Accessing Microbiological Data: A User’s Perspective

Mark Segal, Ph. D.US Environmental Protection Agency

Designing the Microbial Research Commons:An International Symposium

8-9 October 2009

Washington, DC

Unique Data Perspective of Microbiologists

• Range of Data and Information Types Routinely Used by Microbiologists– Text– Numerical– Binary– Graphical

• Images– Macroscopic (e.g. colony morphology)– Microscopic (e.g. cell structure)

• Charts and graphs• Diagrams and Cartoons• Molecular structures

– Sequence– Olfactory

Digital Microbiological Data Users Who Are Not

Researchers

• Examples– Government Regulators– Research Funders – Contract Support Personnel– Evaluators for NGOs– Science Media

Where Government Regulators Use Microbiological Data

• Public Health and Pandemics– Analysis of outbreaks– Evaluation of drugs and vaccines

• Food Security– Evaluation of products of food biotechnology– Diagnostics– Antiterrorism

• Bioremediation– Evaluation of microorganisms used for cleanup

• Biofuel and Bioproducts– Evaluation of microorganisms used to make biocatalysts, enzymes– Evaluation of microorganisms used to make fuels– Evaluation of microorganisms used to make chemical substances

Environmental and Energy Applications Using Microbiology

– Bioremediation– Fuels

• Biomass conversion• Biofuel production• Pretreatment enzymes• Desulfurization of petroleum• Oil recovery

– Specialty Chemicals and Co-Products– Waste treatment– Biofertilizers– Biosensors– Biomining / mineral leaching

What Microbiological Data Are Particularly Useful

• Strain Identity– Systematic name, synonyms and relationships– History of strains in collections– Cross references to ‘identical’ strains– Sources of initial isolates– Tracking modifications made to derivatives

• Strain Characteristics – Pathogenicity/Toxigenicity– Metabolic characteristics– Stability of features– Survival adaptations

• Strain/Taxon Historical Information– Outbreaks– Safe Uses

• Potential New Uses of Strains

Sources of Microbiological Data

• Open Literature• Grey Literature• Company Confidential Files• Public Data Banks• Other Web Resources

Microbiological Data Source Issues

• Open Literature– Lack of subscriptions due to cost– Language

• Grey Literature– Finding it!!

• (We also generate it!!)

• Company Confidential Files– Restricted uses

• (We also keep it!!)

• Public Data Banks– Completeness– Accuracy – Stove-piped coverage

Benefits of Development of a Microbial Research Commons

• Accessibility to Researchers and Other Microbiological Data Users

• One Stop Shopping!– A portal that will send us to the resources we

need.• For strain ID we use StrainInfo.net as a starting point.• For whole genome sequences GOLD is a useful pointer.• NCBI/EBI have many useful resources.• Uniprot helps for proteins.• Many of these are tied together but sometimes

awkwardly and often not to other resources which have to be searched independently.

Data Areas Where Government Users Have Some Influence

• Grey Literature– Improved access on government web

sites?

• Confidential Business Information– Limited use/enhanced exchange?

• E.g. “TSCA reform should include stricter requirements for a manufacturer’s claim of Confidential Business Information (CBI). Manufacturers should be required to substantiate their claims of confidentiality. … EPA should be able to negotiate with other governments (local, state, and foreign) on appropriate sharing of CBI with the necessary protections, when necessary to protect public health and safety.” (Principles announced by Administrator Lisa P. Jackson, 9/29/09)