Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group

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 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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

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 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

5. News and Hypotheses Semantic tagging APP Biological Processes Experts Pathways Videos/images Antibodies Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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 https://twitter.com/DomeoTool • Ciccarese et al, 2012 • Open semantic annotation of scientific publications using DOMEO http://www.jbiomedsem.com/content/3/S1/S1 http://annotationframework.org Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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…’ Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

8. APPs for the Semantic Resources Project, May 2010 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

9. Reagents (reproducibility) antibodyregistry.org Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

10. Annotation of Argumentation Semantic Web Applications in Neuromedicine (SWAN) project [2007] classic publication scientific discourse ‘semantic’ representation http://tinyurl.com/cgyna2m Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

11. graph representation Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

12. Annotation Sharing Dynamic inventory of Web-based neuroscience resources http://www.neuinfo.org/ Video Annotation Tools Viz. ann. systems Drupal Framework for building online scientific communitieshttp://sciencecollaboration.org/ Analysis Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

14. Annotation Ontology Network Biotea Annotations at Harvard The Living Document Project Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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/ Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting 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 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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

19. Participants 54 Participants From more than 30 institutions Additional users interact through the mailing list Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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

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

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 Paolo Ciccarese, PhD 2012 CNI Fall Membership Meeting

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