Presentation for the Open Annotation Collaboration workshop, Chicago, March 24, 2011

1. OAC Workshop, March 24, 2011 History and Overview of AO (Annotation Ontology) Paolo Ciccarese, PhD paolo.ciccarese@gmail.com Mass General Hospital Harvard Medical School

2. MIND Informatics Group Focusing on online scientific communities: AlzSWAN(http://hypothesis.alzforum.org/) StemBook.org(http://www.stembook.org/) PDOnline(http://www.pdonlineresearch.org/) SCF Genomic Experiments Repository (http://bloodprogram.hsci.harvard.edu/) Neuropathic Pain Forum (with Harvard NeuroDiscovery Center) We work with pharmaceutical companies, publishers and NIH funded projects. We are heavily involved with W3C HCLS. Director Tim Clark.

3. AlzSWAN (SWAN for Alzheimer’s Disease) http://hypothesis.alzforum.org/ + Online since beginning 2008 + Approx. 2400 manually curated statements about Alzheimer Disease + Linked to approx. 2550 publications -Not fully document centric and missing the link to the original document fragments

4. Our current goal is to enable…

5. …individual scientists to visually and effectively annotate (better semantically annotate) any digital resource and resource fragment, while performing their regular activities decide to keep the annotation private or share it with colleagues, groups, communities or the web run text mining and entities recognition algorithms on scientific documents and benefit from crowdsourcing their curation efficiently search and reuse the annotation retrieve additional content (mashups)

6. …scientific communities curators to annotate scientific publications and resources publish such annotation to their members and trigger valuable discussions and feedback use such annotation to link their internal content or external resources (mashups) embed the stand off annotation in the actual document as part of the content (publication process) benefit from annotation produced by related and trusted communities

7. …text mining providers to provide the results to users in a standardized way, displaying them on top of the documents collect feedback from users that can provide judgment on the accuracy of such results use the feedback to improve their services

8. …everybody tobenefit from the network effect including ontologists, data miners …

9. Our recipe AO (Annotation Ontology) SWAN Framework SWAN Annotation Tool (which integrates with PubMed, BioPortal, AntibodyRegistry, AlzSWAN, UIMA, TextPresso, SIOC, CiTO/FaBiO, ORB and other W3C HCLS efforts…) Semantic Search Bibliographic Management Hypothesis Management … http://purl.org/ao/home

10. Annotation Ontology (AO) OWL vocabulary for representing and sharing annotation of digital resources and their fragments First version on May 2009, current on May 2010 Who already uses AO The Living Document Project Tags4Lab Project

11. Some AO Design Principles Traceability: completeness of the information about every step of the annotation process Orthogonality: designed to leverage existing domain ontologies, the way they are Extensibility: designed with extension points because nothing is complete, ever Full list: http://tinyurl.com/6j8yuz2 http://tinyurl.com/6j8yuz2

13. Annotating a document AlzSWAN: http://tinyurl.com/18r aof:annotatesDocumentsubPropertyOfann:annotates

14. Annotating a document fragment [1]

15. Annotating a document fragment [2] Protein Ontology – PRO: http://purl.org/obo/owl/PRO

16. Annotating a Claim [1]

17. Annotating a Claim [2] Icons by: Everaldo Coelho and Agapeh

18. SWAN Ontology 2.0: http://code.google.com/p/swan-ontology/

19. Claim into triples (nanopublications) <http://example.info/alzswan:statement_f3556dcfc331d9b9af9d5c0cfc570ba6_event_1> Event of type GO "chaperone binding" rdfs:label rdf:type <http://bio2rdf.org/go:0051087> <prefix:actor_1> <http://bio2rdf.org/chebi:53002> rdf:type rdfs:label “Beta amyloid” <prefix:target_1> <http://bio2rdf.org/mesh:D008565> rdf:type rdfs:label “Membrane protein” <http://bio2rdf.org/go:0005886> <prefix:location_1> rdf:type rdfs:label “Plasma membrane” G8 From: http://www.slideshare.net/paolociccarese/alzswan-hyque-and-nanopublications Triples provided by Nigam Shah

20. Integrating with the ecosystem

21. It might look complicated but… you can do all this and more, visually and with minimum effort, with the SWAN Annotation Tool a customizable and extensible web application… not only for biomedicine Image source: http://tinyurl.com/4lk7ynw

22. Bibliography Management See screencast: http://vimeo.com/20438490

23. Annotation Provenance See screencast: http://vimeo.com/20438490

24. Semantic Tags or Qualifiers [1]

25. Semantic Tags or Qualifiers [2]

26. Semantic Tags or Qualifiers [2]

27. Semantic Tags or Qualifiers [2]

28. Antibodies Annotation [1] See screencast: http://vimeo.com/20438490

29. Antibodies Annotation [2] See screencast: http://vimeo.com/20438490 AntibodyRegistry.org search

30. Text Mining Results Curation [1]

31. Text Mining Results Curation [2]

32. Additional resources on the SWAN Annotation Tool NIF Webinar recording (full demo March 15, 2011) http://nif.adobeconnect.com/p19866142/ Slides on Text Mining Results curation http://tinyurl.com/23eavtw Screencasts about integration with Utopia http://tinyurl.com/46mwg4k http://tinyurl.com/4owy348 Screencast of new features in build 7 http://vimeo.com/20438490