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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)
  • Transcript

    • 1. OAC Workshop, March 24, 2011
      History and Overview of AO (Annotation Ontology)
      Paolo Ciccarese, PhD
      paolo.ciccarese@gmail.com
      Mass General Hospital
      Harvard Medical School
    • 2. MIND Informatics Group
      Focusing on online scientific communities:
      AlzSWAN(http://hypothesis.alzforum.org/)
      StemBook.org(http://www.stembook.org/)
      PDOnline(http://www.pdonlineresearch.org/)
      SCF Genomic Experiments Repository
      (http://bloodprogram.hsci.harvard.edu/)
      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)
      http://hypothesis.alzforum.org/
      + 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

      http://purl.org/ao/home
    • 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
      Project
      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: http://tinyurl.com/6j8yuz2
      http://tinyurl.com/6j8yuz2
    • 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
      AlzSWAN: http://tinyurl.com/18r
      aof:annotatesDocumentsubPropertyOfann:annotates
    • 14. Annotating a document fragment [1]
    • 15. Annotating a document fragment [2]
      Protein Ontology – PRO: http://purl.org/obo/owl/PRO
    • 16. Annotating a Claim [1]
    • 17. Annotating a Claim [2]
      Icons by: Everaldo Coelho and Agapeh
    • 18. SWAN Ontology 2.0: http://code.google.com/p/swan-ontology/
    • 19. Claim into triples (nanopublications)
      <http://example.info/alzswan:statement_f3556dcfc331d9b9af9d5c0cfc570ba6_event_1>
      Event of type GO "chaperone binding"
      rdfs:label
      rdf:type
      <http://bio2rdf.org/go:0051087>
      <prefix:actor_1>
      <http://bio2rdf.org/chebi:53002>
      rdf:type
      rdfs:label “Beta amyloid”
      <prefix:target_1>
      <http://bio2rdf.org/mesh:D008565>
      rdf:type
      rdfs:label “Membrane protein”
      <http://bio2rdf.org/go:0005886>
      <prefix:location_1>
      rdf:type
      rdfs:label “Plasma membrane”
      G8
      From: http://www.slideshare.net/paolociccarese/alzswan-hyque-and-nanopublications
      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: http://tinyurl.com/4lk7ynw
    • 22. Bibliography Management
      See screencast: http://vimeo.com/20438490
    • 23. Annotation Provenance
      See screencast: http://vimeo.com/20438490
    • 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: http://vimeo.com/20438490
    • 29. Antibodies Annotation [2]
      See screencast: http://vimeo.com/20438490
      AntibodyRegistry.org 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)
      http://nif.adobeconnect.com/p19866142/
      Slides on Text Mining Results curation
      http://tinyurl.com/23eavtw
      Screencasts about integration with Utopia
      http://tinyurl.com/46mwg4k
      http://tinyurl.com/4owy348
      Screencast of new features in build 7
      http://vimeo.com/20438490