Paolo Ciccarese - 2012
Paolo Ciccarese, PhD

About Me

I am a senior scientist and software engineer, working in the bio-medical informatics field since the year 2000. My extensive background in software engineering, knowledge management and biomedical informatics, together with my great interest in cutting edge technologies provides the necessary scaffold for me to transform the ideas and needs of fellow scientists into production-quality software enabling technological innovations in research environments.


Email   paolo.ciccarese -at- gmail -dot- com
ORCID   0000-0002-5156-2703
Current Residency   Brookline, MA, USA
Citizenship   Italian (US Permanent Resident)

Appointments

Mar 2014-today Assistant Professor of Neurology (Medical Informatics)
Harvard Medical School, Harvard University
, Boston, USA.
Jan 2008-today Assistant in Neuroscience
Neurology Department, Massachusetts General Hospital, Boston, USA.
Jan 2013-today Senior Information Scientist
Massachusetts General Hospital Biomedical Informatics Core
, Boston, USA.
Jan 2011-today Co-chair of the W3C Open Annotation Community Group

Past

Dec 2007-Feb 2014 Instructor of Neurology (faculty)
Harvard Medical School, Harvard University, Boston, USA.
Oct 2006-Dec 2007 Postdoctoral fellowship in Neurology
Neurology Department, Massachusetts General Hospital, Boston, USA.
Oct 2006-Nov 2007 Postdoctoral fellowship in Bioinformatics
Harvard Medical School, Harvard University, Boston, USA.
Mar 2006-Nov 2007 Postdoctoral fellowship in Bioinformatics
Department of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy
Oct 2002-Sep 2007 Lecturer, Department of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy
2005-2007 Object Oriented Analysis and Programming (undergraduate)
2004-2007 Java Fundamentals (undergraduate)
2003-2007 Artificial Intelligence in Medicine: computerized clinical guidelines representation-dissemination-enactment and workflow technologies (graduate)
2002-2005 Medical Informatics: eXtended Markup Language technologies (undergraduate)

Education

2006 PhD in Bioengineering and Bioinformatics, University of Pavia, Italy.
Thesis: The Guide Project: A Clinical Knowledge Management Framework.
2002 Italian national boards for the qualification to the profession of Engineer
2001 Computer Science and Engineering Master Degree, University of Pavia, Italy.
Thesis: A tool for Clinical Practice Guidelines formalization - Score: 110 out of 110).
1992 High School. Diploma from Istituto Tecnico Commerciale (school specializing in commercial subjects and accounting),
Chiavenna, Sondrio, Italy (Score: 60 out of 60).

Research Visits

  • Massachusetts Institute of Technology, MIT Libraries, Cambridge, MA, USA (October 2005)
  • Stanford University School of Medicine, Stanford Medical Informatics, CA, USA (September 2004)

CURRENT Scientific Projects and Collaborations

Since Jan 2014 Linked Data For Libraries (Principal Investigator for MGH), ontologies and software architectures. The Andrew W. Mellon Foundation awarded a nearly $1 million, two-year grant to Cornell to support an investigation using Linked Data and the Semantic Web to improve discovery and access of scholarly information by the three libraries of Cornell, Stanford and Harvard.
Since Jan 2014 Annotopia, as software architect. Annotopia is a generalized version of CATCH and will provide the technologies for creating networks of annotation storage nodes. These notes will be able to serve a veriety of application producing annotation. Annotopia will start by serving the Domeo Annotation Tool and the Utopia PDF tool. The Annotopia technology will be deployed in multiple environments (pedagogical, biomedical...). Annotopia will also provide the technology to the future releases of the CATCH project. Paolo Ciccarese I Annotate 2014 Annotopia at I Annotate 2014
Since Jan 2014 Open edX Annotation Tools, as software architect. These annotation tools offer multiple means of engagement with the edX course material and introduce new models of online, peer-to-peer and student-instructor interactions inside the platform. Digital annotation tools allow contextual commentaries and conceptual tagging of media fragments within MOOCs, thereby transforming the unidirectional delivery of the online course content.
Since Dec 2013 CATCH for HarvardX, as architect of the annotation back-end. Implementation of the CATCH server tailored for HarvardX annotation needs. Server deployed in production at the end of January 2014 for the HarvardX Poetry in America course. Paolo Ciccarese CATCH - Harvard presentation video
Since Jan 2010 Domeo (former SWAN Annotation Tool), as project lead and architect. It is a platform allowing annotating content published in web pages. At Mass General, we are focusing particularly on web pages with scientific content related to health care and life sciences. The annotation can be performed manually or through a pool of text mining services. The results of the annotation process together with their detailed provenance data are persisted and shared in RDF format.
Technologies: Java, Lucene, Groovy, Spring, Grails, Ivy, JavaScript, GWT, Ajax, HTML, CSS, SVN, OWL/ RDF, SPARQL, Virtuoso.
Since Sep 2008 Scientific Discourse Task Force - Semantic Web for Health Care and Life Sciences Interest Group at W3C. The group aims providing a Semantic Web platform for biomedical discourse which can be evolved over time into a more general facility for many types of scientific discourse, and which is linked to key biological categories specified by ontologies. I am involved in two different working groups: rhetorical structure - for developing a formal structure describing discourse knowledge items in scientific literature - and bibliographic citations ontologies alignments.
Technologies: OWL, RDF, RDFS, RDFa, XML, XHTML
.

Open-Source Ontologies

Since Mar 2011 Collections Ontology (CO), as conceiver and author. Originally developed as part of the SWAN ontology ecosystem, it defines a generic vocabulary for unordered (Set) and ordered collections (List) in OWL-DL. Since March 2011, it became an independent project managed by a community of people. Documentation and updates are available in the wiki.
Technologies: OWL2, RDF, RDFS, Pellet, Protege, SPARQL.
On Oct 2010 Porting of the FRBR (Functional Requirements for Bibliographic Records) model from the RDF to the OWL2 DL format, as co-author. The porting is now used by FaBiO (FRBR-aligned Bibliographic Ontology).
Technologies: OWL2, RDF, FRBR model.
Since Sep 2010 CiTO (Citation Typing Ontology) and FaBiO (FRBR-aligned Bibliographic Ontology) ontologies, as contributor.
Technologies: OWL2, PRISM model, FRBR model.
Since Sep 2010 ORB (Ontology for Rhetorical Blocks), as co-author. Developed as part of the Scientific Discourse Task Force - Semantic Web for Health Care and Life Sciences Interest Group at W3C, the ORB ontology provides a model for capturing the coarse-grained rhetorical structure of scientific publications.
Technologies: OWL2.
Since Jan 2010 Antibodies Ontology, as contributor. Developed as part of the Semantic Resources project, the Antibodies ontology is an OBI-compliant model for representing: the antibody itself, an antigen for an antibody, the solution which is offered by an organization, the offering organization, and the process by which the antibody was created.
Technologies: OWL2, OBO, OBI.
Since Nov 2009 Annotation Ontology (AO), as author and project lead. This is a model for documents annotation that permits users including journal or web community editorial staff, individual scientists, and computational web agents to construct and persist scientific document annotation as RDF, linking text strings or image portions within the document to term URIs in available ontologies.
Technologies: OWL, RDF, RDFS.
In 2009 SWAN (Semantic Web Applications in Neuroscience) and SIOC (Semantically-Interlinked Online Communities) integration module, as co-author. This integration work provides a complete model to represent scientific discourse in online communities at different levels of granularity (discourse elements and content items).
Technologies: OWL, RDF, RDFS, Pellet.
Since Jan 2008 PAV (Provenance, Authoring and Versioning) Ontology, as author. Originally developed as part of the SWAN ontology ecosystem, it defines a vocabulary for defining provenance, authoring and versioning in knowledge management application that are heavily based on integration of data from different sources. PAV has been selected as one of the reference ontologies by the W3C Provenance Incubator Group.
Technologies: OWL, RDF, RDFS, Pellet.
Jan 2008-Mar 2011 SWAN Collections, as author. Originally developed as part of the SWAN ontology ecosystem, it defines a generic vocabulary for unordered (Set) and ordered collections (List) in OWL-DL. It has been used in projects such as AlzSWAN, the SWAN Annotation Tool, EARMARK and FaBiO (FRBR-aligned Bibliographic Ontology). Since March 2011, it has been renamed Collections Ontology (CO) and is now developed by several contributors as a separate project.
Technologies: OWL, RDF, RDFS, Pellet.
Since Sep 2006 SWAN Ontology, as author and project lead. The collection of ontologies, created in collaboration with AlzForum, and used by the SWAN (Semantic Web Applications in Neuromedicine), AlzSWAN and Scientific Collaboration Framework (SCF) software ecosystems to create, manage and share knowledge bases for scientific research.
Technologies: OWL, RDF, RDFS, Pellet.

Open-Source Software Development Projects

Since August 2011 Apache Clerezza module for UIMA, as contributor. Clerezza is a service platform based on OSGi (Open Services Gateway initiative) which provides a set of functionality for management of semantically linked data accessible through RESTful Web Services and in a secured way. I am working to extend the current functionalities of the UIMA module to better serve text mining services and applications oriented to semantics. I also co-wrote a converter that serializes UIMA results into Annotation Ontology (AO) RDF format.
Technologies: Java, OSGi, UIMA, RDF, Annotation Ontology.
Since 2010 Ontology Term Request Broker (obro), as analyst and developer. The broker is a web service for annotation software, used by the annotator, to find existing ontological terms and to create requests for new terms using provisional identifiers. The broker accepts requests for new ontology terms in a way that does not depend on the immediate availability of the ontology maintainer.
Technologies: Java, Lucene, Ant.
Since 2006 SIMILE Vicino, as developer. Vicino is a library to perform nearest neighbor searching and clustering. Vicino is one of the toolsl developed in the context of the SIMILE (Semantic Interoperability of Metadata and Information in unLike Environments) project at the Massachusetts Institute of Technology (MIT). For a brief period, Vicino has been integrated in Freebase Gridworks (now Google Refine) before being replaced by an algorithm implementing a different approach.
Technologies: Eclipse, Java, VPTree, SVN.
Since 2005 Java Data Processing Framework (JDPF), as architect and developer. Evolution of the project Tempo. It allows in the definition, generation and execution of standard and custom data processing.
Technologies: Eclipse, Java, OSGi, Eclipse RCP, Apache Felix, Eclipse Equinox, Maven, SVN.
Since 2004 SIMILE Welkin RDF browser, as developer. Welkin is one of the tool developed in the context of the SIMILE (Semantic Interoperability of Metadata and Information in unLike Environments) project at the Massachusetts Institute of Technology (MIT).
Technologies: Java, Swing, Sesame, RDF, SVN.
Since 2004 Genius graphical software tool for visualizing genetic networks, as conceiver and developer. Conceived in 2004 and put on hold, after a long period of inactivity the project as been put back in development in 2010.
Technologies: Java, Swing, JFreeChart, XML, SVN.

Past Scientific Projects and Collaborations

Sep 2013-Dec 2013 Library Cloud (Harvard Library Innovation Lab), as member of the architectural committee. LibraryCloud is a metadata server that gathers library metadata from multiple institutions and makes it available through open APIs and as Linked Open Data.
Dec 2012-Sep 2013 CATCH: Common Annotation, Tagging, and Citation at Harvard (Harvard Library Labs), as Co-Principal Investigator and architect. Common Annotation,Tagging and Citation (CATC) API is a unified public open API that enables storing, searching, discovering, sharing and analyzing scholarly annotations produced on four digital media types - text, image, audio and video - across existing pedagogical and research tools at Harvard.
Jun 2010-Jun 2013 MS Discovery Forum: An Advanced Scientific Web Community for Multiple Sclerosis Research, as bioinformatician. MS Discovery Forum will be a web community for multiple sclerosis (MS) researchers to share and discuss current research results, reagents, protocols and compendia of other information including genetic epidemiology.
Sep 2010-Aug 2013 Document Annotation Services for the Neuroscience Information Framework, as project manager for Mass General Hospital and developer. A collaboration with the Neuroscience Information Framework (NIF) project - at the University of California San Diego - for the customization and extensions of DOMEO (previously named SWAN Annotation Tool) for serving the need of the NIF community. The list of features includes the integration with the NIF Antibody Registry.
Technologies: Java, Groovy, Grails, Spring, Spring Security, OpenID, JavaScript, GWT, Ajax, HTML, CSS, SVN, OWL/RDF, Web Services.
Feb 2011-Jan 2012 Architectures of Nanopublications, as contributor. Collaboration for applying nanopublications to practical examples in research in biology. My contribution is directed to ensure the possibility of publication of SWAN content and appropriate provenance as nanopublication.
Nov 2010-Oct 2012 Elsevier Annotation Framework collaboration, as developer. In collaboration with the publisher Elsevier. Application of the Domeo (former SWAN Annotation Tool) for curation of text mining services results. The project goals include the integration of the Annotation Tool with the Apache UIMA framework through the translation of the UIMA results into Annotation Ontology format.
Technologies: Java, Groovy, Spring, Grails, JavaScript, GWT, Ajax, HTML, CSS, SVN, OWL/ RDF, Web Services, UIMA.
Oct 2010-Sep 2011 Build provenance-aware model of mappings between sections of non-SemWeb documents, and terms in SemWeb ontologies, as subtask coordinator. Subtask Homepage - Scientific Discourse Task Force - Semantic Web for Health Care and Life Sciences Interest Group at W3C.
Mar 2010-Dec 2011 SWAN 2.0: Hypothesis Management for Drug Discovery, as project lead and head developer. Developed in collaboration with a major pharma, the projects is combining in a single framework the expressiveness of the first version of the SWAN platform - hypotheses management - with the power of the SWAN Annotation Tool - document centric, semantic content creation.
Technologies: Java, Groovy, Grails, Lucene, GWT, JavaScript, Ajax, HTML, CSS, SVN, RDF, OWL, REST, SPARQL, SpringSource Tool Suite.
Jan 2009-Dec 2010 Semantic Resources Project, as Project manager and senior researcher for Mass General Hospital: collaboration between Mass General Hospital and Science Commons and with the goal of extending the Neurocommons project and enabling its facilities to be easily used from within the SWAN and SCF projects and by other scientific communities. Taking best advantage of emerging Semantic Web technologies, we developed a set of resources or interlinked knowledge bases considered of high value for the bio-informatics world. Examples of resources are: antibodies, for which we developed an OBO/OBI compliant OWL model, and PRotein Ontology (PRO), for which we worked with the maintainers for developing extensions of the model and for including proteins related to the Alzheimer's disease.
Technologies: OWL, RDF, OBO, SPARQL, Virtuoso, Pellet, Java, Lucene
Sep 2009-Sep 2010 SWAN (Semantic Web Applications in Neuromedicine) - CiTO (Citation Typing Ontology) - FaBiO (FRBR aligned Bibliographic Ontology) - PRISM (Publishing Requirements for Industry Standard Metadata) alignment/integration , as responsible. The project has been developed as part of the Scientific Discourse Task Force - Semantic Web for Health Care and Life Sciences Interest Group at W3C. A single, integrated, model for representing citations and bibliographic objects has been created extended CiTO/FaBiO with some of the features provided by PRISM and the former SWAN Ontology Citations module. Both CiTO/FaBiO and SWAN ontologies have been built on top of the FRBR (Functional Requirements for Bibliographic Records) model.
Technologies: OWL, RDF, Pellet reasoner.
Jan 2008-Sep 2009 SCF (Science Collaboration Framework), as semantic technologies catalyst. The Science Collaboration Framework (SCF) is a software toolkit to establish web-based virtual team organizations for researchers in biomedicine. It enables researchers to publish and discuss on-line content such as articles, news, and perspectives, and to provide shared semantic context for this content using established scientific vocabularies and automated text mining.
Technologies: JavaScript, OWL, RDF.
2008 SWAN (Semantic Web Applications in Neuromedicine) - SIOC (Semantically-Interlinked Online Communities) ontologies alignment/integration, as responsible and editor of the W3C HCLS note. The project has been developed as part of the Scientific Discourse Task Force - Semantic Web for Health Care and Life Sciences Interest Group at W3C. SWAN-SIOC enables semantic interoperability of discourse across scientific communities with intersecting but distinct research interests.
Technologies: OWL, RDF, Pellet reasoner.
Sep 2006-Sep 2009 SWAN (Semantic Web Applications in Neuromedicine), as project lead and developer - Developed in collaboration with AlzForum, SWAN is a collaborative web application that aims to organize and annotate scientific knowledge about Alzheimer disease and other neurodegenerative disorders. SWAN facilitates the formalization of hypotheses about the disease and allows to manage the evolving universe of data and information about Alzheimer disease in such a way that researchers can easily comprehend the larger context ("what hypothesis does this support or contradict?"), compare and contrast hypotheses ("where do these two hypotheses agree and disagree?"), identify unanswered questions and synthesize concepts and data into ever more comprehensive and useful hypotheses and treatment targets for this disease. You can browse SWAN for Alzheimer or AlzSWAN here.
Technologies: Java, Groovy, Hibernate, Spring, Lucene, OWL, RDF, SPARQL, OpenAnzo, JavaScript, Ajax, Dojo, Exhibit, Struts2, Tiles, JSP, JAXB, HTML, Maven, SVN.
2006 ROL (Rete Oncologica Lombarda or Lombardia Oncological Network), as developer: The project consisted in the developement of an evidence-based decision support system focused on checking cancer treatments compliance with clinical protocols.
2005-2007 Amyloidosis Network Project , as project manager and developer: Analysis, design and developement of i. an infrastructure for managing communication and patient data collection from a network of hospitals; ii. an innovative electronic patient record with an unstructured database and archetypes/templates meta models; iii. a decision support system for computerizing the clinical protocol. Development of the original version of the Amiloidosi.it website that is still online with few changes.
Technologies: Eclipse, Tomcat, MySQL, Java, Struts2, JavaScript, jQuery, Prototype, Scriptaculous, HTML, CSS, iBatis, Spring, SVN.
2003-2005 E-Heart Failure Project. A model for the integrated management of care for cardiac decompensation patients, based on computerized guidelines as responsible for the computerizable model of the clinical practice guideline and responsible for the design and developement of the guideline-based decision support system - The project has been funded by the Autonomous Province of Trento and coordinated by the ITC-Irst in collaboration with the Universities of Pavia, Florence and Trento, the Fraunhofer IBMT and the Health Care Service Trust of the Province of Trento. The overall aim of the project was to design, develop and assess computerized guidelines for an integrated care management model. A web structure acts as a virtual environment in which information services are delivered to various categories of user. This cooperative framework, based on innovative techniques, supports all those involved in the care process (hospital doctors, nurses, and general practitioners) by furnishing information, providing access to data according to need, and enabling the exchange of information.
Technologies: Guide Technology, Eclipse, Tomcat, MySql, SQL, JDBC, Java, Swing, J2EE, JBoss, WebServices, SOAP, WSDL, XML, XMLSchema, Struts, JSP, HTML, CSS, JavaScript, Castor, CVS.
2002-2005 MIUR - FIRB: Le tecnologie dell'informazione e della comunicazione per la gestione dei processi di prevenzione, cura e riabilitazione - Information and communication technologies for the management of health care processes for prevention cure and rehabilitation, as resposible for modeling and computerization of clinical practice guidelines.
Technologies: Guide Technology, Eclipse, Tomcat, MySql, SQL, JDBC, Java, Swing, J2EE, JBoss, WebServices, SOAP, WSDL, XML, XMLSchema, Struts, JSP, HTML, CSS, JavaScript, Castor, CVS.
Nov 2001-Dec 2007 The Guide Project, as conceiver, architect and developer: 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: Eclipse, Tomcat, MySql, SQL, JDBCJava, Swing, J2EE, JBoss, WebServices, SOAP, WSDL, XML, XMLSchema, Servlets, JSP, HTML, CSS, JavaScript, Castor, CVS.

Publications

Journals

  1. 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)
  2. 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 (Accepted)
  3. 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)
  4. Ciccarese P, Soiland-Reyes S and Clark T
    Web Annotation as a First-Class Object.
    IEEE Internet Computing. 10/2013;
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. Kumar A, Ciccarese P, Smith B, Piazza M.
    Context-Based Task Ontologies for Clinical Guidelines.
    Stud Health Technol Inform. 2004;102:81-94 (PubMed)
  16. 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)
  17. 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)
  18. 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)
  19. 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. Ciccarese P, Clark T
    Annotopia: An Open Source Universal Annotation Server for Biomedical Research.
    Demo Paper at SWAT4LS 2014
  2. 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)
  3. 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
  4. 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
  5. 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)
  6. Sanderson R, Ciccarese P, Van de Sompel H
    Designing the W3C Open Annotation Data Model.
    Paper and poster at WebSci2013 (OPEN ACCESS)
  7. Sanderson R, Ciccarese P
    W3C Open Annotation Community Group Position Statement
    . (text)
    eBooks: Great Expectations for Web Standards A W3C Workshop on Electronic Books and the Open Web Platform
  8. 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
  9. 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.
  10. 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).
  11. 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)
  12. 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
  13. 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
  14. 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)
  15. 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)
  16. 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
  17. 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
  18. Larizza C, Ciccarese P.
    An Extensible Software Framework for Temporal Data Processing.
    Intelligent Data Analysis in Medicine and Pharmacology (IDAMAP) 2007 Proceedings
  19. 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
  20. Ciccarese P, Wu E, Clark T.
    An Overview of the SWAN 1.0 Discourse Ontology.
    WWW2007/HCLSDI Workshop
  21. 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
  22. Ciccarese P, Larizza C.
    A Framework for Temporal Data Processing and Abstractions.
    AMIA Annu Symp Proc. 2006:146-50 (PubMed, PMCID: PMC1839476).
  23. Ciccarese P, Larizza C.
    Tempo: a Framework for temporal data processing and abstractions.
    I Workshop on Technologies for Healthcare & Healthy Lifestyle, Valencia, Spain. (2006)
  24. 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.
  25. 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.
  26. 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)
  27. 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.
  28. 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)
  29. Ciccarese P, Quaglini S, Kumar A.
    New-Guide: Architecture.
    Proceedings of Open Clinical Workshop: Methods for the Representation of Clinical Guidelines. (2001)

Technical

  1. 2014 ~ Contributor to IDPF Informational Document: Open Annotation in EPUB (Draft).
  2. 2013 ~ Editor of the W3C Open Annotation Community Group: Open Annotation Data Model.
  3. 2012 ~ Contributor to the Discovery Informatics Workshop final report
  4. 2012 ~ Editor of the W3C Open Annotation Community Group: Open Annotation Core Specification. (Draft)
  5. 2012 ~ Editor of the W3C Open Annotation Community Group: Open Annotation Extension Specification. (Draft)
  6. 2011 ~ Contributor to the Force 11 Manifesto:Improving Future Research Communication and e-Scholarship.
  7. 2011 ~ Editor of the W3C Health Care and Life Sciences Interest Group note: Ontology of Rhetorical Blocks (ORB). (Draft)
  8. 2009 ~ Editor of the W3C Health Care and Life Sciences Interest Group note: Semantic Web Applications in Neuromedicine (SWAN) Ontology.
  9. 2009 ~ Editor of the W3C Health Care and Life Sciences Interest Group note: SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies.

Theses

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


Scientific ACTIVITIES AND INTERESTS GROUPS

Organization of Events (Steering Committee)

Organization of Events (Program Committee and Scientific Program Committee)

Editorial Boards

Revision Activities

Interest Groups

INVITED TALKS, SELECTED Presentations, PANELS and WORSHOPS

2014

Oct 28 Participant at the Web Annotation Working Group F2F, Santa Clara, CA
Part of TPAC 2014
Aug 8 Invited Talk at VIVO 2014 Conference, Austin, TX
Title: Knowledge networks, Social networks… Annotation… Learning and Discovery -
Jun 24 Invited Talk at Ontology and Imaging Informatics, Amherst, NY
Title: Interoperable Biomedical Image Annotations. Describing and Linking Biomedical Images through Open Annotation and Domain Ontologies - Annotopia: universal annotation server with Open Annotation heart. Slides
Apr 29 Participant at the Annotopia Workshop at EMBL-EBI, Cambridge, UK
Apr 4 Talk at iAnnotate 2014, San Francisco, CA
Title: Annotopia: Open Annotation server - Annotopia: universal annotation server with Open Annotation heart. Slides - Paolo Ciccarese I Annotate video
Apr 2 Participant at the W3C Annotation Workshop, San Francisco, CA, USA
Jan 30 Invited expert to the kick-off meeting of the Linked Data Project for Libraries, Stanford, Palo Alto, CA, USA

2013

Dec 11 Invited talk at the Baker Library of Medicine, Harvard Buseinss School, Boston, MA
Title: On Annotation standard and tools
July 25 Participant at the NIF Hack-a-thon 2013, UCSD, San Diego, CA, USA
July 12 Keynote speaker at DILS (Data Integration in Life Sciences) 2013, Montreal, Canada
Title: Open Annotation in Biomedicine: annotation, semantic annotation and how to keep the right crowd in the loop
June 25 Participant at the Open Annotation Community Group F2F, University of Manchester, Manchester, UK
June 24 Invited speaker at the Open Annotation Data Model rollout, University of Manchester, Manchester, UK
Jun 21 Invited speaker at NFAIS (National Federation of Advanced Information Services) workshop:
Update on Content: Fostering Practical Usage, Philadelphia, USA
Jun 20 Co-organizer of session at Workshop on Innovations in Scholarly Communication (OAI8), Geneva, Switzerland
Title: Open Annotations
May 14 Talk at the Cambridge Semantic Web Monthly Meetup, MIT, Cambridge, MA
Title: Open Annotation Core Data Model
May 6 Invited speaker at the Open Annotation Data Model rollout, MITH, U. of Maryland, College Park, MD
May 5 Panelist at the MiT8 (Media in Transition International Conference), MIT, Cambridge USA
Title of the panel: Shared Knowledge Creation: Talking Back to Online Content
Apr 10 Invited talk at iAnnotate 2013, San Francisco, CA
Title: Semantic annotation on the web using Domeo - Paolo Ciccarese I Annotate video
Apr 9 Invited speaker at the Open Annotation Data Model rollout, Stanford, CA
Mar 28 Speaker at Annotations @ Harvard: Convergence Workshop
Talk: The Domeo Annotation Tool
Talk: Open Annotation (OA) Data Model - Open Annotation (OA) Data Model slides - Paolo Ciccarese I Annotate video
Mar 19 Speaker at Beyond the PDF 2, Amsterdam, Netherlands
Talk: The W3C Open Annotation Model: Interoperability for Scholarly Annotation
Demo: The Domeo Annotation Tool v.2 Alpha
Mar 1 Talk at Conference on Semantics in Healthcare and Life Sciences (CSHALS) 2013, Boston, MA
Title: Domeo Web Annotation Tool: Linking Science and Semantics through Annotation
Feb 14 Invited talk at the Countway Library of Medicine, Harvard Medical School, Boston, MA
Title: Open Annotation and Domeo: Annotations in Biomedicine
Feb 12 Talk at eBooks: Great Expectations for Web Standards. W3C Workshop on Electronic Books and the Open Web Platform, New York
Title: Open Annotation: Bridging the Divide? (with R. Sanderson) - Domeo: a web-based tool for semantic annotation of online documentsslides

2012

Dec 10 Talk at 2012 Fall CNI (Coalition for Networked Information) Membership Meeting, Washington DC
Title: Open Annotation Update: Open Annotation Collaboration Experiment Results & Ongoing Work of the W3C Open Annotation Community Group - Domeo: a web-based tool for semantic annotation of online documentsslides
Nov 1 Talk at Site Visit of Take Note Conference, Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA
Title: Pervasive, Transferable Annotation for Science Content on the Web
Nov 1 Talk at Site Visit of Take Note Conference, Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA
Title:Connected Collective Knowledge: The New Annotation-Citation Paradigm
Oct 17 Poster presentation AntibodyRegistry.org & Domeo: a toolset for robust identification and linking of specific antibody catalog information to the scientific literature. at Neuroscience 2012, SfN, New Orleans, LA
Sep 18 Co-chair of the Open Annotation Community Group Face to Face Meeting, Chicago, IL
Jul 26 Invited at the OAC Project Review Meeting, Chicago, IL
Jun 12 Speaker at the Preconference Workshop at 2012 NMC (New Media Consortium) Summer Conference
Title: Connected Collective Knowledge
Jun 4 Tutorial with Stéphane Corlosquet at SemTechBiz (The Semantic Technology & Business Conference)
Title: Leveraging the Semantic Web with Drupal 7 - Domeo: a web-based tool for semantic annotation of online documentsslides
May 31 Speaker at the NIF (Neuroscience Information Framework) all hands meeting 2012, San Diego, CA, USA
Title: Domeo: Progress report
Feb 17 Invited talk at School of Computer Science, Manchester University, Manchester UK
Title: Linking science and semantics through annotation
Feb 2 Invited participant at 2012 NSF Workshop: Discovery Informatics: Science Challenges for Intelligent Systems, Washington DC, USA
Jan 30 Talk at Scientific Discourse Task Force, W3C HCLS Interest Group
Title: Creating, visualising, sharing, curating and discussing text mining results with Domeo Annotation Toolkit, Apache UIMA and Apache Clerezza - Domeo and Text Miningslides

2011

Nov 7 Invited speaker at New Tools and Methods for Notetaking Workshop, Radcliffe Institute for Advanced Study, Cambridge, MA, USA
Oct 4 Participant at Alzforum / Protein Ontology Kick-Off Meeting, Buffalo, NY, USA
Aug 15 Participant at The Future of Research Communication (FoRC) workshop, Schloss Dagtuhl, Germany
Aug 9 Talk at Cambridge Semantic Web Gatherings, Cambridge, MA, USA
Title: Annotating online documents with DOMEO and Annotation Ontology
Jul 15 Talk at Bio Ontologies 2011, Vienna, Austria
Title: DOMEO: a web-based tool for semantic annotation of online documents.
Jun 27 Judge at the Elsevier/TWC Heath & Life Sciences Hackathon, RPI, Albany, NY, USA
Event: 24-hour Health and Life Sciences Semantic Web Hackathon
Jun 23 Panelist for for the Harvard IT Summit, Cambridge, MA, USA
Title of the Panel: Scholarly Annotations
Jun 16 Speaker at the NIF (Neuroscience Information Framework) all hands meeting 2011, San Diego, CA, USA
Title: Progress and future developments of DOMEO (SWAN Annotation Tool) within NIF
Jun 15 Talk at NCBO (National Center for Biomedical Ontology) Webinar Series
Title: Linking science and semantics with Annotation Ontology and the SWAN Annotation Tool
May 11 Lecture at MassGeneral Institute for Neurodegenerative Disease (MIND), Charlestown, MA, USA
Title: Annotating Online Scientific Literature
Mar 24 Invited talk at OAC Workshop, Chicago, IL, USA
Title: History and Overview of AO (Annotation Ontology) - Semantic Resources Project Slidesslides
Mar 15 Invited talk at NIF webinars
Title: Annotation Ontology (AO) and SWAN Annotation Tool - webinar recording
Jan 19 Participant at Beyond the PDF workshop, San Diego, CA, USA

2010

Dec 1 Invited talk at AstraZeneca, Waltham, MA, USA
Title: Hypothesis Management and Supervised Automated Annotation of Web Documents
Oct 12 Invited talk at Eli Lilly and Company, Indianapolis, IN, USA
Title: Drug Discovery and Supervised Automated Annotation of Web Documents
Oct 8 Invited talk at Pfizer, Cambridge, MA, USA
Title: Hypothesis Management and Supervised Automated Annotation of Web Documents
Jul 9 Talk at BioOntologies 2010: Semantic Applications in Life Sciences, Boston, MA, USA
Title: AO: an open Annotation Ontology for science on the web - AO Annotation Ontology Slidesslides
Apr 26 Invited talk at 2010 Protein Ontology 3th Annual Meeting, Newark, Delaware
Title: Semantic Resources Project: PRO (Protein Ontology) Use Cases for Scientific Communities - Semantic Resources Project Slidesslides

2009

Nov 7 Invited talk at WONCA (GP branch of WHO) committee for the ICPC classification meeting, Brasov, Romania
Title: The medical terminology-classifications ecosystem. Ontoterminologies for semantic interoperability
Jun 23 Invited talk at EU Workshop: Ontology-Driven Semantic Interoperability in eHealth, Brussels, Belgium
Title: Semantics is not a luxury: Building the new generation of Clinical Information Systems - Semantics is not a luxuryslides
Jun 25 Talk at 3rd Tinnitus Research Initiative Meeting, Stresa, Italy
Title: Tinnitusbook: a proposal for an advanced scientific web community for tinnitus research - Scientific communities slidesslides
Apr 30 Talk at HCLS F2F Meeting, Cambridge, MA, USA
Title: Controlled vocabularies definition method for bridging formal ontologies development - HCLS slidesslides
Mar 10 Talk at Cambridge Semantic Web Gatherings, Cambridge, MA, USA
Title: SWAN Ontology 1.2

2008

Sep 3 Participant at the Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes workshop, Dallas, TX
May 6 Talk at European conference eHealth 2008, eHealth without frontiers, Portoroz, Slovenia
Title: Medicognos knowledge and software solutions for continuity of care

2007

May 26 Invited talk at the Italian Society for Amyloidosis National Meeting, Venice, Italy
Title: National Electronic Patient Record for Amyloidosis

2006

Nov 12 Talk at AMIA Annual Symposium, Washington DC
Title: A Framework for Temporal Data Processing and Abstractions
Nov 8 Participant at Biomedical Ontology in Action, Baltimore, MD
Jun 20 Invited talk at the Workshop for the European project PIPS, Cambridge, UK
Title: The Guide Project

2004

Sep 9 Talk at MEDINFO 2004, San Francisco, CA, USA
Title: A Guideline Management System
Sep 6 Talk at IDAMAP 2004, Stanford, Palo Alto, CA, USA
Title: GENIUS: A New Tool for Gene Networks Visualization

2003

Oct 19 Talk at AIME 2003, Protaras, Cyprus
Title: The NewGuide Project: Guidelines, Information Sharing and Learning from Exceptions.
Oct Participant at the Workshop on Medical Ontologies, Rome

Professional Activities

Jan 2014-Jun 2014 Semantic Web technologies and Linked Open Data consultant for Harvard Business School, Cambridge, MA. Leveraging Semantic Web technologies for improving library services.
Jan 2012-Mar 2012 Semantic Web technologies consultant for Fidelity Biosciences, Inc, Boston, MA. Leveraging Semantic Web technologies for building scientific portals.
Sep 2007-Dec 2009 Clinical Information Systems and Knowledge Management consultant for 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 communication between the different components is made possible by contracts and formal representation of clinical, medical, and patients knowledge. 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.
Jan 2003-Nov 2007 Information Technology and Knowledge Management consultant for Laboratory for Medical Informatics, University of Pavia, Italy.
Development of a production quality version of "The Guide Project" 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. The communication between the different components is regulated by a set of contracts and made possible through exchange of structured data. The need of semantically representing clinical data - back in 2001 when I completed the first draft of this architecture - motivated my initial interest for Semantic Web technologies.
Technologies: Clinical Workflow, Electronic Patient Records, Clinical Terminologies (ICD9, 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.
Sep 2006-Nov 2007 Information Technology consultant for Policlinico S. Matteo, research hospital in 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.

Mar 2005-Sep 2006 Knowledge Architect at Medicognos, SA Development of a knowledge based distributed Electronic Patient Record with workflow and Decision Support capabilities.
Mar 2005-Mar 2006 Clinical Information Systems and Knowledge Management consultant for Medilogix PgmbH, Belgium.
Analysis and design of the Medilogix innovative process-based electronic patient record. The platform allow health care professionals to efficiently perform their daily activities while keeping track, in a very formal way, of every step of the care process. The platform enables collaborative work through creation of networks for continuity of care. It also includes features for managing medical documentation and planning medical and organizational activities.
Technologies: UML, Poseidon for UML, Relational Databases, OpenEHR, and Database Design Studio.
2005 Founder at Medicognos, SA Development of a knowledge based distributed Electronic Patient Record with workflow and Decision Support capabilities.
2003 Software Developer consultant for 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, MySQL.
Nov 2001-Nov 2002 Information Technology consultant for 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.
2000 Software Developer consultant for the EUProject 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.

Last updated on: October 28, 2014