Your SlideShare is downloading. ×
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
AO: Annotation Ontology for science on the web
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

AO: Annotation Ontology for science on the web

7,160

Published on

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

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

Published in: Technology, Education
1 Comment
5 Likes
Statistics
Notes
No Downloads
Views
Total Views
7,160
On Slideshare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
0
Comments
1
Likes
5
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide
  • After having clear the list of all our application requirements the first thing I’ve done is investigating for existing ontologies that were covering the same topic or similar topics. The best contribution I’ve found has been an old project called Annotea.
  • Transcript

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

    ×