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BioCat:Operat ional Biosu rvei l lance ModelEvaluat ions and Catalog

Courtney D. Corley, Ph.D.Pacific Northwest National [email protected]://biocat.pnl.gov

Funded by the Threat Characterization and Attribution Branch,

Chemical and Biological Defense Division, Science and Technology

Directorate of the U.S. Department of Homeland Security

Monday 14-November 2011

PNNL-SA-82311
mailto:[email protected]:[email protected]://biocat.pnl.gov/http://biocat.pnl.gov/mailto:[email protected]:[email protected]


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BioCat Overview

Motivated by Needs of National Biosurveillance

What methodology was followed?

What is BioCat?

What are our next steps?

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Questions That National and GlobalBiosurveillance Must Answer

We think there may be a problem

Are the indicators real?

There could be a problem

How would we know?

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NBIC Mission

NBIC was established IAW PL 110-53

as the operational hub for the NBIS

community. NBIC provides trained

analysts and a 24/7 capability to

examine worldwide biosurveillance

data across multiple health domains,

integrates and assesses real-world

bio-events, and provides situational

awareness to the Secretary,

the DHS NOC and otherNBIS participants.

National Biosurveillance Integration System (NBIS) andNational Biosurveillance Integration Center (NBIC)

NBIS Mission

The NBIS enhances the identification,

location and tracking of biological

events potentially impacting

homeland security by uniquelyintegrating information and data and

leveraging interagency

communications and relationships.

NBIS supports prevention and

mitigation of such events by

providing timely notifications and

ongoing situational awareness to

enhance response of government

agencies.

Homeland Security

Advisors

SLTT Govt Agencies

Critical Infrastructure

DHS

USDA

DOJ

DOT

DOI

HHS

Non-Government

Organizations

Allies

DOD

USPS

Private Sector

EPA

DOSVA

DOC

State Fusion Centers

NBIC

Federal*

INTERNATIONAL

SLTT = State,Local, Tribal,

Territorial

*Formal NBIS Member Agencies and other Federal Participants

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A Biosurveillance Event in Scope of this Project

A chemical, biological, and radiological event that significantly impact

the One Healthlandscape. Biosurveillance events are characterized by

evidence of condition and risk. These are neither mutually exclusive

nor limited to the following examples:

Evidence of conditionperson-to-person transmission(e.g., Mycobacterium tuberculosis)

zoonoses (e.g., influenza A/H5N1,Francisella tularensis)

food-borne pathogens (e.g., Salmonella)vector-borne pathogens(e.g., equine encephalitis, Plasmodium falciparum)

water-borne pathogens(e.g., Vibrio cholerae)

air-borne pathogens (e.g., influenza)

animal-to-animal transmission(e.g.,Aphtae epizooticae [FMD])

plant pathogens(e.g., soybean and wheat rusts, citrus canker, etc.)

Evidence of riskeconomically motivated adulteration of the food supply and pharmaceutical supply

accidental or deliberate events effecting air/water quality(e.g., particulate matter,

pesticide runoff, consequences of a natural disaster, etc.)

intentional release (e.g., Bacillus anthracis, Yersinia pestis [plague])

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What is a Biosurveillance Model?

A biosurveillance model is an abstract computational,

algorithmic, statistical, or mathematicalrepresentationthat produces informative output related to CBR event-riskorevent-detection.

A biosurveillance model is formulated with a prioriknowledge and may ingest, process and analyze data.

A biosurveillance model may:be proactiveor anticipatory(e.g., used to detect orforecast an event, respectively);

assess risk(e.g., contextualized products arising from

disparate data sources, surrogate markers, and SMEanalysis);

be descriptivein nature (i.e., used to understand thedynamics or drivers of an event).

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Example Biosurveillance Models

HumanBayesian modeling of unknown diseases for biosurveillance. Y. Shen and G. F. Cooper.

2009. AMIA Annu Symp Proc, San Francisco, CA, AMIA.Prediction of a Rift Valley fever outbreak.Anyamba, et al. 2009. Proc Natl Acad Sci USA.2009 106(3): 955959.

Animal and ZoonoticAvian GIS models signal human risk for West Nile virus in Mississippi. W. H. Cooke III, etal. 2006. International Journal of Health Geographics 5: Article 36.

Predicting the risk of bluetongue through time: climate models of temporal patterns ofoutbreaks in Israel.B. V. Purse, et al. 2004. Revue Scientifique Et Technique-OfficeInternational Des Epizooties 23(3): 761-775.

Plant and FoodModeling the public health system response to a terrorist event in the food supply. E.Hartnett, et al. 2009. Risk Analysis 29(11): 1506.

Climatic models to predict occurrence of Fusariumtoxins in wheat and maize.A. W.Schaafsma and D. C. Hooker. 2007. Int J Food Microbiol 119(1-2): 116-25.

Use of field-integrated information in GIS-based maps to evaluate Moko disease(Ralstonia s olanacearum) in banana growing farms in Colombia. Munar-Vivas, et al. 2010.Crop Protection 29(9): 936-941.

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Presentation Overview


Discovery methodology

What is BioCat?

What are our next steps?

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Characterizing Event-Based BiosurveillanceModels have been developed and complex systems have evolved with abreadth of disparate data to detect or forecast biosurveillance events.

Event-based biosurveillance attributes

were derived via a two-day workshop held at Pacific Northwest NationalLaboratory by a broad set of distinguished scientists and researchers

were designed to help a biosurveillance researcher or decision makerassess what types of models may be best applied to their problem

space describe operating parameters and characteristics of the candidate

models

Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science: To Appear

Assessing the Continuum of Event-Based Biosurveillance Through an Operational Lens

Short Title: Assessing Event-Based Biosurveillance

Courtney D. Corley1, Mary J. Lancaster1, Robert T. Brigantic1 James S. Chung1 , Taylor McKenzie, Ronald A. Walters1, Ray R. Arthur2, Cynthia

Bruckner-Lea1, Gus Calapristi1, Glenn Dowling3, David M. Hartley4, Shaun Kennedy5, Amy Kircher6, Sara Klucking7, Eva K. Lee8, Noele P.

Nelson4, Jennifer Olsen9, Carmen Pancerella10, Teresa N. Quitugua11, Jeremy T. Reed12, Carla S. Thomas13

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http://www.google.com/imgres?imgurl=http://upload.wikimedia.org/wikipedia/commons/thumb/e/ed/United_States_Northern_Command_emblem.png/300px-United_States_Northern_Command_emblem.png&imgrefurl=http://forum.prisonplanet.com/index.php?topic=144019.0&usg=__ik-WzA1P9a1GVZRPex-1xh-D1l0=&h=300&w=300&sz=92&hl=en&start=2&zoom=1&um=1&itbs=1&tbnid=uC_QJg1sj__rmM:&tbnh=116&tbnw=116&prev=/images?q=USNORTHCOM+Office+of+the+Surgeon+General,+U.S.+Department+of+Defense&um=1&hl=en&sa=N&rls=com.microsoft:*:IE-SearchBox&rlz=1I7SUNA_en&tbs=isch:1http://www.sandia.gov/index.htmlhttp://www.google.com/imgres?imgurl=http://sphotos.ak.fbcdn.net/hphotos-ak-snc4/hs170.snc4/37817_410485596855_176724106855_5103319_6896710_n.jpg&imgrefurl=http://www.facebook.com/note.php?note_id=10150220025790346&usg=__22NFkyCEyDbaGg8Q28O5ZhCBZ0c=&h=250&w=250&sz=27&hl=en&start=10&zoom=1&um=1&itbs=1&tbnid=HhiBk0-qkzlCGM:&tbnh=111&tbnw=111&prev=/images?q=Office+of+Preparedness+and+Emergency+Operations,+DHHS&um=1&hl=en&rls=com.microsoft:*:IE-SearchBox&rlz=1I7SUNA_en&tbs=isch:1http://www.google.com/imgres?imgurl=http://federalpatches.com/ESW/Images/360px-US_Department_of_Homeland_Security_Seal.svg.png&imgrefurl=http://federalpatches.com/&usg=__FwX4tONgCutgc1MMAe-VbZArfdA=&h=359&w=360&sz=82&hl=en&start=5&zoom=1&um=1&itbs=1&tbnid=tSixPj7ZH-EkLM:&tbnh=121&tbnw=121&prev=/images?q=u.s.+department+of+homeland+security+logo&um=1&hl=en&rls=com.microsoft:*:IE-SearchBox&rlz=1I7SUNA_en&tbs=isch:1http://www.google.com/imgres?imgurl=http://www.defendingfoodsafety.com/uploads/image/USDA%20-%20FSIS.jpg&imgrefurl=http://www.defendingfoodsafety.com/2009/07/articles/food-safety-news/vilsack-names-jerold-mande-as-deputy-under-secretary-for-food-safety/&usg=__DXdhv4b3Vt4THEDKYbr_wZdix8o=&h=547&w=683&sz=46&hl=en&start=7&zoom=1&um=1&itbs=1&tbnid=PZGK6CVmFEyHUM:&tbnh=111&tbnw=139&prev=/images?q=Food+Safety+&+Inspection+Service,+U.S.+Department+of+Agriculture&um=1&hl=en&rls=com.microsoft:*:IE-SearchBox&rlz=1I7SUNA_en&tbs=isch:1http://www.google.com/imgres?imgurl=http://assets.studynation.com/study_abroad_logo_images/georgia_institute_of_technology.png&imgrefurl=http://www.studynation.com/studyabroad/study-options/fashion_design/page-2&usg=__KEfm6i76wz5V320qIooSOtNYzjM=&h=200&w=200&sz=19&hl=en&start=14&zoom=1&um=1&itbs=1&tbnid=Duh2SzNhzsKEAM:&tbnh=104&tbnw=104&prev=/images?q=Georgia+Institute+of+Technology+logo&um=1&hl=en&rls=com.microsoft:*:IE-SearchBox&rlz=1I7SUNA_en&tbs=isch:1http://www.google.com/imgres?imgurl=http://www.azdhs.gov/phs/oids/vector/images/cdc_logo.jpg&imgrefurl=http://www.azdhs.gov/phs/oids/vector/worldrabiesday07.htm&usg=__vCI2rtEzZ32ikVv7qA0DOzG8sKw=&h=355&w=484&sz=139&hl=en&start=2&zoom=1&um=1&itbs=1&tbnid=1dE4mlldwpp3jM:&tbnh=95&tbnw=129&prev=/images?q=Centers+for+Disease+Control+and+Prevention&um=1&hl=en&rls=com.microsoft:*:IE-SearchBox&rlz=1I7SUNA_en&tbs=isch:1


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Biosurveillance Model Search

Subject matter experts and agency contacts

Visualization tools combined with subject matter expertiseLiterature A literature searchis the active identificationof existing information sources most relevant to theresearch question or need

Subject matter experts were asked to supply keywordsand phrases salient to the research topic and which wouldenable the information analyst to identify relevantliterature

Scientific databases

Google harvestLand grant universities, agriculture programs, etc.

Others

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Database Description of Coverage/ScopeAcademic Search

Complete

Scholarly, multi-disciplinary full-text database, with more than 7,900 full-text periodicals, including more than 6,800 peer-

reviewed journals. In addition to full text, this database offers indexing and abstracts for more than 11,900 journals and a total

of more than 12,000 publications including monographs, reports, conference proceedings, etc. The database features PDF

content going back as far as 1887, with the majority of full text titles in native (searchable) PDF format. Searchable citedreferences are provided for more than 1,400 journals.

Environment Index More than 1,957,000 records from more than 1,700 domestic and international titles going back to the 1940s (including 1,125

active core titles) as well as more than 120 monographs.

International Security &

Counter Terrorism

Reference Center

ISCTRC provides a comprehensive Open Source Intelligence Resource for analysts, risk management professionals, and

students. Content includes hundreds of full text journals and periodicals, hundreds of thousands of selected articles, news

feeds, reports, summaries, books, FAQs, and proprietary Background Information Summaries that pertain to terrorism and

security.

GreenFILE This database offers well-researched information covering all aspects of human impact to the environment. Its collection of

scholarly, government and general-interest titles includes content on global warming, green building, pollution, sustainable

agriculture, renewable energy, recycling, and more. The database provides indexing and abstracts for more than 384,000records, as well as Open Access full text for more than 4,700 records.

MEDLINE The U.S. National Library of Medicine (NLM) premier life sciences database. Explore biomedicine and life sciences,

bioengineering, public health, clinical care, and plant and animal science. Search precisely with MesH terms and CAS registry

numbers; link to NCBI databases and PubMed Related Articles. Backfiles to 1950.

Military & Government

Collection

Designed to offer current news pertaining to all branches of the military and government, this database offers a thorough

collection of periodicals, academic journals, and other content pertinent to the increasing needs of those sites. The Military &

Government Collection provides cover-to-cover full text for nearly 300 journals and periodicals and indexing and abstracts for

more than 400 titles.

Open Source Center The Open Source Center (OSC) is the US Government's premier provider of foreign open source intelligence. OpenSource.gov

provides information on foreign political, military, economic, and technical issues beyond the usual media from an everexpanding universe of open sources. Our website contains sources from more than 160 countries in more than 80 languages

and hosts content from several commercial providers, as well as content from OSC partners. Access to the database is

restricted.

Scopus SciVerse Scopus is the worlds largest abstract and citation database of peer-reviewed literature and quality web sources. The

database contains 41 million records, 70% with abstracts. Nearly 18,000 titles from 5,000 publishers worldwide. 70% of content

is pulled from international sources. Includes over 3 million conference papers.

Web of Science +

Conference Proceedings

Citation Index

Science Citation Index Expanded: Over 7,100 major journals across 150 disciplines, from 1900-present.

Conference Proceedings Citation Index:Over 110,000 journals and book-based proceedings in two editions: Science and

Social Science and Humanities, across 256 disciplines.

Databases QueriedOver 13,000

citations collected

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Extract Operational Biosurveillance Models Separating the wheat from the chaff

Encountered an oceanof relevant citations

Analyst tools used to extract relevant citations

Analysis with IN-SPIRE

Citations discovered during search phase are correlatedwith pathogen and toxin list

Visualization with IN-SPIRE

Subject Matter Expert

Reviews correlated modelsConfirms or rejects relevant citation based on his/herdomain knowledge

Result is a curated list of models

6,500 relevant

citations

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IN-SPIRE ThemeView of Citations

health, security, food

Dengue, fever population

epidemics, leaf, damage

E. coli O157:H7

virus, infection, hepatitis

spatial, patients, clinical

avian, influenza, pathogenic

blood, defense, evidence

risk, risk analysis, pathogen

This view provided the overall information map from which to browse and later down select

the appropriate citations

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W d Cl d f Titl f th


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Word Cloud of Titles from theCurated Publication List

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BioCat Overview


Discovery Methodology

Event-Based Biosurveillance Model Catalog

What are the biosurveillance modeling gaps?

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BioCat.pnl.govEvent-Based Biosurveillance Model Catalog

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BioCat.pnl.gov: Curated Publications Interface

Curated bio su rvei l lance model ci tat ions in queue to be

character ized. On-cl ick so rt by feature shown in beige box

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BioCat.pnl.gov: Cataloged Model Interface

Basic Inform ation19


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BioCat Outline


Discovery Methodology

Event-Based Biosurveillance Model Catalog

Gaps

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Model Types

35%

32%

13%

11%

5%4% Risk Assessment

Spatial Epidemiological

Experimental or Clinical

Event DetectionSpread or Response

Disease Forecast

Review


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Agents

49%

31%

14%

6%

Airborne, Droplet,Aerosolized

Vector-borne

Water-, Soil-borne

Not Specific


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Data Sources

0

5

10

15

20

25

30


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Variables

0

5

10

15

20

25


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0

2

4

6

8

10

12

14

Airborne

0

2

4

6

8

10

12

14

Water-, Soil-borne

0

2

4

6

8

10

12

14

Vector

Variables by agent


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Validation Methods

30%

13%

20%

13%

4%

11%

7%

2%

Statistically Validated

Not Validated

Training Data

Temporally IndependentData

Spatially andTemporallyIndependent Data

Sensitivity Analysis

Specificity andSensitivity

Simulated Data


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Operational Viability

0

5

10

15

20

25

30

Level 1 Level 2 Level 3 Level 4 Level 5 Level 6


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National Biosurveillance Opportunities

There is a critical need to train qualified human capital

There is no comprehensive picture of US and Global BiosurveillanceThere is no common language to discuss biosurveillance

What are the capability layers (e.g., sensors, models, astute clinician,syndromic or surrogate reports, etc.)?

Biosurveillance models and systems are rarely interoperable and

information interchange is stymied by technology and policy factorsThere are very few event-based biosurveillance models that forecastevidence of condition or risk with epidemiological data (i.e., not merelydata correlations)

There is inadequate knowledge and models that understand the naturalhistory of disease (e.g., endemic and epidemic patterns, at riskpopulations, environmental determinants, etc.)

There are very few mature models that understand social, behavioraland cultural determinants of biosurveillance events (e.g., riskassessment, food adulteration, social media impact, etc.)

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PNNL Biosurveillance Project Team

Core Team Members

Dr. Courtney D. Corley [PI]

Dr. Robert T. Brigantic [co-PI]

Dr. Mary J. Lancaster

James S. Chung

Project Advisors

Dr. Teresa N. Quitugua

Dr. Ronald A. Walters

Gus Calapristi

Dr. Cindy Bruckner-Lea

Information Analysts

Christine Noonan

John Schweighardt

Shy Brown

BioCat Wiki Team

Dr. Andrew J. Cowell

Keith A. Fligg

Andrew Piatt

Peter Ellis

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This work is funded by theU.S. Department of Homeland SecurityThreat Characterization and Attribution Branch

Chemical and Biological Defense DivisionScience and Technology Directorate

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http://biocat.pnl.gov

[email protected]
http://biocat.pnl.gov/mailto:[email protected]:[email protected]://biocat.pnl.gov/


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BioCatEvent-Based Biosurveillance Model Catalog

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BioCat: Curated Publications Interface

Curated bio su rvei l lance model ci tat ions in queue to be

character ized. On-cl ick so rt by feature shown in beige box

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BioCat: Publications Interface

Technical Reports published in 1998, 1999, 2000, or 2001

Down-select from 6501 to 28 articles

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BioCat: Biological Model Catalog Interface

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BioCat: Cataloged Model Interface

Basic Inform ation35


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Edit Cataloged Modelwi th form36


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Requirements37


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Readiness and Coverage38


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Inpu t Data and Outp ut39


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Documents

biosurveillance 2