Considerations in designing a national or regional microbiological data archiving system Micah I. Krichevsky Bionomics International Wheaton, MD USA

Many sources of microbiological data are unavailable as a public good or for exploitation of the genetic pool they describe.

Summary ▪ Start discussion ▸ To enhance access and archiving of basic observational data ▸ Their interpretation ▸ Meet local needs ▪ Distributed system for national microbiological data ▸ Capture ▸ Manage ▸ Archive for permanent access

Observations Database Structure Conditions of obtaining data Data interpretation Data Context Metadata Communication

John Locke, English philosopher (August 29, October 28, 1704), in “An Essay Concerning Human Understanding: Book 3: Chapter V: Of the Names of Mixed Modes and Relations” “This shows species to be made for communication.” Paraphrasing further: Nature does not define species, we do. Further, neither nature nor we define the boundaries of species.

Taxonomy and Identification The dividing line between data and their interpretation is critical to any study All taxonomies and identifications are subjective interpretations of observations. cannot Thus, there cannot be an objectively correct identification. can There can be a consensus which lends credence to the identification.

The What of Culture Collections Authenticated, living cultures Cell & tissue cultures Hybridomas Fungi Yeasts Bacteria Algae Viruses Others

The Why of Culture Collections Basic to many research and technical activities Microbiology Molecular biology Epidemiology Biotechnology R&D and production Industrial fermentation Biodiversity conservation Environmental protection & remediation

Collections as Data Repositories Potential and kinetic information ● Potential: the biological material ➔ Little use without data ● Kinetic: the known data on the attributes of the material ➔ Some small use (e.g., biodiversity studies) without biological material ● Maximum utility requires distribution of both in usable form

National Microbiological Data Repository (NMDR) ▪A backup repository ▸ Each contributor submits a copy of data ▸ Each contributor updates the submitted data ▪ An online information resource ▪ A mechanism for combining data sets for cooperative studies ▪ The data may be: ▸ Freely accessible, or ▸ Accessible with restriction, or ▸ Held as a private, secure database

OFTEN, SINGLE WORDS ARE MEANINGLESS IN ISOLATION RKC Codes for MANNOSE Features : : D-Mannose is catabolized : D-Mannose is catabolized aerobically : D-Mannose is catabolized anaerobically : D-Mannose is utilized : D-Mannose is oxidized : D-Mannose is reduced : Acid is produced from D-mannose : Gas is produced from D-mannose : D-Mannose can be used as the sole source of carbon.

50110 Taxonomy Taxonomic rank superdomain domain subdomain superempire empire subempire superkingdom kingdom subkingdom superphylum phylum Codes for Taxonmic Rank genus subgenus species subspecies variety cultivar biovar serovar pathovar chemovar isolate culture clone Top Level Lower Level

50121 Isolation history Study Survey Start date Start time End date End time Sampling date Sampling time Place of sampling sample site description Sample designation sample pH sample Temperature sample salinity sample color sample physical appearance Sampling

Possible Components of a National Microbiological Data Repository Final delivery of information and services must become, and remain, a local responsibility.

Links to Special Content Consultants International Data Sources (mirrored or linked) University Collections Commercial Laboratories (confidential repository ) Clinical Microbiology Laboratories Agriculture Collections (research andsurvey) Government Laboratories National Culture Collection Repository

Users of Data in National Data Repository Students Primary through Secondary University Graduate School Postdoctoral Commercial National Regional International Educators Collections Press Regulators NGOs Public Agriculture Medical Laboratories ResearchInvestigators Government Laboratories Note: Some categories of users overlap

Steering (Policy) Committee (User as Chair ) Components : Repository, Data providers, Data Users, Government Representative Repository NDR Data Service Providers Secretariat (Administrative Services) User Feedback Group on Functionality Help Desk Consultant Panels System Design Microbial Coding, Training, Data Analysis User System Training Education & Hands on Training in Microbial Coding, Data Analysis Personnel Key: Repository Personnel External Personnel Mixed (Repository & External) Personnel

Final delivery of information and services must become, and remain, a local responsibility.