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

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

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

4.
Our current goal is to enable…<br />

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

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

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

8.
…everybody tobenefit from the network effect <br />including ontologists, data miners …<br />

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

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

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

12.
A simplified view of AO<br /><ul><li>AO annotates:</li></ul>Resources: documents (HTML, PDF, Word, Excel), Images, <br /> Databases, Web Services... (and their fragments)<br /><ul><li>With (or without) a:</li></ul>Topic: free text, structured text, URIs, RDF entities, <br /> RDF graphs, domain ontologies…<br /><ul><li>Tracing:</li></ul>Provenance: who created what, when, with what<br /> software, with what expectations… <br />

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

14.
Annotating a document fragment [1]<br />

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

16.
Annotating a Claim [1]<br />

17.
Annotating a Claim [2]<br />Icons by: Everaldo Coelho and Agapeh<br />

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

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

20.
Integrating with the ecosystem<br />

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

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

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

24.
Semantic Tags or Qualifiers [1]<br />

25.
Semantic Tags or Qualifiers [2]<br />

26.
Semantic Tags or Qualifiers [2]<br />

27.
Semantic Tags or Qualifiers [2]<br />

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

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

30.
Text Mining Results Curation [1]<br />

31.
Text Mining Results Curation [2]<br />

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