Database and network for genome data

--Ed Coe

A prototype for a database on maize is being developed as part of the recently authorized and funded Plant Genome Initiative. Dr. Jerome P. Miksche, Director of the Office of Plant Genome Mapping with USDA-ARS, has asked me to develop a proposal to plan and to initiate this prototype. One of the targets of the PGI is development of database and network systems for genetic data, analysis of data, and linked access to sequences, clones, biosynthetic pathways, and the like, for crop plant species. Prototypes are being defined that will include selected monocot species (i.e., maize), a dicot (soybean), and a gymnosperm (loblolly pine), to be developed in coordination among the species insofar as possible and with mutually effective components. Of course we expect to benefit from substantial parts of the structure and rationale of the effort in humans and in microbial species, especially E. coli. Following is a brief sketch of the maize prototype project I have proposed, following discussions on short turnaround with a number of Cooperators. Your comments, suggestions, and advice will be appreciated.

Objectives: Define data and resources needed in the database, assemble first-priority components, and implement trials of accessing and usage, by September, 1992.

Approach: (1) Examine database strategies, analyses, and software that have been developed for other genome initiatives, including those for human and for bacterial genetics, and for other comparable programs (e.g., biotech and seed industry); (2) Evaluate adaptability of existing products for this project; and (3) Initiate programming modifications and new software needed for mapping, searching, pedigreeing, and information accessing; (4) Develop, initiate, and enhance an on-line database and interfaced network that provides access to current resources and data on the genetics of maize and is readily available to research scientists; (5) Ensure that genetic stock materials (variant strains; intensively characterized populations) and molecular materials (clones; probes) are documented in the database and that the materials are maintained with backup reserves. Solicit from specialists (1) identification and prioritization of user needs; (2) standardizations and defining of data resource structures (example: QTL data); (3) releases of data and scheduled updating; (4) surveys and inventories and compilations of key data; (5) accomplishment of essential cyological, morphological, molecular, and physiological characterizations; (6) essential laboratory analyses; and (7) derivation of key stock materials.

A preliminary outline of the primary components that should be available for access via the prototype:

Variants and reference points
(Mutations & variations; loci & alleles; translocations, inversions, deficiencies; centromeres & telomeres; knobs, etc.; QTLs)
Expression, modifiers, regulation, biochemistry
Mapping Data
Strains and Stocks
Probes and Clones

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

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