AO and Annotation Tool for AOC

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Presentation for the Open Annotation Collaboration workshop, Chicago, March 24, 2011

Presentation for the Open Annotation Collaboration workshop, Chicago, March 24, 2011

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  • The topic can be an antibody (NIF Antibody registry)


  • 1. OAC Workshop, March 24, 2011
    History and Overview of AO (Annotation Ontology)
    Paolo Ciccarese, PhD
    Mass General Hospital
    Harvard Medical School
  • 2. MIND Informatics Group
    Focusing on online scientific communities:
    SCF Genomic Experiments Repository
    Neuropathic Pain Forum
    (with Harvard NeuroDiscovery Center)
    We work with pharmaceutical companies, publishers and NIH funded projects. We are heavily involved with W3C HCLS. Director Tim Clark.
  • 3. AlzSWAN (SWAN for Alzheimer’s Disease)
    + Online since beginning 2008
    + Approx. 2400 manually curated statements about Alzheimer Disease
    + Linked to approx. 2550 publications
    -Not fully document centric and missing the link to the original document fragments
  • 4. Our current goal is to enable…
  • 5. …individual scientists to
    visually and effectively annotate (better semantically annotate) any digital resource and resource fragment, while performing their regular activities
    decide to keep the annotation private or share it with colleagues, groups, communities or the web
    run text mining and entities recognition algorithms on scientific documents and benefit from crowdsourcing their curation
    efficiently search and reuse the annotation
    retrieve additional content (mashups)
  • 6. …scientific communities curators to
    annotate scientific publications and resources
    publish such annotation to their members and trigger valuable discussions and feedback
    use such annotation to link their internal content or external resources (mashups)
    embed the stand off annotation in the actual document as part of the content (publication process)
    benefit from annotation produced by related and trusted communities
  • 7. …text mining providers to
    provide the results to users in a standardized way, displaying them on top of the documents
    collect feedback from users that can provide judgment on the accuracy of such results
    use the feedback to improve their services
  • 8. …everybody tobenefit from the network effect
    including ontologists, data miners …
  • 9. Our recipe
    AO (Annotation Ontology)
    SWAN Framework
    SWAN Annotation Tool (which integrates with PubMed, BioPortal, AntibodyRegistry, AlzSWAN, UIMA, TextPresso, SIOC, CiTO/FaBiO, ORB and other W3C HCLS efforts…)
    Semantic Search
    Bibliographic Management
    Hypothesis Management
  • 10. Annotation Ontology (AO)
    OWL  vocabulary for representing and sharing annotation of digital resources and their fragments
    First version on May 2009, current on May 2010
    Who already
    uses AO
    The Living Document
    Tags4Lab Project
  • 11. Some AO Design Principles
    Traceability: completeness of the information about every step of the annotation process
    Orthogonality: designed to leverage existing domain ontologies, the way they are
    Extensibility: designed with extension points because nothing is complete, ever
    Full list:
  • 12. A simplified view of AO
    • AO annotates:
    Resources: documents (HTML, PDF, Word, Excel), Images,
    Databases, Web Services... (and their fragments)
    • With (or without) a:
    Topic: free text, structured text, URIs, RDF entities,
    RDF graphs, domain ontologies…
    • Tracing:
    Provenance: who created what, when, with what
    software, with what expectations…
  • 13. Annotating a document
  • 14. Annotating a document fragment [1]
  • 15. Annotating a document fragment [2]
    Protein Ontology – PRO:
  • 16. Annotating a Claim [1]
  • 17. Annotating a Claim [2]
    Icons by: Everaldo Coelho and Agapeh
  • 18. SWAN Ontology 2.0:
  • 19. Claim into triples (nanopublications)
    Event of type GO "chaperone binding"
    rdfs:label “Beta amyloid”
    rdfs:label “Membrane protein”
    rdfs:label “Plasma membrane”
    Triples provided by Nigam Shah
  • 20. Integrating with the ecosystem
  • 21. It might look complicated but…
    you can do all this and more, visually and with minimum effort, with the
    SWAN Annotation Tool
    a customizable and extensible web application… not only for biomedicine
    Image source:
  • 22. Bibliography Management
    See screencast:
  • 23. Annotation Provenance
    See screencast:
  • 24. Semantic Tags or Qualifiers [1]
  • 25. Semantic Tags or Qualifiers [2]
  • 26. Semantic Tags or Qualifiers [2]
  • 27. Semantic Tags or Qualifiers [2]
  • 28. Antibodies Annotation [1]
    See screencast:
  • 29. Antibodies Annotation [2]
    See screencast: search
  • 30. Text Mining Results Curation [1]
  • 31. Text Mining Results Curation [2]
  • 32. Additional resources on the SWAN Annotation Tool
    NIF Webinar recording (full demo March 15, 2011)
    Slides on Text Mining Results curation
    Screencasts about integration with Utopia
    Screencast of new features in build 7