PLASMA: THE PLANT SECONDARY METABOLIC ARCHIVE

¹ National Center for Genome Resources, 1800A Old Pecos Trail, Santa Fe, NM 87505 USA

² Molecular Biology Program, New Mexico State Unversity, Las Cruces, NM 88003 USA

³ National Biotechnology Information Facility, New Mexico State University, Las Cruces, NM 88003 USA

Discussions in the scientific community have emphasized the need for a better understanding of plant biochemical processes as related to attempts at plant genetic engineering. We are developing the Plant Secondary Metabolic Archive (PlaSMA) to specifically address the needs of the plant biochemistry community. PlaSMA supports the acquisition, storage, and viewing of plant secondary metabolic data, employing software technology that can be used to support any metabolic pathway data. PlaSMA is being designed to represent specific reaction and pathway data, including experimental parameters and taxon information, rather than limiting the scope to the representation of generic pathways based on consensus. PlaSMA's model for data input and curation relies on distributed experts serving as curators. For this reason the first PlaSMA product was the Plant Secondary Metabolism Input Device (PlaSMID), currently in beta 3 release to a group of plant biochemists. This tool provides biochemists a natural interface to input data into the system by drawing biochemical pathways on the screen and then using them to enter data by calling up forms. We are currently developing an integrated browser and query tool to support complex biochemical queries with both graphical and text-based output. In addition to storing and representing experimental data, we are in the process of integrating GEPASI, the leading software system for modeling chemical and biochemical reaction networks. GEPASI charaterizes steady-state kinetics using Metabolic Control Analysis and stability analysis, and provides a user-freindly means for advanced exploration of a model's behaviour in multi-dimensional parameter space. This research was supported in part by the US ARO grant number DAAH04-96-1-0415.