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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

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  • 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.

AO: Annotation Ontology for science on the web AO: Annotation Ontology for science on the web Presentation Transcript

  • 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/
  • 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
  • Annotation Framework Brief Demo
    Annotation Ontology at work
  • 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
  • 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
  • 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
  • … 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
  • 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
  • Annotation Example
    http://code.google.com/p/annotation-ontology/wiki/Annotation
  • Annotation of a document
    http://code.google.com/p/annotation-ontology/wiki/Annotation
  • Document Provenance
    http://code.google.com/p/annotation-ontology/wiki/SourceDocument
  • Annotation Provenance
    http://code.google.com/p/annotation-ontology/wiki/Annotation
  • Annotation Type
    http://code.google.com/p/annotation-ontology/wiki/Annotation
  • 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
  • Example with Text Selector
    http://code.google.com/p/annotation-ontology/wiki/Qualifiers
  • Example with Image Selector
    http://code.google.com/p/annotation-ontology/wiki/Qualifiers
  • 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
  • Example of Note
    http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes
  • Example of Qualifiers usage
    http://code.google.com/p/annotation-ontology/wiki/SKOS
  • 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’
  • 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
  • Annotation Curation
    http://code.google.com/p/annotation-ontology/wiki/Curation
  • Annotation Curation Tokens
    http://code.google.com/p/annotation-ontology/wiki/Curation
  • 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
  • Annotation Sets 2
  • 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
  • Annotation Perspective or Document Annotation 2
  • 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