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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 />email@example.com<br />http://code.google.com/p/annotation-ontology/<br />
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 />
Annotation Framework Brief Demo<br />Annotation Ontology at work<br />
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 />
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 />
… 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 />
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 />
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 />
Example with Text Selector<br />http://code.google.com/p/annotation-ontology/wiki/Qualifiers<br />
Example with Image Selector<br />http://code.google.com/p/annotation-ontology/wiki/Qualifiers<br />
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 />
Example of Note<br />http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes<br />
Example of Qualifiers usage<br />http://code.google.com/p/annotation-ontology/wiki/SKOS<br />
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 />
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 />
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 />
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 />
Annotation Perspective or Document Annotation 2<br />
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 />
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.