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AO: Annotation Ontology for science on the web

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AO: an open Annotation Ontology for science on the web, Bio Ontologies 2010, July 9, 2010

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AO: Annotation Ontology for science on the web

  1. 1. AO: an open Annotation Ontology for science on the web<br />Bio-Ontologies 2010: Semantic Applications in Life Sciences<br />Paolo Ciccarese, PhD<br />July 9, 2010<br />Mass General Hospital<br />Harvard Medical School<br />paolo.ciccarese@gmail.com<br />http://code.google.com/p/annotation-ontology/<br />
  2. 2. Background <br />Collaboration with a major pharma (hypothesis management for drug discovery) <br />Capitalizes the experience we accumulated with the SWAN project (hypothesis based representation of scientific discourse)<br />Is meant to serve scientific online communities such as <br />PDOnline http://www.pdonlineresearch.org<br />StemBook http://www.stembook.org<br />Science Collaboration Framework 2.0<br />
  3. 3. Annotation Framework Brief Demo<br />Annotation Ontology at work<br />
  4. 4. Annotation Ontology Features 1<br />Annotate any document on the web (text, images, audio, video, …) and their parts<br />Perform different kind of annotations: notes, semantic tags, errata, examples, hypotheses, citations…<br />Use existing domain ontologies (AO is a catalyst for the Semantic Web world)<br />Allow creation of manual annotation and integration of text mining results<br />
  5. 5. Annotation Ontology Features 2<br />Persist the annotation<br />Allow multiple annotation perspectives on the document at the same time<br />Allow curation of manual and automatic annotation<br />Allow organizing the annotation in various ways for improving the authoring and the publication process<br />
  6. 6. Starting from Annotea…<br />1<br />1<br />annotates<br />context (XPointer)<br />2<br />2<br />3<br />body<br />3<br />4<br />4<br />hasTopic<br />recalls<br />5<br />http://www.w3.org/2001/Annotea/<br />5<br />6<br />description<br />6<br />
  7. 7. … here comes AO<br />Annotation and Bookmark are combined in the same model<br />the context can be still defined through pure XPointer but we provide a consistent mechanism for referring to parts of text, images, audio files, video files... <br />it is possible to create annotation types not only by sub-classing but also by composition<br />we provide mechanisms for managing annotation curation <br />we provide mechanisms for managing collections of annotation items<br />we provide mechanisms for managing annotation publishing <br />http://code.google.com/p/annotation-ontology/wiki/Background<br />
  8. 8. Before looking into the details<br />AO is reusing the following ontologies:<br />Annotea/Bookmarks<br />PAV (Provenance, Authoring and Versioning) or DC (Dublin Core)/DCT (Dublin Core Terms)<br />FOAF (Friend Of A Friend)<br />And integrating with the following ontologies:<br />SKOS (Simple Knowledge Organization System)<br />SIOC (Semantically-Interlinked Online Communities)<br />Tag Ontology<br />MOAT (Meaning Of A Tag)<br />SWAN (Semantic Web Applications in Neuromedicine)<br />CiTO coming soon<br />
  9. 9. Annotation Example<br />http://code.google.com/p/annotation-ontology/wiki/Annotation<br />
  10. 10. Annotation of a document<br />http://code.google.com/p/annotation-ontology/wiki/Annotation<br />
  11. 11. Document Provenance<br />http://code.google.com/p/annotation-ontology/wiki/SourceDocument<br />
  12. 12. Annotation Provenance<br />http://code.google.com/p/annotation-ontology/wiki/Annotation<br />
  13. 13. Annotation Type<br />http://code.google.com/p/annotation-ontology/wiki/Annotation<br />
  14. 14. Context and Selectors<br />In AO we can still use XPointer as Annotea was doing <br />But Selectors are the real AO way to define the context within a document (text, image, audio, video…)<br />Multiple kinds of selectors can be defined for each kind of document<br />http://code.google.com/p/annotation-ontology/wiki/Selectors<br />
  15. 15. Example with Text Selector<br />http://code.google.com/p/annotation-ontology/wiki/Qualifiers<br />
  16. 16. Example with Image Selector<br />http://code.google.com/p/annotation-ontology/wiki/Qualifiers<br />
  17. 17. Annotation Types<br />As it was happening in Annotea, in AO the Annotation can be sub-classed in more specific annotation types: <br />Comment<br />Erratum<br />Question<br />Explanation<br />Definition<br />Note<br />Qualifier:<br />ExactQualifier<br />BroadQualifier<br />NarrowQualifier<br />CloseQualifier<br />http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes<br />Parallel to SKOS<br />
  18. 18. Example of Note<br />http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes<br />
  19. 19. Example of Qualifiers usage<br />http://code.google.com/p/annotation-ontology/wiki/SKOS<br />
  20. 20. We could infer that<br />BroadQualifier for<br />BACE1<br />BIRNLex:Protein<br />PRO:BetaSecretase 1<br />BACE1<br />ExactQualifier for<br />BIRNLex:Protein<br />skos:broadMatch<br />PRO:BetaSecretase 1<br />Also: BACE1 possible synonym for ‘Beta-Secretase 1’<br />
  21. 21. Annotation by Composition<br />Annotation types can be sub-classed or created by composition (like multiple inheritance). SWAN Example:<br />http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes<br />http://hypothesis.alzforum.org/<br />HP:Human Phenotype Ontology <br />
  22. 22. Annotation Curation<br />http://code.google.com/p/annotation-ontology/wiki/Curation<br />
  23. 23. Annotation Curation Tokens<br />http://code.google.com/p/annotation-ontology/wiki/Curation<br />
  24. 24. Annotation Sets 1<br />Are grouping annotation items<br />Can be useful for grouping annotation items with the same provenance (for example the annotation produced by text mining services)<br />Can be useful for grouping annotation items with the same topic (for example the annotation regarding life science entities)<br />Allow to define access restrictions for the grouped annotation<br />http://code.google.com/p/annotation-ontology/wiki/AnnotationSet<br />
  25. 25. Annotation Sets 2<br />
  26. 26. Annotation Perspective or Document Annotation 1<br />Is a collections of annotation sets – within all those available - that have been combined for a specific purpose – usually for publication - by a particular user/group/content provider<br />Multiple ‘Document Annotation’ instances can be defined for the same document by the same of different publishers<br />
  27. 27. Annotation Perspective or Document Annotation 2<br />
  28. 28. Acknowledgements<br />Tim Clark, Marco Ocana, Sudeshna Das<br />LeylaJaelGarcía Castro (E-Business & Web Science Research Group, UniversitätderBundeswehr) and Alexander García Castro (Computational Linguistics Department, University of Bremen) for additional use cases<br />Jonathan Rees (Science Commons) and Eric Prud'hommeaux (W3C) for fruitful discussions<br />Anita de Waard (Elsevier) for the support<br />

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