Published in Probe Volume 4(1-2): July 1993-July 1994
Mary Polacco, Database Developer
Curtis Hall, University of Missouri
Columbia, MO 65211
The Maize Genome Database, or MaizeDB, is curated as a Sybase database at the University of Missouri-Columbia and provides user-friendly, Internet access to the maize genome and the biology of maize.
Information includes 142 genetic maps, with 4,864 mapped loci, recombination and map score data (2,164 entries), 986 probes, 1,701 genetic/cytogenetic stocks, 7994 locus variations, 4,662 stock pedigrees, 5,600 bibliographic references indexed to genetic objects, and addresses of maize researchers.
Gene functionality may be queried by mutant phenotype, trait, confirmed or putative gene products, metabolic pathways, induction conditions and text descriptions of genes. Work is in progress to document quantitative trait loci. Users with Internet connections may access the data by several procedures that are described more fully below: guest login, gopher, World Wide Web, or file transfer of a special graphics, ACEDB format.
Data is input from various sources, including specially formatted, electronic lab notebooks of researchers who focus on mapping or mutant characterization. The contributors are international and from academic, government, and industrial research groups. Information, especially regarding gene function and expression, is also taken from the scientific literature, both electronic and printed.
Connecting To Other Databases
Using Mosaic, a type of free software that connects users to information on the World Wide Web (WWW), users connected to MaizeDB may retrieve information, including images and graphics, from other databases around the world, as easily as if the data existed in the MaizeDB records. If desired, they may store the information on their machines.
For example, while browsing the MaizeDB, you may read that the function of maize gene, dps1, was confirmed by transgenic complementation of E. coli mutations in dap1. By clicking on dap1, you would retrieve the record from the E. coli Stock Center at Yale University. Clicking on the EC number for gene products that are enzymes connects you to the ENZYME database. ENZYME describes the reaction, and in turn, connects to all Swiss-Prot entries corresponding to that EC number, as well as to OMIM (On-line Mendelian Inheritance in Man).
WWW connectivity requires precise matching of records in MaizeDB to records in other databases around the world. It permits curators of distinct datasets to combine data in a seamless fashion without actually importing the data. The ability to extract distinct formats of data from MaizeDB makes preparing files of matching identifiers relatively easy, so that external databases may use the WWW to connect to us, as occurred in June 1994 with SwissProt.
WWW/MaizeDB currently accesses external data in the following databases:
GenBank ....... nucleotide sequences
SwissProt ..... protein sequences; connects to Prosite (motifs, signature sequences), MedLine, EMBL
dbEST.........random cDNA's partial sequences, with periodically updated homology searches
E. coli Stock Center....... E. coli genetic stocks, map
ENZYME .......reactions, comments; connects to SwissProt, OMIM
AAtDB ........ Arabidopsis Genome Database
Accessing MaizeDB - Requirements
Guest login only requires that your machine have Internet connectivity, direct or indirect. Modem connections are supported, as are connections using any computer, including PC, Macintosh, and Unix. guest login protocol:
telnet teosinte.agron.missouri.edu
login: guest
password: corncob
Guest login provides access to:
Guests are encouraged to leave comments on the Note form of the database. While not required, leaving your e-mail address will permit us to contact you directly for further clarification.
NOTE: Users with X-Windows (this is not the same as Microsoft Windows)
software will enjoy the most user-friendly access to the database. If
connecting by modem, the X-Window will not function, and users should
select the vt100 emulation.
NOTE: If using the vt100 emulation of MaizeDB/Sybase, type "r" while
holding down the "control" (aka "CTRL") key to access the commands
required to query or browse the database. The command utilities are
described in more detail in the "help" option that appears or after
successful login as a guest.
Gopher
Gopher makes available hierarchical collections of information across the Internet. Gopher client (user) software provides easy access to all gopher data servers. All words in a record, except commonly used words, are indexed and thus may be used to query records.
Free gopher client software for Unix, PC, or Macintosh machines is available by anonymous ftp (file transfer protocol)* from boombox.umn.edu. Once installed, open server teosinte.agron.missouri.edu, port 70 or use gopher to find us by location in Columbia, Missouri. On-line help is provided by the gopher software and is in a file on the MaizeDB gopher server.
World Wide Web (WWW)
WWW is a hypermedia retrieval system which allows users to traverse on-line documents by clicking on hyperlinks-terms, icons, or images that point to other related documents. Hyperlinks permit retrieval of any document anywhere on the Internet. Retrieved "documents" may include text files, graphics, and videos. Connecting to the WWW currently works best if users have access to Mosaic software installed on a Unix machine. Macintosh and PC Mosaic software are rapidly approaching the capability of the Unix version.
Users without WWW software may access the WWW-linked format of MaizeDB by selecting the Lynx option after "guest login."
Mosaic software supports mouse capability and is available without charge by anonymous ftp from ftp.ncsa.uiuc.edu. The Unix version, but not the Macintosh or PC version, requires an X-Window on the user's machine; it will require a systems administrator to install. To access MaizeDB from Mosaic software, use our WWW address, otherwise known as URL or uniform resource locator:
http://teosinte.agron.missouri.edu/top.html
The WWW formatted data is dynamically extracted from the most current version of the database, which is continuously updated.
ACEDB Format
This is a special graphical format and requires a UNIX machine. The database may be retrieved by anonymous ftp from the National Agricultural Library, probe.nalusda.gov in directory pub/maize. This format is static, and periodically extracted from MaizeDB. It does not support the robust queries of the Sybase database, accessible by the guest login service.
ANONYMOUS FTP requires that the user have ftp or file transfer software to connect to another machine. Once connected, login as "anonymous" and use your e-mail address as the password. If using a Unix machine, type: cd pub/maize, and to transfer the database, type: get mace.tar.Z
History Of MaizeDB Design: Some Landmarks
Fall 1991
First prototype MaizeDB operational. Some 24,000 records created the first 6 months, largely from data summaries in the Maize Genetics Cooperation Newsletter (MNL), volume 65. The database currently contains over 78,000 records.
December 1992
First public access to the data, a gopher server established. First access was 100-200 connections/month, and has grown to over 1,000 connections/month.
March 1993
Maize Gene List, MNL, vol 67, pp. 134-15, extracted from MaizeDB Version 2 of MaizeDB implemented.
June 1993
ACEDB formatted data extracted from MaizeDB.
August 1993
Tool developed for loading references from PC and Macintosh reference manager formats.
December 31, 1993
Guest login to MaizeDB established.
Winter 1994
MaizeDB placed on the World Wide Web; currently there are 600-1,100
connections/week.
WWW connections made to external databases, listed above.
March 1994
Genetic indexing of 1993 references extracted from the MaizeDB, published as hardcopy in MNL, vol 69. pp 148-153. Information was indexed to chromosome, gene or allele and trait.
June 1994
SwissProt connects to MaizeDB using a file extracted from MaizeDB per specifications of SwissProt curators.
Developers and Curators of the Database Include:
E.H. Coe (PI), P. Byrne, G. Davis, D. Hancock, M. Polacco (Columbia,
MO)
M. Berlyn, S. Letovsky (New Haven, CT)
C. Fauron (Salt Lake City, UT)
S. Rodermel, C. Wetzel (Ames, IA)
M. Sachs (Urbana, IL)
For further help in accessing the database, please e-mail db_request@teosinte.agron.missouri.edu or contact Denis Hancock, (314) 882-1722 (phone), (314) 874-4063 (FAX).