V. MAIZE GENOME DATABASE
MaizeDB currently presents 15,515 loci, including quantitative trait loci and gene candidates; 14,460 references; 4,071 colleague addresses; 489 traits; 2,789 genetic stocks; 5,449 elite germplasm pedigrees; 21,399 variations with 3803 images, and 771 phenotypes; 1055 (putative) gene products; 62,783 links to 41 external databases from 13,582 records; GRIN, SwissProt and GenBank (Entrez format) link reciprocally to MaizeDB pages. The WWW page 'What's New' provides an historical listing of data and design changes, with hypertext links to database records. Since Jan 1995 there have been 2,913,414 accesses, with 202,824 in Mar 1997, more than double last year. A more detailed usage analysis is accessible from the database homepage.
The Maize Genetics Newsletter (MNL), years 1992-current, is newly on-line, linked to MaizeDB authors and other objects. Links to new external databases were made: MedLine (1921 links), EcoCyc(298), AGIS-EC#(297). Medline provides access to published abstracts, related articles and GenBank records; EcoCyc accesses E. coli metabolic pathway data and links to the Coli Genetic Stock Center; and AGIS-EC# accesses plant metabolic pathway and gene product data.
Of the loci with map locations, 1270 are genes, 4133 are probed sites, and 651 are QTL; 93 hybridize to clones from various Triticeae species; 126 to rice. Of the 1804 EST's or partially sequenced cDNA's in maize, 669 have been placed on the BNL or the UMC maps. Of the mapped sites using clones from other species, there are 93 marked by probes from the Triticeae and 181 with rice probes.
Accessing the data: WWW access modes include (a) 4 styles of precision query forms, including one that provides user-specified subsets of Mapmaker formatted data; (b) full text query; (c) browser access to special lists, computed regularly, which dynamically extract data from MaizeDB. These special lists include map-indexed lists of genes, probes, microsatellite primers, genetic stocks, mutant images; cooperators; current literature; new data. Most of the browsing lists are accessible from the 'Of Interest to Maize Cooperators' page.
In addition to various WWW routes, MaizeDB supports access by gopher, ACEDB and ad hoc SQL. There is guest Internet login by modem to all routes, including access by clients without gopher or WWW software on their computers.
The fastest way to become acquainted with how MaizeDB represents information in areas of your interest is to use the full-text query option, prior to utilizing the all-attributes precision query pages. Detailed help is available on-line. Please email us at firstname.lastname@example.org, for help, suggestions, and anything related.
Following is a proposed criterion key for designating and naming cDNAs and their genes. Please respond to MaizeDB, at email@example.com, with any comments about the proposal.
Principle: Whenever appropriate, seek a mnemonic in Mendel, check MaizeDB for prior usage and for the same map location or potential equivalence, assign a new mnemonic (e.g., mnm1) if justified, and request MaizeDB (firstname.lastname@example.org) to reserve the mnemonic. Mendel may be accessed from the MaizeDB home page, under 'Of Interest to Maize Cooperators', and then the Commission for Plant Gene Nomenclature (CPGN) (http://jii06.jic.bbrsc.ac.uk).
For a sequenced cDNA, synopsis of the nomenclature syntax:
[mnemonic, gene or institution][integer][letter, if multiple site][mnemonic or gene family number in parentheses]
Before Mapping, use the anonymous acronym of the institution or laboratory with a sequential number, e.g. int###.
Single Copy: If probability/score for the sequence indicates this is a cDNA from a new gene with defined function, assign a new mnemonic (e.g., mnm1), and request MaizeDB to reserve it and to maintain the int### as a synonym. If this is a cDNA homologous to a named gene mapping at a different location, designate a new, homologous gene (e.g., mnm2).
Multiple Copy, with independent evidence indicating that the map site is uniquely the site for the cDNA: Assign a mnemonic. For other mapped sites, use int###b(mnm), etc.
Multiple Copy, with no independent evidence of uniqueness, append a mnemonic in parentheses -- e.g. int###(mnm) -- thus, csu123(abc). In the absence of a mnemonic, include the Mendel Family number, in (). These numbers will soon be made available in the public Mendel database.
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