Curriculum Vitae

ORCID 0000-0002-5156-2703   paolo.ciccarese -at- gmail   Boston, MA, USA


Currently

Since 02/15 | Principal Software and Knowledge Engineer, PerkinElmer Innovation Lab, Cambridge, USA

Since 03/14 | Assistant Professor of Neurology (Informatics), Harvard Medical School, Harvard University, Boston, USA

Since 02/15 | Visiting Scientist, Neurology Department, Massachusetts General Hospital, Boston, USA

Since 01/11 | Co-chair of the W3C Open Annotation Community Group

Past Academic Positions

01/08-02/15 | Assistant in Neuroscience, Neurology Department, Massachusetts General Hospital, Boston, USA

12/07-02/14 | Instructor of Neurology (faculty), Harvard Medical School, Harvard University

10/06-12/07 | Postdoctoral researcher in Neurology, Neurology Department, Massachusetts General Hospital

10/06-12/07 | Postdoctoral researcher in Bioinformatics, Harvard Medical School, Harvard University

03/06-11/07 | Postdoctoral researcher in Biomedical Informatics, University of Pavia, Pavia, Italy

10/02-09/07 | Lecturer, Department of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy

  • Object Oriented Analysis and Programming | Undergraduate 2005-07
  • Java Fundamentals | Undergraduate 2005-07
  • Artificial Intelligence in Medicine: evidence-based clinical information systems | Undergraduate 2003-07
  • Medical Informatics: eXtended Markup Language technologies | Graduate 2003-07

Education

Education
2006 PhD in Bioengineering and Bioinformatics, University of Pavia, Italy. 2002 Italian national boards for the qualification to the profession of Engineer. 2001 Computer Science and Engineering Master Degree, University of Pavia, Italy. Score: 110/110. 1992 High School Diploma. Istituto Tecnico Commerciale (school specializing in commercial subjects and accounting), Chiavenna, Sondrio, Italy. Score: 60/60.
Research Visits
2005 Massachusettts Institute of Technology, MIT Libraries, Cambridge, MA, USA. 2004 Stanford University School of Medicine, Stanford Medical Informatics, CA, USA.
Continuous Education
2016 Oct Genes and the Human Condition (From Behavior to Biotechnology), University of Maryland, College Park, USA.

Big Data Specialization - UC San Diego - Coursera

2016 Feb Graph Analytics for Big Data, UC San Diego, USA.
With Neo4J and GraphX.
2016 Jan Machine Learning With Big Data, UC San Diego, USA.
Naive Bayes, Decision Trees, Association Rules and K-means clustering with KNIME and Spark.
2015 Dec Introduction to Big Data Analytics, UC San Diego, USA.
Hive, Pig, Splunk, Spark DataFrames, Spark SQL, Spark SQL and Hive.
2015 Nov Hadoop Platform and Application Framework, UC San Diego, USA.
Hadoop HDFS, HDFS2, YARN, Map/Reduce, HBase, Spark and PySpark.
2015 Oct Introduction to Big Data, UC San Diego, USA.

Past Activities As Entrepreneur and Consultant

11/14-05/15 Data Management and Semantic Technologies Consultant Sanofi-Aventis Deutschland GmbH. Semantic technologies and information management.

01/13-02/15 Senior Information Scientist Biomedical Informatics Core, Massachusetts General Hospital. Information management and scientific social media.

01/14-06/14 Semantic Web technologies and Linked Open Data Consultant Baker Library - Bloomberg Center, Harvard Business School, Cambridge MA. Assisted the Baker library staff in the definition of a roadmap for the adoption Semantic Web technologies for improving the availability and crosslinking of internally curated content with harvested public content.

12/13-05/14 Annotation technologies for education HarvardX, Harvard University, Cambridge MA. Designed and boostrapped the development of the annotation server for the HarvardX platform. Technologies: Grails, Java, Groovy, REST, Spring Security, HTML, CSS, JavaScript.

01/12-03/12 Semantic Web technologies for scientific portals Consultant Fidelity Biosciences, Inc, Boston MA. Use of Semantic Web technologies for improving scientific web portals. Technologies: RDF, RDFs, OWL, Pellet reasoner, Protege, Jena and Sesame.

09/07-12/09 Principal Clinical Inf. Systems and Knowledge Management Engineer Medicognos SA, Spa, Belgium. Analysis and design of the Medicognos clinical process management platform, which has been conceived as an evolution of "The Guide Project" component-based architecture. The system has been designed to make full use of clinical decision support for quality and safety management of clinical workflows. Technologies: UML, Electronic Patient Records, Clinical Terminologies (ICD9, SNOMED), Clinical Workflow, Computerized Clinical Guidelines, Windows Workflow Foundation, OpenEHR, RDF, OWL, Pellet reasoner.

01/03-11/07 Senior Information Technology and Knowledge Management Engineer Laboratory for Medical Informatics, Department of Computer Engineering and Systems Science, University of Pavia, Italy. Development of a component-based multi-level architecture designed to integrate a formalized model of the medical knowledge contained in clinical guidelines and protocols with both workflow management systems and electronic patient record technologies. Technologies: Clinical Workflow, Electronic Patient Records, Clinical Terminologies (ICD9/ICD10, SNOMED), Eclipse, CVS, Java, Struts, Struts2, JavaScript, Prototype, Scriptacolous, jQuery, HTML, CSS, iBatis, Spring, OpenEHR, J2EE, JSP, JMS, JBoss, XML, XMLSchema, MySQL, WSDL, Web Services, User Interface Design.

09/06-11/07 Clinical Information Technology Consultant Policlinico San Matteo (research hospital), Pavia, Italy. Analysis, design and implementation of (i) the website for the Italian network for amyloidosis and (ii) of a web infrastructure for managing communication and patient data collection from a network of hospitals dealing with the rare pathology. Technologies: Eclipse, CVS, Java, iBatis, Castor, Struts2, Web Programming, HTML, CSS, Javascript, JQuery, Ajax, MySQL, SQL, User Interface Design.

03/05-09/06 Knowledge and Process Management Architect Medicognos SA, Spa, Belgium. Development of a knowledge based distributed Electronic Patient Record with workflow and Decision Support capabilities. Technologies: C#, Windows Workflow Foundation, UML, Relational Databases, OpenEHR, Database Design Studio, XML, XSLT and clinical terminologies (ICD9/ICD10, SNOMED).

03/05-03/06 Principal Clinical Inf. Systems and Knowledge Management Engineer Medilogix PgmbH, Belgium. Analysis and design of the Medilogix process-based electronic patient record. Technologies: UML, Poseidon for UML, Relational Databases, OpenEHR, Database Design Studio, XML, XSLT, medical terminologies such as SNOMED and ICD9/ICD10.

2005 Founder Medicognos SA, Belgium Medicognos SA, Spa, Belgium. Medicognos clinical information systems brought the state of the art Electronic Patient Records (EPRs) and Computerized Physician Order Entry (CPOE) models a step forward by transforming them into a distributed clinical workflow management system with built-in context-aware evidence-based decision support.

2003 Software Development Consultant Sergio Elia, Vendite e Finanziamenti Immobiliari, Milano, Italy. Design and developement of a client-server information and reporting system for a chain of real estate agencies. Technologies: Eclipse, CVS, Java, Swing, Jasper Reports, JDBC, XML, MySQL.

09/01-11/02 Clinical Information Technology Engineer Consorzio di Bioingegneria e Informatica Pavese, Pavia, Italy. Design and development of an application for formally modeling the knowledge embedded in clinical practice guidelines. Technologies: UML, Poseidon for UML, Java, Swing, Castor, ICD9, SNOMED, UMLS, Oracle Database, XML, XSLT.

2000 Software Development Consultant European Community Project MAIDS (Motorcycle Accidents in Depth Study). Design and development of the software for data exchange between data entry tools and statistical analysis tools. Technologies: C++, Borland C++, C++ Standard Library

Publications

Journals

  1. Smith B, Arabandi S, Brochhausen M, Calhoun M, Ciccarese P, Doyle S, Gibaud B, Goldberg I, Kahn CE, Overton J, Tomaszewski J, Gurcan M. Biomedical imaging ontologies: A survey and proposal for future work. J Pathol Inform 2015, 6:37 (23 June 2015)
  2. Clark T, Ciccarese P, Goble C. Micropublications: a semantic model for claims, evidence, ar guments and annotations in biomedical communications. Journal of Biomedical Semantics 5 (1) 2014, 28 doi:10.1186/2041-1480-5-28 (Open Access)
  3. Merrill E, Corlosquet S, Ciccarese P, Clark T and Das S. Semantic Web repositories for genomics data using the eXframe platform. Journal of Biomedical Semantics 2014 Jun 3;5(Suppl 1):S3. doi: 10.1186/2041-1480-5-S1-S3
  4. Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray A J G, Goble C and Clark T. PAV ontology: Provenance, Authoring and Versioning Highly Accessed Journal of Biomedical Semantics 2013, 4:37 doi:10.1186/2041-1480-4-37 (Open Access)
  5. Ciccarese P, Soiland-Reyes S and Clark T. Web Annotation as a First-Class Object. IEEE Internet Computing. 10/2013;
  6. Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, and Wilbur WJ. BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. Database (Oxford). Database (2013) 2013 : bat064 doi: 10.1093/database/bat064 (Open Access)
  7. Ciccarese P, Peroni S. The Collections Ontology: creating and handling collections in OWL 2 DL frameworks. Semantic Web Journal. 2013 (accepted on July 23rd, in press)
  8. Ciccarese P, Shotton D, Peroni S, Clark T. CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships. Semantic Web Journal. 2013 Feb 04 [doi:10.3233/SW-130098] (OPEN ACCESS)
  9. Ciccarese P, Ocana M, Clark, T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S1. (OPEN ACCESS) (PubMed)
  10. Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database (Oxford). 2012 Mar 20;2012:bas005. Print 2012. (OPEN ACCESS) (PubMed)
  1. Ciccarese P, Ocana M, Castro LJG, Das S, Clark, T. An Open Annotation Ontology for Science on Web 3.0 Highly Accessed J Biomed Semantics 2011, 2(Suppl 2):S4 (17 May 2011) [doi:10.1186/2041-1480-2-S2-S4] (OPEN ACCESS) (PubMed)
  2. Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, Clark T. The SWAN biomedical discourse ontology. J Biomed Inform. 2008 Oct;41(5):739-51. Epub 2008 May 4. [doi: 10.1016/j.jbi.2008.04.010] (OPEN ACCESS) (PubMed)
  3. Quaglini S, Ciccarese P. Models for guideline representation. Neurol Sci. 2006 Jun;27 Suppl 3:S240-4. [doi: 10.1007/s10072-006-0627-6] (PubMed)
  4. Ciccarese P, Caffi E, Quaglini S, Stefanelli M. Architectures and tools for innovative Health Information Systems: the Guide Project. Int J Med Inform. 2005 Aug;74(7-8):553-62. Epub 2005 Mar 25. [doi: 10.1016/j.ijmedinf.2005.02.001] (PubMed)
  5. Ciccarese P, Caffi E, Boiocchi L, Quaglini S, Stefanelli M. A Guideline Management System. Stud Health Technol Inform. 2004;107(Pt 1):28-32. (PubMed)
  6. Kumar A, Ciccarese P, Smith B, Piazza M. Context-Based Task Ontologies for Clinical Guidelines. Stud Health Technol Inform. 2004;102:81-94 (PubMed)
  7. Quaglini S, Ciccarese P, Micieli G, Cavallini A. Non-Compliance with Guidelines: Motivations and Consequences in a case study. Stud Health Technol Inform. 2004;101:75-87. (PubMed)
  8. Kumar A, Quaglini S, Stefanelli M, Ciccarese P, Caffi E. Modular representation of the guideline text: an approach for maintaining and updating the content of medical education. Med Inform Internet Med. 2003 Jun;28(2):99-115. (PubMed)
  9. Kumar A, Ciccarese P, Quaglini S, Stefanelli M, Caffi E, Boiocchi L. Relating UMLS semantic types and task-based ontology to computer-interpretable clinical practice guidelines. Stud Health Technol Inform. 2003;95:469-74. (PubMed)
  10. Peleg M, Tu S, Bury J, Ciccarese P, Fox J, Greenes RA, Hall R, Johnson PD, Jones N, Kumar A, Miksch S, Quaglini S, Seyfang A, Shortliffe EH, Stefanelli M. Comparing computer-interpretable guideline models: a case-study approach. J Am Med Inform Assoc. 2003 Jan-Feb;10(1):52-68. (PubMed, PMCID: PMC150359)

Proceedings

  1. Bukhari SAC, Nagy ML, Ciccarese P, Krauthammer M, and Baker C. iCyrus: A Semantic Framework for Biomedical Image Discovery. Paper at SWAT4LS 2015, Cambridge, UK
  2. Schneider J, Brochhausen M, Rosko S, Ciccarese P, Hogan W, Malone D, Ning Y, Clark T, Boyce R. Formalizing knowledge and evidence about potential drug-drug interactions. Paper at BDM2I 2015 (ISWC2015).
  3. Ciccarese P, Clark T. Annotopia: An Open Source Universal Annotation Server for Biomedical Research. Demo Paper at SWAT4LS 2014 (Open Access)
  4. Schneider J, Ciccarese P, Clark T, Boyce R. Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge basey. Paper at LISC 2014 (ISWC2014)
  5. Bukhari SAC, Nagy ML, Ciccarese P, Klein A, Krauthammer M, and Baker C. An Interoperable Framework for Biomedical Image Retrieval and Knowledge Discovery. Poster (Best Poster Award) at Conference on Semantics in Healthcare and Life Sciences (CSHALS) 2014, Boston, MA
  6. Bukhari SAC, Nagy ML, Krauthammer M, Ciccarese P, Klein A and Baker C. Next-generation semantic search platform for biomedical images. Abstract at 5th Atlantic Workshop on Semantics and Services (AWoSS 2014), Saint John, NB
  7. Merrill E, Corlosquet S, Ciccarese P, Clark T and Das S. eXframe: A Semantic Web Platform for Genomics Experiments. Bio-Ontologies 2013. July 20, 2013, Berlin Germany. (OPEN ACCESS)
  8. Sanderson R, Ciccarese P, Van de Sompel H. Designing the W3C Open Annotation Data Model. Paper and poster at WebSci2013 (OPEN ACCESS)
  9. Sanderson R, Ciccarese P. W3C Open Annotation Community Group Position Statement. eBooks: Great Expectations for Web Standards A W3C Workshop on Electronic Books and the Open Web Platform (Open Access)
  10. Corlosquet S, Das S, Merrill E, Ciccarese P, Clark T. Drupal as a Semantic Web platform. International Semantic Web Conference (ISWC) 2012, Industry Track, Boston, MA, USA
  11. Ciccarese P, Clark T, Bandrowski A, Astakhov V, Grethe JS, Martone M. AntibodyRegistry.org & Domeo: a toolset for robust identification and linking of specific antibody catalog information to the scientific literature. Poster at Neuroscience 2012, New Orleans, LA.
  12. Ciccarese P, Ocana M, Clark, T. DOMEO: a web-based tool for semantic annotation of online documents. Paper at Bio-Ontologies 2011, Vienna, Austria (full text).
  13. Clark T, Ciccarese P, Attwood T, de Waard A, Pettifer S. A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications. Paper at Workshop: Beyond the PDF, January 19-21, 2011. University of California San Diego (full text)
  14. Ciccarese P, Ocana M, Das S, Clark T. AO: An Open Annotation Ontology for Science on the Web. Paper at Bio-ontologies 2010, Boston, USA
  15. Passant A, Ciccarese P, Breslin J, Clark T. SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics. Workshop on Semantic Web Applications in Scientific Discourse (co-located with the 8th International Semantic Web Conference) - 26 October 2009 - Washington, D.C. - CEUR-ws.org, Vol. 523
  16. Clark T, Ciccarese P. An agile model for semantic integration of biomedical web communities.Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics [doi: 10.3389/conf.neuro.11.2009.08.139]. (2009)
  1. Attanasio G, Ciccarese P, Wu E, Clark T, Pecis E. Tinnitusbook: a proposal for an advanced scientific web community for tinnitus research. Presentation and Poster at 3rd Tinnitus Research Initiative Meeting. (2009)
  2. Kinoshita J, Wong G, Wu E, Ocana M, Ciccarese P, Clark T. SWAN, a shared knowledge base for Alzheimer Disease research. Poster at Neuroscience 2007
  3. Quaglini S, Caffi E, Ciccarese P, Ghittori S, Mazzoleni M C. E-learning for Occupational Medicine through an Interactive Guidelines Tool. Poster at MEDINFO 2007
  4. Larizza C, Ciccarese P. An Extensible Software Framework for Temporal Data Processing. Intelligent Data Analysis in Medicine and Pharmacology (IDAMAP) 2007 Proceedings
  5. Samwald M, Bug W, Rees J, Mungal C, Barkley J, Hookway R, Chen H, Stephens S, Bodenreider O, Cheung K, Ciccarese P, Clark T, Doherty D W, Forsberg K, Kashyap V, Kinoshita J, Luciano J, Marshall M S, Neumann E, Prud'hommeaux E, Rubin D, Travers M, Wong G, Wu E, Ruttenberg A. The Semantic Web Health Care and Life Sciences Interest Group work in progress: A large scale, OBO inspired, repository of biological knowledge based on Semantic Web technologies. Poster at Bio-Ontologies SIG Workshop 2007
  6. Ciccarese P, Wu E, Clark T. An Overview of the SWAN 1.0 Discourse Ontology. WWW2007/HCLSDI Workshop
  7. Wong G T, Gao Y, Wu E, Ciccarese P, Ocana M, Kinoshita J, Clark T. Developing SWAN, a shared knowledge base for Alzheimer's Disease research. Poster at Neuroscience 2006
  8. Ciccarese P, Larizza C. A Framework for Temporal Data Processing and Abstractions. AMIA Annu Symp Proc. 2006:146-50 (PubMed, PMCID: PMC1839476).
  9. Ciccarese P, Larizza C. Tempo: a Framework for temporal data processing and abstractions. I Workshop on Technologies for Healthcare & Healthy Lifestyle, Valencia, Spain. (2006)
  10. Ciccarese P, Mazzocchi S, Ferrazzi F, Sacchi L. Genius: a new tool for gene networks visualization. Intelligent Data Analysis in Medicine and Pharmacology (IDAMAP) 2004 Proceedings, ed Blaz Zupan, John H. Holmes , pag. 107 - 111.
  11. Ciccarese P, Caffi E, Boiocchi L, Halevy A, Quaglini S, Kumar A, Stefanelli M. The NewGuide Project: guidelines, information sharing and Learning from Exceptions. Artificial Intelligence in Medicine, Proceedings AIME 2003 ,ed Springer ,pag. 163 - 167.
  12. Kumar A, Quaglini S, Stefanelli M, Ciccarese P, Caffi E, Boiocchi L. A framework for representing and executing a clinical practice guideline for the management of high blood pressure in pregnancy. Technology and Health Care, vol. 10 ,pag. 517 - 519. (2002)
  13. Kumar A, Quaglini S, Stefanelli S, Ciccarese P. Modularized service-oriented guidelines in a distributed web-based environment : A data model and architecture for managing bioterrorism and its continuous surveillance. International Conference on emerging infectious diseases 2002, Programs and Abstracts Book.
  14. Ciccarese P, Quaglini S, Kumar A. New-Guide: a new approach to representing clinical practice guidelines. Proceedings of Advances in Clinical Knowledge Management 5. (2002)
  15. Ciccarese P, Quaglini S, Kumar A.
    New-Guide: Architecture. Proceedings of Open Clinical Workshop: Methods for the Representation of Clinical Guidelines. (2001)

:: Erdös Number: 4 (Erdös – Leeb – Wolfgang Degen – Barry Smith - Ciccarese) ::

Technical

  1. 2016 ~ Editor of the W3C Specification: Selectors and States . (W3C Public Working Draft)
  2. 2016 ~ Editor of the W3C Specification: Web Annotation Vocabulary. (W3C Public Working Draft)
  3. 2014-2016 ~ Editor of the W3C Specification: Web Annotation Data Model. (W3C Public Working Draft)
  4. 2014 ~ Contributor to IDPF Informational Document: Open Annotation in EPUB (Draft).
  5. 2013 ~ Editor of the W3C Open Annotation Community Group: Open Annotation Data Model.
  6. 2012 ~ Contributor to the Discovery Informatics Workshop final report
  7. 2012 ~ Editor of the W3C Open Annotation Community Group: Open Annotation Core Specification.
  8. 2012 ~ Editor of the W3C Open Annotation Community Group: Open Annotation Extension Specification.
  1. 2011 ~ Editor of the W3C Health Care and Life Sciences Interest Group note: Ontology of Rhetorical Blocks (ORB).
  2. 2009 ~ Editor of the W3C Health Care and Life Sciences Interest Group note: Semantic Web Applications in Neuromedicine (SWAN) Ontology.
  3. 2009 ~ Editor of the W3C Health Care and Life Sciences Interest Group note: SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies.

Others

Theses

  • The Guide Project: A Clinical Knowledge Management Framework. PhD Thesis, University of Pavia, Pavia, Italy, 2006. In English.
  • A tool for Clinical Practice Guidelines formalization. Master Thesis, University of Pavia, Pavia, Italy, 2001. In Italian

SCIENTIFIC ACTIVITIES AND INTERESTS GROUPS

Organization of Events (Program Committee and Scientific Program Committee)

Organization of Events (Steering Committee)

Editorial Boards

Revision Activities

  • IEEE Transactions on Information Technology in BioMedicine.
  • Briefings in Bioinformatics, Oxford University Press.
  • Artificial Intelligence in Medicine Europe.
  • Journal of Biomedical Informatics, Elsevier
  • Journal of Web Semantics, Elsevier
  • Journal of Biomedical Semantics, BioMed Central
  • Semantic Web Journal
  • BMC Bioinformatics

Interest Groups

Last updated on: Oct 17, 2016