Report of the Workshop on Integration of Microbial Databases
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Table of Contents
1.0 Introduction
2.0 Goals
Microbiologists and biochemists face a daunting task when seekingup-to-date information on the biochemistry, physiology, ecology, or phylogeny of microorganisms or their macromolecules. There are currently some 100-200 databases in existence containing data about microorganisms. This large and quickly growing mass of complementary information is currently geographically scattered and organized in about as many ways as there are databases. To assist in the retrieval of information and to make complex queries of data about microorganisms possible, a coordinated effort of database curators, computer scientists, and funding agencies is proposed to create an Integrated Microbial Database (IMD) system which would provide a framework in which different microbial databases could conceivably be accessed as if they were one. The proposed initiative differs from current international microbial culture collection database efforts in several important respects. First, the proposed system does not begin with strain databases and so is not limited to consideration of microbes currently maintained in culture collections. This is an important distinction, because there is considerable phenotypic and genotypic data available about microorganisms that are not maintained by culture collections, including, for example, any microorganism that has not been cultivated but whose metabolic activity, distribution or involvement in a symbiotic relationship may be well known. Second, the proposed database effort would provide phylogenetic information through molecular phylogenies. Establishing a phylogenetic perspective will support the ability for a user to make complex queries, the third unique feature of the proposed database.
The potential user community for an integrated microbial database system would include: (i) microbial ecologists exploring the patterns and extent of global microbial biodiversity; (ii) biochemists who could use information about an organisms phylogeny and physiology to select appropriate organisms for comparative studies; (iii) medical microbiologists looking for rapid access to comprehensive information about pathogenic microorganisms; (iv) taxonomists working on microbial classification; (v) educators and students of microbiology needing an updated resource ofmicrobiological information; and (v) industrial microbiologists seekingmore efficient means to recognize new diversity.
3.0 IMD Prototypes Demonstration
4.0 Recommended Activities
4.1 Organization and Administration
4.2 System Design and Implementation
4.3 Data to be Integrated
4.3.1 First Priority Data
a. Nomenclatural Database
b. Phylogenetic Trees
c. Phenotypic Data
4.3.2 Existing Databases
a. Publicly Accessible On-Line Databases
b. Independently Curated, Specific Databases
4.3.3 Databases Needing Development
a. ARDRA
b. Habitat
c. Databases Obtained with Commercial Test Kits or Systems
d. Images
4.3.4 Other Groups Which Have Microbial Strain Data
5.0 Federation Membership and Responsibilities
6.0 Workshop Participants
7.0 Summary
More information about the integrated database project is available in insights, the CME Newsletter.
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