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

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