Report of the Workshop on Integration of Microbial Databases



CME is interested in any comments you may have about the contents of this report.
Please contact niels@vitro.cme.msu.edu with any questions or comments you may have.
Table of Contents

1.0 Introduction

2.0 Goals

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
The IMD will require access to polyphasic data maintained by various institutions throughout the world. These data are specialized in distinct fields. The fundamental on-line data resources contain sequence data, strain data and environmental data. Sequence data are maintained by the consortium of GenBank/EMBL/DDBJ and value-added sequence databases like SwissProt, PIR, etc. Little phenotypic strain data are on-line. However, access to strain-oriented databases is possible and of high priority. These include numerous culture collection databases and directory services including WDCM, MSDN, and MINE.

Environmental data exist on-line. Such databases (e.g. WCMC) will have to be explicitly identified and linked. The initial effort is to provide entry pointers to these information sources. These links, in their simplest initial form, will allow users to utilize the facilities within these resources. A second stage effort will provide more complete links utilizing data elements in common. Such common elements such as taxonomic trees and phenotypic descriptors will be provided as part of the IMD services.

b.) Independently Curated, Specific Databases
There are several specific databases of special interest to microbiologists that are either on-line or could be so in the near future. These include the metabolic pathway database prepared by Ross Overbeek and Evgeni Selkov's team, the quinone database of Komagata, the gyrB sequence database of Harayama (which appears to be particularly useful at the species level), and perhaps others such as those held by the Belgian group.

These specialty databases would remain curated by those groups specifically interested in them and will most likely not be comprehensive. But they can be extremely useful for certain organism groups and may gain wider use and development if conveniently linked and accessible.

It is recommended that the IMD explore the state of these databases, their development and curation, plans for on-line access, and linkage issues with their developers. The federation would like to encourage linkages to such databases and should work in collaboration with the developers/curators to solve linkage problems.

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.

Return to CME Publications.