Considerations in designinga national or regional

microbiological data archiving system

Micah I. KrichevskyBionomics 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

Datainterpretation

Data

Context

Metadata

Communication

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.

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 cannotcannot be an objectively correct identification. • There cancan be a consensus which lends credence to the identification.

The What of Culture Collections

Authenticated, living cultures

Cell & tissue culturesHybridomas Fungi Yeasts Bacteria Algae Viruses Others

The Why of Culture CollectionsBasic 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 ISOLATIONRKC 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.

50110 Taxonomy50111 Taxonomic rank150111001 superdomain150111002 domain150111003 subdomain150111004 superempire 150111005 empire 150111006 subempire150111007 superkingdom 150111008 kingdom 150111009 subkingdom150111010 superphylum 150111011 phylum

Codes for Taxonmic Rank

50111029 genus 150111030 subgenus150111038 species150111039 subspecies150111041 variety150111043 cultivar150111044 biovar150111045 serovar150111046 pathovar150111047 chemovar150111051 isolate150111052 culture150111053 clone

Top Level Lower Level

50121 Isolation history150121001 Study150121002 Survey550121003 Start date650121004 Start time550121005 End date650121006 End time550121007 Sampling date650121008 Sampling time150121009 Place of sampling150121010 sample site description150121011 Sample designation250121012 sample pH250121013 sample Temperature250121014 sample salinity150121015 sample color150121016 sample physical appearance

Sampling

Possible Components of a National Possible Components of a National Microbiological Data RepositoryMicrobiological Data Repository

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

Links to SpecialContent

Consultants

InternationalData Sources

(mirrored or linked)

UniversityCollections

CommercialLaboratories(confidentialrepository)

Clinical

MicrobiologyLaboratories

Agriculture Collections

(research andsurvey)

GovernmentLaboratories

NationalCulture Collection

Repository

National

Culture

CollectionRepository

Repository ofData

Public

Private

Build MicrobialDiversityDatabase

Database ofMaterial Transfer

Agreements

Public

Private

Data ProducerEducation &

User Training

Data Tools

ControlledVocabulary

SoftwareLibrary

DataManagement

SpecialAnalysisSoftware

Access to Data

Open

RestrictedUse

Services

Workshops

Help Desk

Users of Datain National

DataRepository

Students

Primarythrough

Secondary

University

GraduateSchool

Postdoctoral

Commercial

National

Regional

International

Educators

Collections

Press

Regulators

NGOs

Public

AgricultureMedical Laboratories

Research Investigators

GovernmentLaboratories

Note: Some categories of users overlap

DataProducers

ComputerEntry &

Normalization

Exchange ofData

Communicationwith other

stakeholders

Open

RestrictedUse

BackupFacility

Open

Confidential

NationalFederation for

CultureCollections

NationalScientificSocieties

WorldFederation for

CultureCollections

Other NationalFederations(USA, UK,

Japan, etc.)

Other National &International

ScientificSocieties &

Unions

Steering (Policy) Committee(User as Chair) Components

:

Repository, Dataproviders, Data

Users,Government

RepresentativeRepository

NDR DataService

Providers

Secretariat(Administrative

Services)

User FeedbackGroup on

Functionality

Help DeskConsultant

Panels

SystemDesign

MicrobialCoding,

Training, DataAnalysis

UserSystemTraining

Education & Handson Training in

Microbial Coding,Data Analysis

Personnel Key: RepositoryPersonnel

ExternalPersonnel

Mixed(Repository &

External)Personnel

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