Considerations in designing a national or regional microbiological data archiving system

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

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

3. 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

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

5. John Locke, English philosopher (August 29, 1632 - 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.

6. 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. • Thus, there cannot be an objectively correct identification. • There can be a consensus which lends credence to the identification.

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

8. 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

9. 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

10. 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

11. OFTEN, SINGLE WORDS ARE MEANINGLESS IN ISOLATION RKC Codes for MANNOSE Features: 024506: D-Mannose is catabolized. 024507: D-Mannose is catabolized aerobically. 024508: D-Mannose is catabolized anaerobically. 025022: D-Mannose is utilized. 025080: D-Mannose is oxidized. 025138: D-Mannose is reduced. 025196: Acid is produced from D-mannose. 025254: Gas is produced from D-mannose. 025312: D-Mannose can be used as the sole source of carbon.

12. Codes for Taxonmic Rank Top Level Lower Level 50110 Taxonomy 50111 Taxonomic rank 150111001 superdomain 150111002 domain 150111003 subdomain 150111004 superempire 150111005 empire 150111006 subempire 150111007 superkingdom 150111008 kingdom 150111009 subkingdom 150111010 superphylum 150111011 phylum 50111029 genus 150111030 subgenus 150111038 species 150111039 subspecies 150111041 variety 150111043 cultivar 150111044 biovar 150111045 serovar 150111046 pathovar 150111047 chemovar 150111051 isolate 150111052 culture 150111053 clone

13. 50121 Isolation history 150121001 Study 150121002 Survey 550121003 Start date 650121004 Start time 550121005 End date 650121006 End time 550121007 Sampling date 650121008 Sampling time 150121009 Place of sampling 150121010 sample site description 150121011 Sample designation 250121012 sample pH 250121013 sample Temperature 250121014 sample salinity 150121015 sample color 150121016 sample physical appearance Sampling

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

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

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

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

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