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OAC Workshop, March 24, 2011<br />History and Overview of AO (Annotation Ontology) <br />Paolo Ciccarese, PhD<br />email@example.com<br />Mass General Hospital<br />Harvard Medical School<br />
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 />
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 />
…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 />
…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 />
…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 />
…everybody tobenefit from the network effect <br />including ontologists, data miners …<br />
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 />
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 />
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 />
Annotating a document<br />AlzSWAN: http://tinyurl.com/18r<br />aof:annotatesDocumentsubPropertyOfann:annotates<br />
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 />
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 />
The topic can be an antibody (NIF Antibody registry)