IX. Maize Genome Database, a USDA-ARS Plant Genome Database
http://www.agron.missouri.edu/
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. August 1995 records included 240 genetic maps; 6227 mapped loci; 3498 map data entries, both recombination and map score data; 2335 probes; 1985 genetic/cytogenetic stocks; 19,821 locus variations, including 2800 mutants from the Neuffer collection, allozyme typing for 21 loci and 437 elite stocks; 4662 stock pedigrees; 6785 bibliographic references, indexed to genetic objects; 2430 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 guest login to the relational APT query forms; gopher; World Wide Web; or by file transfer of a special graphical format, ACEDB. Any data retrieved may be saved to a file on your computer(gopher, WWW) or e-mailed (gopher, WWW, relational query).

Data input is from various sources, including specially formatted, electronic lab notebooks of researchers who focus on mapping or mutant characterization; direct entry by off-site curators into the APT forms; electronic updates of pointers to external databases. These contributors are international and from academic, government , and industrial research groups. Data, especially regarding gene function and expression, are also taken from the scientific literature, both electronic and printed. The WWW and APT fill-in-the-blanks forms execute direct queries on the underlying Sybase tables, and therefore, any information entered, by off- or on-site curators, is instantly available to WWW or relational queries.

New in 1994-95 -- boxes enclose hints on retrieving information from MaizeDB using forms(WWW or APT)

1. Mapping; Maps; Data; Core(Anchor) Markers
Mappers may identify the chromosome region corresponding to their mapping data by pasting their scores into the Scores field on the MapScore (by locus) form and clicking on the Probed Site for each MapScore retrieved. When a precise match is not found, piecemeal groups representing stretches of 10 or so individuals work best. The better the match, the tighter the linkage. Sample queries--note the use of %, the Sybase wild-card:

 For bnl maps (recombinant inbred or RI populations)
SCORES: %2131213312
or SCORES: %2131213312%2212

For umc 95 maps (immortal F2 or IF2 populations)
SCORES: %BHHHAHHHB
OR SCORES: %BHHHAHHHB%AABBH

New Maps
Mycogen (365 markers)
UMC 1995 RFLP (602 markers)--with map scores
CIMMYT (346 markers)
Mitochondrial (two normal and T-cytoplasm restriction fragment maps)
A table of core or anchor markers that define mapping bins is stored as a hypertext file on the WWW and may be accessed from the top page for MaizeDB under 'Of Interest to Maize Cooperators'. A Probe request form is also accessible from that page.

Map retrieval. Retrieve the above maps and the previously entered BNL maps from the Map form after typing within the Name, Source or Linkage Group field:
NAME: Mycogen to retrieve all Mycogen maps
NAME: Mycogen%2 to retrieve Mycogen chromosome 2
NAME: umc 95 [or NAME: umc 95%2 ] for umc 95 maps [chromosome 2 only]
SOURCE: CIMMYT all CIMMYT maps
LINKAGE GROUP: mito
NAME: bnl [or NAME: bnl%2] for bnl 1993 map [chromosome 2 only]
NAME bins [or NAME: bins%2] for bins maps [chromosome 2 only]
NAME: % for a list of all the maps
 

Retrieve Complete Map Scores, in order by chromosome and coordinate, for umc 95 maps on the WWW from the Map Score Tables form, by selecting Panel Type: Immortal F2 . Retrieve BNL map score panels similarly, but select Panel Type: Recombinant Inbred. The dynamically extracted table of map scores is currently accessible only by WWW.

2. Representation of QTL Data
Design has been completed and data entry is on-going. QTL representation will facilitate comparisons with genome information obtained from classical, biochemical and molecular genetic studies. Traits where public information is available include yield and yield components, quality attributes, such as kernel protein and starch concentrations, developmental characteristics and responses to pests and abiotic stress. A full description of how to access the data is provided in an on-line JQTL article accessible as a QTL Experiment form 'hint' on the MaizeDB WWW directory of focused query forms.

 A list of QTL experiments that have been entered into the database may be retrieved from the QTL Experiment form, by typing within the name field:
Name: %

3. Allozyme variations
These data were provided in electronic form by either Charles Stuber or Alex Kahler and include both null alleles and electrophoretic variants or allozymes for some 21 loci, as surveyed across 437 maize lines.

A list of the germplasm or stocks with characterized allozymes or null alleles may be retrieved on the Stock form by typing within the 'phenotype' field :
Phenotype: electro
(or
Phenotype: electrophoretic mobility)
Phenotype: null

4. WWW; connections to 18 other databases
The MaizeDB World Wide Web server is seamlessly connected to files, including images and graphics, from other databases around the world, as though the data existed in the MaizeDB records. Free software, Mosaic or Netscape, is required to browse files on the WWW, or to store the information on your machine. 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 to another database, ENZYME, which describes the reaction and in turn, connects to all SwissProt entries corresponding to that EC number and, also, 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 and maintaining updates. The ability to extract distinct formats of data from MaizeDB make it relatively easy to prepare files of matching identifiers so that external databases may use the WWW to connect to us, as occurred June 1994 with SwissProt.

MaizeDB records currently access external data in the following databases (-> indicates further connections through the external database). Generally connections are made by clicking on the 'Key' for the external database record; clicking on the database name provides access to the external database home-page. Other connections, such as gene product EC# or related genes in other databases, 'hop' directly to the external database.

Sequences
dbEST random cDNA's partial sequences (EST's), with periodically updated similarity (BLAST) searches; updates of connecting identifiers automatically delivered to MaizeDB
GenBank nucleotide sequences 
GSDB nucleotide sequences 
SwissProt protein sequences; -> Prosite (motifs, signature sequences); -> MedLine 
PIR protein sequences
GenoBase nucleotide sequences, -> other sequences submitted by same researcher; performs updated (BLAST) similarity searches on retrieved sequences (if less than 4000 bp); useful for updates on EST sequenced EST's (see dbEST above)

Genomes, Germplasm
AAtDB Arabidopsis Genome Database
E. coli Stock Center E. coli genetic stocks, map; -> ENZYME; -> GenBank
GrainGenes Wheat, Barley, Oats, etc. Genome Database
GRIN Germplasm Resources Information Network
RiceGenes Rice Genome Database
SGB Saccharomyces Genome Database
Xlocus Multi-genome database

Metabolism
ENZYME reactions, comments; -> SwissProt (all species); -> OMIM 
Klotho metabolic compounds database

References
J Biol Chem abstracts, articles (since April 1995)
JQTL on-line journal sponsored by Crop Science Society of America
Agricola abstracts (connection made; electronic matching tool under development).

Sequenced Locus Retrieval. A list of loci with sequences in GenBank may be retrieved from the Locus form typing within the field External Database,
EXTERNAL DATABASE: Gen or GenBank
This query may be further constrained to only loci with mutant phenotypes by additionally typing within the Phenotype field:
PHENOTYPE: %
Or for loci with sequences in GenBank, and with some map location, type within the map coordinates field:
VALUE: %

5. E-mail to cooperators. Using the WWW server, clicking on the e-mail address of a Person record will activate an e-mail form addressed to that Person.

DEVELOPERS AND CURATORS OF THE DATABASE INCLUDE: EH Coe (PI), P. Byrne, G. Davis, D. Hancock, M. Polacco (Columbia, MO) M. Berlyn (New Haven, CT), S. Letovsky (Baltimore, MD) C. Fauron (Salt Lake City, UT), S. Rodermel, C. Wetzel (Ames, IA) M. Sachs (Urbana, IL)

For technical 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).

ACCESSING MaizeDB - WHAT IS REQUIRED.
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 is the UNIX command, not needed for other machine software):
telnet teosinte.agron.missouri.edu
login(user name): guest
password: corncob
Guest login provides access to:
gopher
Sybase APT forms; both X-Window and vt100 emulation users supported
Lynx, a WWW browser that does not require an X-Window
help
Guests are encouraged to type 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 or to provide help.

NOTE: Users with X-Windows (this is not the same as Microsoft Windows) software will enjoy the most user-friendly access to the APT Sybase forms for fully relational queries of 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', or '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 after login as a guest.

->gopher makes available hierarchical collections of information across the Internet. Gopher client (user) software provides easy access to all gopher data servers on the Internet. 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 from boombox.umn.edu. Once installed, open server gopher.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 in a file on the MaizeDB gopher server. Our gopher server supports login to the SYBASE format.

->World Wide Web (WWW) WWW is a hypermedia or interactive-file retrieval system and allows users to traverse on-line documents by clicking on hyper links - terms, icons or images that point to other related documents. Hyper links permit retrieval of any document anywhere on the Internet. Retrieved 'documents' may include text files, graphics, and videos. Users without WWW software may access the WWW-linked format of MaizeDB by selecting the Lynx option after 'guest login'. Browsing software, such as Mosaic, 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 versions, requires an X-Window on the user's machine; it will require a systems administrator to install. Netscape software is similar to Mosaic and available by anonymous ftp from ftp.mcom.com. Netscape on a machine with SLIP connections to the Internet, may access the World Wide Web by modem. To access MaizeDB on the WWW, use the MaizeDB WWW address, otherwise known as URL or uniform resource locator:
http://www.agron.missouri.edu
The WWW formatted data are dynamically extracted from the most current version of the database, which is continuously updated.

-> ACEDB format This is a special, stand-alone, 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/maizedb and in file macedist950414.tar.Z. ACEDB formatted information is periodically extracted from MaizeDB. It does not support the robust, fill-in-the-blanks form queries of the Sybase database, accessible by the guest login service and by WWW.

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/maizedb and to transfer the database, type binary and, on a separate line, type get macedist950414.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.

Dec 1992 First public access to the data: a gopher server established. First Gopher access was 100-200 transactions/month, and steadily grew over the first 2 years to over 5,000 transactions/month.

March 1993
o Maize Gene List, MNL vol 67 pp 134-15, extracted from MaizeDB
o Version 2 of MaizeDB design implemented

March 30, 1993 40,055 records in the database

June 1993
ACEDB formatted data extracted from MaizeDB

August 1993 Tool developed for electronic reference loading, with matching to authors and previously loaded reference, from PC or MacIntosh reference manager formats. This tool has been used for loading various reference sets, including those of MNL or in Mutants of Maize (in press 1995).

Fall 1993 MaizeDB placed on World Wide Web

Dec 31, 1993 Guest login to MaizeDB(SYBASE) established that permits access by modem or other connection on the Internet, and by any machine with telnet software.

Jan 3, 1994 61,544 records in the database

Winter 1994
o MaizeDB records connected to external databases on the World Wide Web; growth of WWW access has steadily increased from 200 transactions/month to over 20,000 WWW transactions per month.
o WWW connections made to external databases from within individual MaizeDB records

March 1994 Genetic indexing of 1993 references extracted from the MaizeDB, published as hardcopy (Zealand) in MNL, vol 68. 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; updates of connectors exchanged regularly.

December 1994 QTL forms implemented; first data entered.

Jan 1, 1995 96,900 records in the database

January 1995 Permanent curator position established.


Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors

Return to the MNL 69 On-Line Index
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