Liju Fan, PhD

_____________________________________________________________________________
Columbia, MD 21046 Tel: 410-880-8988 Mobile: 443-745-7412 liju.fan@gmail.com

CAREER SUMMARY Senior Ontologist / Information Architect with more than ten years of experience in ontology development, information architecture, system engineering, project management, and consulting. Extensive experience working closely with US government agencies, military services, international partners, and commercial clients on projects with technical solutions that require knowledge representation, ontology engineering, knowledge management, requirement management, semantic web technologies, and related technical standards and disciplines for true semantic interoperability and effective retrieval of information assets. Expertise recognized for critical thinking in the design, development, maintenance, and delivery of robust ontologies to solve clients complex problems. Team lead/player with excellent time-management and organizational skills in delivering projects on-time, within budget, and in scope. Holds a Current Secret Security Clearance and PMP certification. SELECTED ACHIEVEMENTS Led development and delivery of an ontology based on multiple international standards for effective requirements management, leveraging inferencing on complete traceability and change/configuration management for a high-profile project within DoD. Received impressive praises from clients. Led development and delivery of an ontology and related artifacts in a vocabulary package approved by COI Coordination Panel and ESWG for Data Quality Service that validates data elements in USAF financial management data systems with over $170 billion annual budget in an SOA environment. Communicated original project ideas with JCAHO for hospital incident reporting using an ontology. Worked with client to define project scope and objectives and contributed to proposal writing. Enabled client team to win $1.5 million grant award from AHRQ. Led a team in development of an ontology prototype for a Data Analysis Portal with applications in NIH-funded immunology research. Accelerated project schedule and delivered successfully in 4 months what others had not in previous 14 months. Enabled client team to win the next phase competition award of $30 million.

PROFESSIONAL EXPERIENCE Ontology Workshop, LLC 12/2005-Present Senior Consultant/Owner Served as Ontologist for TopQuadrant on a University of Texas project. Analyzed clients needs. Defined project plan. Developed ontologies in TopBraid Composer for interoperability of data systems in CDC Public Health Information Network (PHIN). Modeled PHIN system architecture. Defined using Description Logic (DL) classes related to Key Performance Measures and Functional Requirements for Preparedness compliance and certification. Prepared project reports. Accomplishments: delivered ontologies, co-authored meeting abstract. Served as Coordinator/Core Developer for Ontology of Biomedical Investigations (OBI) OWG. Managed ontology development-related activities. Collaborated with international research communities. Led relations branch efforts. Developed demo on reasoner Pellet and presented to workshop attendees. Made major design decisions. Developed OBI in Protg-OWL using DL. Analyzed use cases for consistent annotation of biomedical investigations. Performed tasks, monitored, evaluated. Accomplishments: improved process, accomplished tasks. Commissioned by World Cancer Research Fund International (WCRF) and authored 10,000-word Narrative Review on nervous system cancers, for Second Report on Food, Nutrition, Physical Activity and the Prevention of Cancer: a Global Perspective. Analyzed needs and requirements. Defined project plan. Searched web-based databases. Analyzed scientific evidence, epidemiological data, cancer classification. Tabulated results. Addressed qualitative issues. Accomplishment: adopted by Advisory Panel for international recommendations. Started up company. Develop business for knowledge management. Received training in Project Management Professional (PMP). Keep abreast of current trends in the field, evaluating Java EE, Stardog, and GATE. Accomplishments: delivered contracts, obtained PMP certification and maintain.

Liju Fan

Tel: 410-880-8988 Mobile: 443-745-7412 liju.fan@gmail.com

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Semantic Strategy, Inc. 9/2011-3/2013 Principal Ontologist Served as Health Care Subject Matter Expert and Ontology Lead for DoD Office of Deputy Chief Management Officer (DCMO). Developed in Protg-OWL preliminary ontology as semantic and data transport standard for enhanced content analysis and correct partner data exchange of medical records in DoD and VA based on USMPECOMs accessions report for medical history. Mapped concepts in OWL to Healthcare Data Dictionary (HDD) and National Information Exchange Model (NIEM) Core. Planned with client on expedited schedule and deliverables in response to sequestration. Authored analysis paper and recommended next steps using reasoner and triple store for implementation. Accomplishments: Delivered to clients full satisfaction, received acknowledgement for good knowledge and value added and referral for next phase. Served as Ontology Lead for Enterprise Information Web (EIW) Program Management Office (PMO) in DCMO. Led development in TopBraid Composer and Protg-OWL and delivered Requirements Ontology for complete traceability and change/configuration management using multiple reasoners. Analyzed and integrated multiple ISO standards (System Life Cycle Processes, Requirements Engineering) and Business Analysis Body of Knowledge (BABOK) Guide in defining OWL classes. Created pertinent ontology questions, triple store with real-life project data instances, configured reasoners, inference, and made SPARQL queries that successfully tested ontology deliverables. Directed and supervised ontology development for DoD Strategic Management Plan, defining OWL classes using DL and linking strategic goals to overarching business goals to key initiatives and measures to business activities and outcome. Defined OWL classes for processes in acquisition business capability lifecycle (BCL) of defense business systems for re-alignment. Accomplishments: Delivered robust and validated ontologies based on best industry practices and received impressive praises from clients for powerful inferencing. Served as Ontology Advisor. Instructed individuals and group made of EIW and corporate staff for trainings on ontology development and tool. Authored article on good ontology criteria as guidelines for PMO evaluation. Evaluated ontology work delivered by contract developers and presented results to client. Evaluated current state of semantic technologies during EIW RFI market research and provided client feedbacks. Evaluated and provided constructive feedbacks to improve DoD Semantic Business Enterprise Architecture (BEA) and Business Process ontologies developed by DCMO working group based on DoD Architecture Framework (DoDAF) logical and conceptual models and Business Process Model and Notation (BPMN). Accomplishments: Effectively trained staff and informed clients. Council for Logistics Research, Inc 6/2009 2/2011 Sr. Ontologist/Sr. Vocabulary Specialist Served on Enterprise Vocabulary Team as Primary Ontologist for USAF Communities of Interest (COIs). Developed ontology in TopBraid for Data Quality Service maintaining current Appropriations Acts symbols and budget codes and descriptions in compliance with USAF approved methodologies for publishing, versioning and discovering SAWSDL services. Analyzed business processes, vocabularies, data tables, data elements, and data dictionary. Conducted searches and elicited knowledge from subject matter experts for validation to ensure robust ontology representation extensible to future requirements. Evaluated and tested ontologies to support ontology management, harmonization, and application for Service Oriented Architectures (SOA), semantic indexing and discovery, interoperability, reuse, and authoritativeness of USAF Transparency initiative. Identified information assets and developed Real Growth prototype ontology based on business process definition. Evaluated ontology prototypes for Global Positioning System (GPS) and Department of Defense Architecture Framework (DODAF) and advised COIs on best practices. Developed and delivered documentation and presentations to clients. Accomplishments: Led development and delivery of an ontology and related artifacts in a vocabulary package approved by COI Coordination Panel and ESWG for Data Quality Service that validates data elements in USAF financial management data systems with over $170 billion budget in 2011. Supported convert and handoff of ontology products to XML and service developers. Identified and resolved technical issues to ensure customer satisfaction. Generated XML schema from OWL and Ontologized Authoritative Data (OAD). Provided data owners feedbacks for added values. Evaluated ontology visualization tool and provided developer critical functional requirements. Accomplishment: improved teamwork.

Liju Fan

Tel: 410-880-8988 Mobile: 443-745-7412 liju.fan@gmail.com

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FDA 7/2008-6/2009 Biologist (GS-13) Reviewed regulatory submissions for human food safety and toxicology of new and investigational drugs for food-producing animals. Searched scientific literature and toxicology databases. Authored toxicology review and food use authorization. Evaluated data. Researched, evaluated, and implemented summarization tools to enhance work efficiency. Served on committee for CVM GRAS (generally recognized as safe) pilot project. Participated in FOI summary project for toxicology reviews. Improved Standard Operating Procedure (SOP) for evaluating toxicities of combinational drugs. Accomplishment: provided recommendations on human food safety of animal drugs to ensure consumer safety. Fujifilm Medical Systems USA 12/2007-7/2008 Information Architect Developed, evaluated, tested ontologies in TopBraid Composer Maestro. Queried & retrieved data based on classified ontologies. Reviewed and organized standards created by ACR and RSNA for radiology reporting. Co-authored meeting abstract. Collaborated with subject matter experts and IT developers to develop and deploy the prototype of a novel system for radiology reporting. Collected and validated system requirements and use cases. Contributed to team hiring decisions. Accomplishments: performance review above expectation, salary increased after 3 months. Served as Coordinator/Core Developer of Ontology of Biomedical Investigations (OBI) Working Group (OWG). Developed OBI in Protg-OWL. Led relations branch efforts. Accomplishments: improved process, accomplished tasks satisfactorily. KEVRIC An IMC Company 2/2002-11/2005 Project Manager, 10/2004-11/2005 Managed and delivered concurrent ontology projects with total budget $345,000/year, 8 professionals on 3 teams. Developed ontologies (ImmPort Ontology, Toxicology Ontology Prototype, Hospital Incident Reporting Ontology) for data interoperability in Immunology Database and Analysis Portal and Chemical Effects in Biological Systems Knowledgebase. Analyzed clients needs/requirements. Defined project scope/objectives. Negotiated contracts. Developed short/long term project plans. Created road maps. Contributed to system design. Recommended implementation feasibility. Prepared status and project reports. Managed content. Analyzed object and relational models. Modeled data elements, data architecture. Trained staff. Directed staff in evaluating several natural language processing (NLP) tools. Planned, scheduled, assigned, coordinated, reviewed team member tasks. Supervised staff/subcontractor in development, implementation, problem resolution. Supervised analysis, design, development, testing and debugging of ontology browser. Worked closely with software developer/information architect for user experience, development, test, and content production. Wrote and tested on-line tutorial for ontology browser. Accomplishments: delivered ontologies; presented demos at meetings. Communicated ontology project ideas with NIEHS/NCT. Analyzed c lients needs. Worked with clients to define project scope and objectives. Wrote proposal. Accomplishment: won $25,000 contract award. Served as OWG member of Functional Genomics Investigation Ontology (FuGO). Developed FuGO in Protg-OWL. Planned approaches. Accomplished tasks. Coordinated with international collaborators. Coauthored article, Accomplishment: published article in OMICS. Principal Investigator, 10/2002-9/2004 Led team, delivered project (NIAID/NGIT - Bioinformatics Service Contract Phase I subcontract). Developed ontology prototype in Protg-OWL for complex computer system and applications in immunology research. Created new action plan. Assigned tasks, monitored, evaluated. Trained staff. Researched and modeled disease susceptible genes, autoimmune disease, clinical data. Debugged Protg-OWL. Delivered in 4 months what others had not in previous 14 months. Accomplishments: accelerated project schedule, enabled client team to win competition for $30 million Phase II award, personal recognition. Evaluated Protg-OWL for feasibility in production environment (NCICB Enterprise Vocabulary Services Protg-OWL project). Accomplishments: satisfactorily completed third-party evaluation of editing/modeling functionalities, enabled further funding of Stanford U. by NCI.

Liju Fan

Tel: 410-880-8988 Mobile: 443-745-7412 liju.fan@gmail.com

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Communicated original ontology project ideas with JCAHO. Worked with client to define project scope and objectives. Helped write proposal to AHRQ. Accomplishment: enabled client team to win $1.5 million grant award. Delivered lectures on techniques and applications in proteomics research. Audiences: NCI/CB client team, KEVRIC staff. Accomplishment: enabled KEVRIC staff to use proteomic approaches in bio-defense proposal. Communicated original program ideas with NIH program officer, wrote white paper. Prepared high-level presentations, debriefed to company executives. Accomplishment: corporate approval for writing grant proposal. Served as OWG member and liaison to World Wide Web Consortium (W3C). Developed Microarray Gene Expression Data (MGED) Ontology in OilED. Planned work, researched and analyzed object models, accomplished tasks. Coordinated with international collaborators, wrote position paper. Recommended new software for implementation feasibility. Accomplishments: team released first stable MO; presented MO at workshop; co-authored, published article in Bioinformatics.

Senior Scientist, 2/2002-10/2002 Served as Subject Matter Expert (NCI/CB-EVS contract). Curated cancer-related concepts and modeled NCI Thesaurus using description logic in TDE. Initiated pharmacokinetics modeling with VA. Accomplishment: maintained NCI Thesaurus in production and expanded. Served as OWG member, NCICB Liaison to MGED. Analyzed users needs. Developed MGED Ontology (MO) in DAML+OIL Mapped NCI Thesaurus to MO. Accomplishments: first applied MO in annotating microarray experiments, first applied NCI Thesaurus in MO, collaborated meeting presentation. Attended training (lecture, lab) on Proteomics: Principles and Methods. Represented NCI/CB and KEVRIC. Performed assays, reviewed and analyzed data, searched proteomics database. Accomplishments: obtained certificate, applied training in lectures. Served as Peer Reviewer, Pediatric Drugs, Adis International Limited, Auckland, New Zealand. Accomplishment: reviewed review manuscript.

EDUCATION (highest degree obtained)

PhD/MS in Toxicology, University of Michigan, Ann Arbor, MI.

CONTINUING EDUCATION AND TRAINING

Certification. Semantic Technology 102. 2011. DCMO, Crystal City, VA. Certification. Semantic Technology 101. 2011. DCMO, Crystal City, VA. Certification. Business Process Management Notations. 2011. DCMO, Crystal City, VA. Certification. Project Management Professional (PMP). 2011. Project Management Institute (PMI). Business Process Management (BPM) in Action. 2011. TechTarget, Newton, MA. Certificate. Introduction to Architecture. 2009. Air Force Institute of Technology, Arlington, VA. Center for Veterinarian Medicine as a High Performance Organization Workshop. 2008. FDA, Rockville, MD. Trainings on Corrective Action and Preventive Action, Software Development, Design Control, and Patent Basics. 2008. Fujifilm Medical Systems, USA, Stamford, CT. Certificate. Business to Government Mastery Program. 2007. B2G Institute. Arlington, VA. Intensive SBIR/SSTR Workshop. 2007. TEDCO, Columbia, MD. Introductory SBIR/STTR Proposal Workshop. 2007. MMRDI, College Park, MD. Workshop. TopMIND Semantic Technology. 2006. TopQuadrant, Alexandria, VA. On-line Training. Introduction to TaskMap. 2005. Harvard Computing Group, Devens, MA. Workshop. Bioinformatics & Advanced Assay Development for Homeland Defense. 2004. DHS HSARPA, Washington, D.C. Certificate. Java Programming. 2001. CyberLearning National Education Foundation, Alexandria, VA. Certificate. Introduction to Unix. 2001. CyberLearning National Education Foundation, Alexandria, VA. Certificate. Oracle 8: Backup and Recovery. 2001. Professional Education & Training, UMBC, Baltimore, MD. Certificate. Oracle 8: Database Administration. 2001. Professional Education & Training, UMBC, Baltimore, MD.

Liju Fan

Tel: 410-880-8988 Mobile: 443-745-7412 liju.fan@gmail.com

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Certificate. Web Publishing: HTML 2001. UMB, Baltimore, MD. On-line CE Course. Basic Bioinformatics: From Sequence Analysis to Genome Analysis. 2001. Society of Toxicology, Reston VA. Certificate. Introduction to Oracle: SQL and PL/SQL. 2001. Professional Education & Training, UMBC, Baltimore, MD.

HONORS AND AWARDS Certificate of Excellence, Community Services Division, Howard County, MD. 2004 The First Annual Immigrant Achievement Award, American Immigration Lawyers Association, Washington, D.C. 1996.

SELECTED PEER-REVIEWED PUBLICATIONS (others available upon request) 1. 2. 3. 4. Fan, L., et. al., Building Requirements Ontology Based on ISO and BABOK Standards for Traceability and Configuration Management. 2013. Manuscript in preparation. Peters, B. and The OBI Consortium. Ontology for Biomedical Investigations. Nature Proceedings. 2009. Fan, L. Nervous Tissue Cancer Review, Second Expert Report, World Cancer Research Fund International/American Institute for Cancer Research (WCRF/AICR). 2007. Fostel, J.M., Burgoon, L., Zwickl, C., Lord, P., Corton, J.C., Bushel, P.R., Cunningham. M., Fan. L., et. al. Towards a checklist for exchange and interpretation of data from a toxicology study. Toxicol. Sci., 99:26-34, 2007. Whetzel, P.L., Brinkman, R., Causton H.C., Fan, L., et. al. Development of FuGO: an Ontology for Functional Genomics Investigations. OMICS A Journal of Integrative Biology, 10(2):199-204, 2006. Whetzel, P.L., Parkinson, H., Causton H.C., Fan, L., et. al. The MGED Ontology; A semantic-based description of microarray experiments. Bioinformatics, 22(7):866-73, 2006. Stoeckert, C., Parkinson, H., Whetzel, T., Spellman, P., Ball, C.A., White, J., Matese, J., Fan, L., et. al. The MGED Ontology. W3C Workshop on Semantic Web for Life Sciences, Cambridge, Massachusetts, 2004.

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RECENT MEETING ABSTRACTS (others available upon request) 1. 2. 3. Fan L., Kesarinath, G. Leveraging ontology in mapping to Health Data Dictionary (HDD) and National Information Exchange Model (NIEM) Core. 2013. Abstract in Preparation. Rocca-Serra, P., Sansone, S.-A., Ruttenberg, A., Brinkman, R., Fan, L., et. al. OBI: The Ontology for Biomedical Investigations. 3rd International Biocuration Conference. Berlin, Germany. 2009. Rocca-Serra, P., Sansone, S.-A., Ruttenberg, A., Brinkman, R., Fan, L., et. al. OBI: The Ontology for Biomedical Investigations. 16th Annual International Conference Intelligent Systems for Molecular Biology. Bio-Ontologies SIG. Toronto, CA, 2008. Mirhaji, P., Coyne, R., Fan, L., et. al. PHIN Preparedness Ontology: Lessons Learned from Knowledge Modeling. The 4th Annual Public Health Information Network (PHIN) Conference, Atlanta, GA, 2006. Fan, L., et. al., Building a Hospital Incident Reporting Ontology (HIRO) in the Web Ontology Language (OWL) using the JCAHO Patient Safety Event Taxonomy (PSET). AMIA 2005 Annual Symposium, Washington, D.C., 2005. Stoeckert, C., Parkinson, H., Whetzel, T., Fan, L., et. al. The MGED Ontology: Providing Descriptors for Microarray Experiments. The 7th Annual Bio-Ontologies Meeting, Detroit, Michigan, 2005. Fan, L., A., et. al., Building a Hospital Incident Reporting Ontology (HIRO) in the Web Ontology Language (OWL) using the JCAHO Patient Safety Event Taxonomy (PSET). Innovation Caf, AHRQ Annual Conference, Washington, DC, 2005. Xu, P., Remennik, L., Thotakura, N.R., Golbeck, J., Fan, L. Prototype development of an immunology ontology that integrates multiple biomedical ontologies. Seventh International Protg Conference, Bethesda, MD, 2004. Corresponded submission and presented demo. Stoeckert, C., Parkinson, H., Whetzel, T., White, J., Matese, J., Fan, L., et. al. OntologyEntry in MAGE. MGED6, Aix-en-Provence, France, 2003.

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Liju Fan

Tel: 410-880-8988 Mobile: 443-745-7412 liju.fan@gmail.com

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RECENT INVITED TALKS (others available upon request) 1. 2. 3. 4. 5. 6. 7. A Semantic Approach to Requirements Management (Approval Process). Enterprise Information Web, Alexandria, VA. 12/2012. A Semantic Approach to Requirements Management (Traceability). Enterprise Information Web, Alexandria, VA. 10/2012. Request for COI Coordination Panel Vocabulary Package Recommendation. USAF Enterprise Vocabulary Team External Technical Review, Arlington, VA 12/2010. Approved. Development of Relations in OBI. Fourth OBI Workshop. NIH, Bethesda, MD, 7/2007 Pellet and Reasoning. Third OBI Workshop. EBI, Hinxton, UK 7/2006. Ontology Development for Semantic Integration in Biomedical Research. Center for Scientific Review, NIH, Bethesda, MD, 2/2006. Building a Hospital Incident Reporting Ontology (HIRO) in the Web Ontology Language (OWL) Using the JCAHO Patient Safety Event Taxonomy (PSET). Collaborative Expedition Workshop, Open Standards for Government Information Sharing, NSF, Ballston, VA, 7/2005. Building a Hospital Incident Reporting Ontology (HIRO) in the Web Ontology Language (OWL) Using the JCAHO Patient Safety Event Taxonomy (PSET). AHRQ Annual Conference, Washington, D.C., 6/2005. Building a Hospital Incident Reporting Ontology (HIRO) in the Web Ontology Language (OWL) Using the JCAHO Patient Safety Event Taxonomy (PSET). Joint Commission for Accreditation of Healthcare Organizations (JCAHO), Park Ridge, IL, 3/2005. Ontology Development: The Tools of the Trade. National Center for Toxicogenomics, NIEHS, Research Triangle Park, NC, 1/2005. Ontology and Semantic Web. Fujitsu Laboratories of America, College Park, MD, 11/2004. The MGED Ontology. W3C Workshop on Semantic Web for Life Sciences, Cambridge, MA, 10/2004. Ontology Development: The Tools of the Trade. Protein Information Resources (PIR), Georgetown University, Washington, DC, 3/2004.

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SKILLS Knowledge Management & Ontology Development: ontology editing & ontology modeling (Requirements Ontology, Business Process Modeling and Notation (BPMN) Ontology, National Information Exchange Model Core Ontology, DD Form 2807-2 Mapping Ontology, Financial Management Data Quality Service Ontology, GPS Ontology, DoDAF Ontology, NCI Thesaurus, MGED Ontology, Hospital Incident Reporting Ontology, FuGO, OBI, ImmPort Ontology, Toxicology Ontology prototype, PHIN Preparedness Ontology, Mammography Ontology), content management, web-based search, information extraction, analysis on business process models, open-source taxonomies/ontologies and data standards (NIEM, Health Data Dictionary, DoDAF Conceptual Model, DoDAF Logical Model, Open Biomedical Ontologies, Basic Formal Ontology, Information Artifact Ontology, HL7 Reference Information Model, UMLS Semantic Network, PHIN Logical Data Model, GO, FMA, IMGT Ontology, Dublin Core), database management (creating and managing databases, manipulating data), web services, service-oriented architecture (SOA) Computer Software and Applications: ontology editing tools (Protg, TopBraid Composer, Altova XML Spy, OilED, TDE, DTS, Metaphrase Authority, Knoodl), ontology reasoners (Pellet, SwiftOWLIM, SPARQLDL, SPIN, Racer), natural language processing (NLP) (ActiveNavigation, MEAD, GATE), enterprise information web (SPARQLizer, Federator), project management (MS Project, MS Excel, MS SharePoint), presentation (MS PowerPoint, Visio), program coordination & collaboration (Groove Virtual Office, Wiki, WebEx, Centra, Citrix, Juniper), word processing (MS Word, WordPad, UltraEdit), operating systems (Windows, Mac), relational databases (Oracle, Access, MySQL), statistics & graphics (GraphPad Prizm, SAS, SoftMix), programming languages & standards (OWL, XML, RDF, SPARQL, SQL, HTML, JAVA), file structure (Window Explorer), web searching (Mozilla Firefox, Internet Explorer), internet mail (FTP, MS Outlook), Project Management and Staff Supervision: complex problem solving (business, technical), budget and resource management, personnel management (scheduling, assigning, coordinating, monitoring, evaluating tasks), training and evaluating subordinate staff.