Sensing the Biological (And Making Sense of the Biological)

1. Sensing the Biological(And Making Sense of the Biological) Regina L. Tan, DVM, MS, DACVPM rtan@MITRE.org This material has been cleared for public release, case number 08-1360

2. What Is MITRE? A Federally Funded Research and Development Center (FFRDC) A unique organization that assists the U.S. government with scientific research and analysis and/or systems engineering and integration A not-for-profit corporation, chartered to work solely in the public interest Address long-term challenges of considerable complexity, analyze technical questions with a high degree of objectivity, and provide creative and cost-effective solutions to government problems

3. Agenda This material has been cleared for public release, case number 08-1360 What’s the Challenge? Sensing the biological Example H5N1 The big picture: building the system The bigger picture: The Biosecurity Enterprise Quick summary

4. The National Challenge Grand Challenge Zero ∆T Biosecurity: Detection, Distinction, Prevention Planning Emergency Planning and Response Biologic response without mitigation Event Consequence Additional Indicators Event T-Zero 1st Indicator Biologic response with mitigation Steady State Steady State Detection of 1st Indicator Response/Clean-up Anomaly and /or Event Detected Investigation/Attribution, Targeted Prevention Implementation Verification, Identification, Alert This material has been cleared for public release, case number 08-1360

5. The Challenge Statement This material has been cleared for public release, case number 08-1360 • Protect our Nation from intentional and unintentional biological threats to humans, animals, and infrastructure • United States as a system • Globalization of trade and biological threats • Tools at hand: • Information to characterize and identify targets and events that is produced by quantitative and qualitative analysis • Information derived from measurements of physical phenomena intrinsic to an object or event

6. The Challenge: Sensing the biological This material has been cleared for public release, case number 08-1360 Mother Nature and the ever-changing state of normal Direct pathogen detection Indirect pathogen detection Prediction of pathogen spread Comprehensive pathogen detection requires a management framework, integration capability, and science-based analysis End goal: enable scientific decisions based on actual science (i.e. Making Sense of the Biological)

7. Example Highly Pathogenic Avian Influenza H5N1 This material has been cleared for public release, case number 08-1360

8. Problem • Large-scale (e.g. international) outbreaks of zoonotic* disease may move and change by unknown mechanisms • End-to-end scientific analysis is difficult; large gapsexist across scientific data sources • Geographic areas • Human, wild, and domestic animal populations • Genetic, epidemiologic, contextual information • Different data collection standards and methods across sources • To fill datagaps, need to combine multiple, disjointed datasets from scientific and non-scientific data collection methods • To analyze combined data, need to combine multiple analytic disciplines • To visualize combined data, need to integrate multi-source data with time/space/net/statistical and decision-support views *diseases transmitted from animals to humans This material has been cleared for public release, case number 08-1360

9. Category Description Attributes Data Source Attribute Preference Select One Field Required Multiple Values 7 2 1 2 3 6 serotype Bioscope Data Concept EVENT WHO WHAT WHERE HOW MSC WHEN Animal tests positive Time of disease case Disease Agent Location of disease case species human Animals affected Agricultural type Source of infection start date longitude Unit type end date country province sub-district Report Number Clinical signs region text dead Causal agent Strain name accession Set date location latitude Risk factors reason onset date # suspect # cases # dead # slaughtered age race Type of record report date sample date Set location Type of record Animal type sex • This material has been cleared for public release, case number 08-1360 PROMED OTHER GENBANK W.C.S. O.I.E. W.H.O.

10. event source case_count species event_id INTEGER  event_date TIMESTAMP  date_source TEXT (64)  start_date TIMESTAMP end_date TIMESTAMP onset_date TIMESTAMP report_date TIMESTAMP sample_date TIMESTAMP event_loc TEXT (256)  loc_type TEXT (64)  country TEXT (256) province TEXT (256) region TEXT (256) district TEXT (256) location TEXT (512) longitude NUMBER latitude NUMBER ag_type TEXT (128) infection_src TEXT (128) animal_type TEXT (128) unit_type TEXT (128) report_no TEXT (128) clinical_signs TEXT (1) text TEXT (1024) risk_factors TEXT (1024) reason TEXT (512) notes TEXT (2048) entered_by TEXT (256) entered_on DATE/TIME vetted_by TEXT (256) vetted_on DATE/TIME source_id INTEGER  name TEXT (64) record_id INTEGER  species_id INTEGER  suspected NUMBER reported NUMBER deaths NUMBER slaughtered NUMBER species_id INTEGER  name TEXT (256) tax_kingdom TEXT (256) tax_phylum TEXT (256) tax_class TEXT (256) tax_order TEXT (256) tax_family TEXT (256) tax_genus TEXT (256) tax_species TEXT (256) person accession person_id INTEGER  age NUMBER race TEXT (128) sex TEXT (1) deceased TEXT (1) accession_id INTEGER  link_text TEXT (128) link_url TEXT (1024) clade clade_id INTEGER  parent_id INTEGER  serotype_id INTEGER  name TEXT (256) description TEXT (1024) strain serotype strain_id INTEGER  clade_id INTEGER  name TEXT (256) path TEXT(1) description TEXT (1024) serotype_id INTEGER  species_id INTEGER  name TEXT (64) description TEXT (1024) Bioscope Database Schema • This material has been cleared for public release, case number 08-1360

11. Tie Table 1 – many relationship Foreign Key 1 – 1 relationship Bioscope Database Schema Notes Tied to event table with tie table which is not shown.  Primary Key Maintained automatically by triggers which use sequence numbers Maintained by triggers No manual entry required. Species may contain generic groupings without taxonomic information such as “Water Fowl” or “Domestic Avian” This material has been cleared for public release, case number 08-1360

12. The Big Picture This material has been cleared for public release, case number 08-1360

13. The National Challenge Grand Challenge Zero ∆T Biosecurity: Detection, Distinction, Prevention Planning Emergency Planning and Response Biologic response without mitigation Event Consequence Additional Indicators Event T-Zero 1st Indicator Biologic response with mitigation Steady State Steady State Detection of 1st Indicator Response/Clean-up Anomaly and /or Event Detected Investigation/Attribution, Targeted Prevention Implementation Verification, Identification, Alert This material has been cleared for public release, case number 08-1360

14. Success Depends on Integration at Every Phase of the Challenge Challenge Vision and Mission • Integrate biosecurity stakeholders, research investments, and strategic thinking through the creation of an innovative, integrative, and relevant “system of systems.” • A situational awareness environment that enables 1) immediate detection and 2) immediate source distinction (natural versus intentional) of emergent biothreats. This material has been cleared for public release, case number 08-1360

15. Biosecurity Challenge Problem Statement This material has been cleared for public release, case number 08-1360 Background: Comprehensive pathogen detection requires a management framework, integration capability, and science-based analysis. Problem: No comprehensive pathogen detection system exists. Solution: An end-to-end system that integrates sensors, information, scientific data, and organizations around biothreat detection and distinction. Job: develop relevant, innovative, and integrative technologies that connect organizations across the end-to-end national enterprise. Goal: End-to-end biosecurity system that informs and coordinates national security decisions.

16. Biosecurity Challenge Phases This material has been cleared for public release, case number 08-1360 • Detection through integration • Sensors • Surveillance • Monitoring • Analysis • Organizations • Distinction • Data collection standards and standardizations • Information security and privacy issues • Sector norms and SOPs • Datasets • Libraries • Baselines

17. The Bigger Picture: The Biosecurity Enterprise This material has been cleared for public release, case number 08-1360

18. This material has been cleared for public release, case number 08-1360

19. This material has been cleared for public release, case number 08-1360

20. Quick Summary This material has been cleared for public release, case number 08-1360 Sensing the biological must be done with respect to “normal” “Normal” changes with Mother Nature Persistent surveillance and understanding suggested Provide technological support to enable responsible analysis Provide responsible analysis for informed decision making and interagency coordination Standardization required to make sense of multitude of biological surveillance systems

21. Thank you