborator's Services; 7). New Draft for Plant Genome III Meeting; 8). New Solanaceae Database Shows Syntenic Relationships
WWW Interface to ACEDB Databases
The Plant Genome Database Project is now offering a collection of ACEDB-based databases for both plant and non-plant genomes. The databases have been installed behind the "Moulon" ACEDB-WWW server and can be browsed and queried interactively. The various databases are listed below:
New Query Capabilities for Plant Genome Data
The ACEDB-based databases can be queried using the ACEDB query language, query-by-example (QBE) and a query-building (QB) tool. The ACEDB query language requires an understanding of syntax, but QBE and QB do not. In addition, all the data from the ACEDB databases has been indexed for searches using WAIS. Finally, data can be searched using agrep--a tool which allows you to make approximate matches (aka, fuzzy searching).
Links to external data: Agricola, GenBank, SwissProt, Images
HTML links are increasingly being used to connect plant genome data with data from external sources, for example AGRICOLA, GenBank, and SwissProt. This allows us to take advantage of the division of labor between databases specializing in different tasks. For example, the receptor kinase sequence object from the Arabidopsis database AAtDB contains a link to GenBank labeled "M80238". Clicking on it will retrieve a GenBank record from a computer at National Institutes of Health.
New Gopher Services
The Plant Genome Information on the Agricultural Genome Gopher has been reorganized. It can be used to access the same information that is presented by the WWW interface to the genome databases, both plant and non-plant.
Telnet access to WWW Lynx Client
Users who are restricted to VT100 or VT200 terminals or emulators can access the WWW services using Lynx, a text-only client (see below for access details). The client is set up so that only NAL data (and data from a few other sources) is available--it cannot be used to surf the Internet (sorry).
Collaborator's Page summarizes Collaborator's Services
A page has been set up with links to resources maintained independently by the plant genome collaborators. The services include ftp archives, gophers and access to databases.
New Draft for Plant Genome III Meeting
There is a new version of a draft describing the next Plant Genome Meeting in San Diego in mid-January 1995 (gopher and WWW).
New Solanaceae Database Shows Syntenic Relationships
SolGenes, a database for pepper, tomato and potato, now shows the syntenic relationships between chromosomes from these members of the Solanaceae. The information is presented as an on-line image of a genetic map. The image responds to mouse clicks enabling one to find out more about a particular locus by clicking on it, then selecting "Show as text". Figure 1 is an example comparing chromosome 9 of tomato and potato. Access to these graphically depicted relationships from the Agricultural Genome home page is via the following sequential menu selections (WWW Interface to ACEDB Data, Browse Solgenes, and Multimap).
Ways to Access the Agricultural Genome Databases
WWW:
http://probe.nalusda.gov:8000/
Gopher:
gopher probe.nalusda.gov
Lynx:
telnet probe.nalusda.gov
login: lynx
password: (none - hit return)
Anonymous FTP:
probe.nalusda.gov