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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources and Associated Information

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

Title: Data management and database structure at the ARS Culture Collection

Author
item Labeda, David

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 31, 2013
Publication Date: May 31, 2013
Citation: Labeda, D.P. 2013. Data management and database structure at the ARS Culture Collection. Meeting Abstract.

Technical Abstract: The organization and management of collection data for the 96,000 strains held in the ARS Culture Collection has been an ongoing process. Originally, the records for the four separate collections were maintained by individual curators in notebooks and/or card files and subsequently on the National Center for Agricultural Utilization Research’s mainframe computer system. A common set of database fields for microbial culture collections was developed during a meeting between the ARS Germplasm Resources Information Network (ARS GRIN) database staff and the three ARS microbial culture collections held at Cornell University in the late 1980’s to provide for future transportability and inter-operability. When our collection databases where migrated into FoxPro before the mainframe was decommissioned, this data structure was adopted for catalog relevant fields. The use of a unified set of field names, size, and content for common catalog information across the 4 original databases facilitated the merging of the bacterial and actinobacterial holdings into a unified database during the last migration to the current PostgreSQL database system in 2001. Increased functionality has been added to the system, providing inventory management of both lyophilized and frozen materials and, most recently, an online order and request processing system. These additions have made the database schema far more complex than the original flat-file database. A new database has been developed to organize and provide public access to gene sequence data for multiple genes generated by studies characterizing collection materials and it is planned that this system will be linked to the collection database in the future.

Last Modified: 9/1/2014
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