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2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC




  Annotations in Biomedicine
&Ongoing Work of the W3C Open
 Annotation Community Group
               Paolo Ciccarese, PhD
                   paolo.ciccarese@gmail.com



                 Mass General Hospital         Harvard Medical School
Annotation in Biomedicine




                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
As (biomedical) scientists…
  • We deal with an increasing amount of digital
    resources:
    documents, images, videos, datasets, vocabul
    aries, databases, software…
       – About 150-200 articles a week
       – 10mins/article ≈ 34 hours/week
       – How can we manage it?



                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Limitations of the Web of Documents
  • Machines don’t do very well in *understanding*
    documents and have difficulties to
    find, present, access, or maintain available
    electronic information on the web
  • Need for a data representation to enable
    software products (agents) to provide access to
    heterogeneous and distributed information
       – Tasks often require to combine data on the Web
       – Humans combine these information easily** even
         ifdifferent terminologies are used and the information
         is incomplete, or buried in images and videos

                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
News and Hypotheses



  Semantic tagging


                                  APP




                                                                                       Biological Processes
                                                                   Experts
Pathways                        Videos/images       Antibodies
                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Document Metadata
                                  Exchange Organizer
  • Domeo is a web application for producing and
    sharing manual and semi-automatic
    (structured/unstructured) stand-off annotation
  • Domeo is designed as an open system
              Ciccarese et al, 2012
              Open semantic annotation of scientific publications using DOMEO
              http://www.jbiomedsem.com/content/3/S1/S1

              http://annotationframework.org
              https://twitter.com/DomeoTool

                         2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Semantic tagging through ontologies



         http://purl.obolibrary.org/obo/PR_000004168
         Label ‘amyloid beta A4 protein’
         Exact synonyms ‘APP’, ‘amyloidogenic glycoprotein’, …
         Related Synonyms ‘A4’, ‘ABPP’,

         Is a
         http://purl.obolibrary.org/obo/PR_000000001
         Label ‘protein’
         Definition ‘An amino acid chain that…’


                          2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
APPs for the Semantic Resources Project, May 2010
                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Reagents (reproducibility)




                                                  antibodyregistry.org


                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Annotation of Argumentation
                                          Semantic Web Applications in Neuromedicine
                                                    (SWAN) project [2007]




          classic publication

                                           scientific discourse ‘semantic’ representation



   http://tinyurl.com/cgyna2m
                           2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
graph representation




                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Annotation Sharing
                   Dynamic inventory of Web-based
                   neuroscience resources                      Video Annotation
                   http://www.neuinfo.org/                     Tools

                                                               Viz. ann. systems




                Drupal Framework for building
                online scientific communities
                http://sciencecollaboration.org/                          Analysis




                            2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Annotation Ontology (AO)
  • OWL vocabulary for representing and sharing
    annotation of digital resources and their
    fragments in RDF format
  • Focus on biomedicine and sciences. But desire
    to make the AO framework more broadly
    usable.

            Ciccarese et al, 2011
            An open annotation ontology for science on web 3.0
            http://www.jbiomedsem.com/content/2/S2/S4


                         2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Annotation Ontology Network

                                                           Biotea




                                                      Annotations
                                                      at Harvard




  The Living Document
         Project

                        2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Open Annotation Collaboration
  • Focus on interoperability for annotations in
    order to allow sharing of annotations across:
       – Annotation clients;
       – Content collections;
       – Services that leverage annotations.
  • Focus on annotation for scholarly purposes.
    But desire to make the OAC framework more
    broadly usable.
     http://openannotation.org/
                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
AO+OAC = W3C Open Annotation
  • Annotation Ontology and Open Annotation
    Collaboration have been merged to create the
    W3C Open Annotation Community Group
  • Officially started in February 2012




                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD                              Take Note Site Visit, November 1st 2012
W3C Open Annotation
                        Community Group
  • Is working towards a common, RDF-based,
    specification for annotating digital resources:
       – Aligned with WWW Architecture & Linked Open
         Data best practices
       – Focus on interoperability – the sharing of
         annotations across clients, servers, repositories
         and applications
       – Annotations are treated as first class Web
         resources, i.e., referenceable and available to
         themselves be annotated

                         2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
http://www.w3.org/community/openannotation/




                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Participants




   54 Participants
   From more than 30 institutions
   Additional users interact through the mailing list




                         2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Public Mailing List




                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Specifications (Drafts)




                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Plans for Open Annotation 1.0 Release
  • Currently working on a new draft and a new
    tutorial that will be published in mid January
    for collecting further feedback
  • We are planning a release of Open Annotation
    Model v. 1.0 for March/April
  • They will have a new structure that we believe
    will help lowering the learning and
    implementation curves

                       2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD
Acknowledgements
  • Tim Clark, Director of MIND Informatics
  • Domeo Support: Maryann Martone, Anita
    Bandrowski, VadimAstakhov, Anita de
    Waard, Bradley Allen, Keith Gutfreund
  • W3C Community Group: Robert
    Sanderson, Herbert van de Sompel and all the
    members
  • Funding: National Institutes of Health, Elsevier
    Laboratories, and Eli Lilly & Co.
                        2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

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2012 CNI Fall Membership Meeting

  • 1. 2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC Annotations in Biomedicine &Ongoing Work of the W3C Open Annotation Community Group Paolo Ciccarese, PhD paolo.ciccarese@gmail.com Mass General Hospital Harvard Medical School
  • 2. Annotation in Biomedicine 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 3. As (biomedical) scientists… • We deal with an increasing amount of digital resources: documents, images, videos, datasets, vocabul aries, databases, software… – About 150-200 articles a week – 10mins/article ≈ 34 hours/week – How can we manage it? 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 4. Limitations of the Web of Documents • Machines don’t do very well in *understanding* documents and have difficulties to find, present, access, or maintain available electronic information on the web • Need for a data representation to enable software products (agents) to provide access to heterogeneous and distributed information – Tasks often require to combine data on the Web – Humans combine these information easily** even ifdifferent terminologies are used and the information is incomplete, or buried in images and videos 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 5. News and Hypotheses Semantic tagging APP Biological Processes Experts Pathways Videos/images Antibodies 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 6. Document Metadata Exchange Organizer • Domeo is a web application for producing and sharing manual and semi-automatic (structured/unstructured) stand-off annotation • Domeo is designed as an open system Ciccarese et al, 2012 Open semantic annotation of scientific publications using DOMEO http://www.jbiomedsem.com/content/3/S1/S1 http://annotationframework.org https://twitter.com/DomeoTool 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 7. Semantic tagging through ontologies http://purl.obolibrary.org/obo/PR_000004168 Label ‘amyloid beta A4 protein’ Exact synonyms ‘APP’, ‘amyloidogenic glycoprotein’, … Related Synonyms ‘A4’, ‘ABPP’, Is a http://purl.obolibrary.org/obo/PR_000000001 Label ‘protein’ Definition ‘An amino acid chain that…’ 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 8. APPs for the Semantic Resources Project, May 2010 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 9. Reagents (reproducibility) antibodyregistry.org 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 10. Annotation of Argumentation Semantic Web Applications in Neuromedicine (SWAN) project [2007] classic publication scientific discourse ‘semantic’ representation http://tinyurl.com/cgyna2m 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 11. graph representation 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 12. Annotation Sharing Dynamic inventory of Web-based neuroscience resources Video Annotation http://www.neuinfo.org/ Tools Viz. ann. systems Drupal Framework for building online scientific communities http://sciencecollaboration.org/ Analysis 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 13. Annotation Ontology (AO) • OWL vocabulary for representing and sharing annotation of digital resources and their fragments in RDF format • Focus on biomedicine and sciences. But desire to make the AO framework more broadly usable. Ciccarese et al, 2011 An open annotation ontology for science on web 3.0 http://www.jbiomedsem.com/content/2/S2/S4 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 14. Annotation Ontology Network Biotea Annotations at Harvard The Living Document Project 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 15. Open Annotation Collaboration • Focus on interoperability for annotations in order to allow sharing of annotations across: – Annotation clients; – Content collections; – Services that leverage annotations. • Focus on annotation for scholarly purposes. But desire to make the OAC framework more broadly usable. http://openannotation.org/ 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 16. AO+OAC = W3C Open Annotation • Annotation Ontology and Open Annotation Collaboration have been merged to create the W3C Open Annotation Community Group • Officially started in February 2012 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD Take Note Site Visit, November 1st 2012
  • 17. W3C Open Annotation Community Group • Is working towards a common, RDF-based, specification for annotating digital resources: – Aligned with WWW Architecture & Linked Open Data best practices – Focus on interoperability – the sharing of annotations across clients, servers, repositories and applications – Annotations are treated as first class Web resources, i.e., referenceable and available to themselves be annotated 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 18. http://www.w3.org/community/openannotation/ 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 19. Participants 54 Participants From more than 30 institutions Additional users interact through the mailing list 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 20. Public Mailing List 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 21. Specifications (Drafts) 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 22. Plans for Open Annotation 1.0 Release • Currently working on a new draft and a new tutorial that will be published in mid January for collecting further feedback • We are planning a release of Open Annotation Model v. 1.0 for March/April • They will have a new structure that we believe will help lowering the learning and implementation curves 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD
  • 23. Acknowledgements • Tim Clark, Director of MIND Informatics • Domeo Support: Maryann Martone, Anita Bandrowski, VadimAstakhov, Anita de Waard, Bradley Allen, Keith Gutfreund • W3C Community Group: Robert Sanderson, Herbert van de Sompel and all the members • Funding: National Institutes of Health, Elsevier Laboratories, and Eli Lilly & Co. 2012 CNI Fall Membership Meeting Paolo Ciccarese, PhD