TBASE is implemented in a fully relational database-management system that is used for curation and for public access. For most investigators, the most convenient access is through Gopher, but TBASE will soon be accessible through the World Wide Web, which will also serve as a route of submission. The Gopher software is widely available and information about its acquisition can be obtained through the Welch Laboratory user support line at (410) 955-9705 or through email at email@example.com. Connectivity to the Johns Hopkins BioGopher is achieved by configuring the client to connect to gopher.gdb.org, port 70. For users who do not have access to computers on the Internet that have a Gopher client, access through a network Gopher client may serve as the alternative method. From a networked machine with standard network software, a client may be reached by typing telnet mouse.gdb.org (login: tbase, password: <return>). Finally, telephone dialup access is available at (410) 614-2665 (vtl00, 8 bits, no parity, 1 stop). When TBASE is fully implemented, by late 1994, it will be available in a full client-server SQL query-compatible mode and be integrated within the complex of genomic databases.
Data acquisition is effected by active literature-scanning and processing of direct submission forms. Literature-scanning refers to direct data extraction from the scientific literature through careful examination of a large number of journals, which have been statistically identified as periodically stable sources of such information. The data are later processed and manually entered into the database by TBASE staff. Active literature-scanning has so far been the primary mode of data accumulation and has ensured that the database accurately reflects the general progress of transgenic research.
The second method of data acquisition is the processing of direct submission forms, which consist of paper and electronic entry forms and templates. Appropriate paper entry forms have been designed for each of the three major TBASE object classes–Laboratory, DNA Construct, and Transgenic Line–closely following the format that is reflected by the recently revised schema. The paper forms may be obtained from the Welch Laboratory. The paper entry forms contain obligatory information (equivalent to the “not null” condition in the data dictionary); this includes contact information and any citations originally describing the founder lines or constructs, which must be clearly and fully provided as cross references. One complete set should be processed per transgenic animal or targeted mutant. Individual forms, however, may be used to modify or update information on a given line or mutant that already exists in the database.
The use of electronic submission forms and templates constitutes the final data-acquisition strategy, which is going to be implemented in the immediate future on satisfactory implementation of the revised schema. Original investigators and submitters will be able to use software submission tools with error-checking capabilities for more efficient and timely contributions to the database.