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Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group
Paolo Ciccarese, PhD
Mass General Hospital Harvard Medical School
2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC
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Annotation in Biomedicine
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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As (biomedical) scientists…
• We deal with an increasing amount of digital resources: documents, images, videos, datasets, vocabularies, databases, software…– About 150-200 articles a week– 10mins/article ≈ 34 hours/week– How can we manage it?
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Limitations of the Web of Documents
• Machines don’t do very well in *understanding* documents and have difficulties to find, present, access, or maintain available electronic information on the web
• Need for a data representation to enable software products (agents) to provide access to heterogeneous and distributed information– Tasks often require to combine data on the Web– Humans combine these information easily** even if different
terminologies are used and the information is incomplete, or buried in images and videos
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Semantic tagging
APP
News and Hypotheses
Biol
ogic
al P
roce
sses
Videos/imagesPathways Expe
rts
Antibodies 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Document Metadata Exchange Organizer
• Domeo is a web application for producing and sharing manual and semi-automatic (structured/unstructured) stand-off annotation
• Domeo is designed as an open system
Ciccarese et al, 2012Open semantic annotation of scientific publications using DOMEO http://www.jbiomedsem.com/content/3/S1/S1
http://annotationframework.org
https://twitter.com/DomeoTool
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Semantic tagging through ontologies
http://purl.obolibrary.org/obo/PR_000004168Label ‘amyloid beta A4 protein’Exact synonyms ‘APP’, ‘amyloidogenic glycoprotein’, …Related Synonyms ‘A4’, ‘ABPP’,
Is a http://purl.obolibrary.org/obo/PR_000000001Label ‘protein’Definition ‘An amino acid chain that…’
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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APPs
for t
he S
eman
tic R
esou
rces
Pro
ject
, May
201
0
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Reagents (reproducibility)
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
antibodyregistry.org
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Annotation of Argumentation
classic publication
scientific discourse ‘semantic’ representation
http://tinyurl.com/cgyna2m
Semantic Web Applications in Neuromedicine (SWAN) project [2007]
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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graph representation
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Drupal Framework for building online scientific communitieshttp://sciencecollaboration.org/
Dynamic inventory of Web-based neuroscience resourceshttp://www.neuinfo.org/
Viz. ann. systems
Analysis
Annotation Sharing
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Video AnnotationTools
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Annotation Ontology (AO)
• OWL vocabulary for representing and sharing annotation of digital resources and their fragments in RDF format
• Focus on biomedicine and sciences. But desire to make the AO framework more broadly usable.
Ciccarese et al, 2011An open annotation ontology for science on web 3.0http://www.jbiomedsem.com/content/2/S2/S4
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Annotation Ontology Network
The Living DocumentProject
Biotea
Annotations at Harvard
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Open Annotation Collaboration
• Focus on interoperability for annotations in order to allow sharing of annotations across:– Annotation clients;– Content collections;– Services that leverage annotations.
• Focus on annotation for scholarly purposes. But desire to make the OAC framework more broadly usable.
http://openannotation.org/ 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Take Note Site Visit, November 1st 2012
AO+OAC = W3C Open Annotation
• Annotation Ontology and Open Annotation Collaboration have been merged to create the W3C Open Annotation Community Group
• Officially started in February 2012
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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W3C Open Annotation Community Group
• Is working towards a common, RDF-based, specification for annotating digital resources:– Aligned with WWW Architecture & Linked Open Data
best practices– Focus on interoperability – the sharing of
annotations across clients, servers, repositories and applications
– Annotations are treated as first class Web resources, i.e., referenceable and available to themselves be annotated
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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http://www.w3.org/community/openannotation/
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Participants
54 ParticipantsFrom more than 30 institutionsAdditional users interact through the mailing list
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Public Mailing List
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Specifications (Drafts)
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Plans for Open Annotation 1.0 Release
• Currently working on a new draft and a new tutorial that will be published in mid January for collecting further feedback
• We are planning a release of Open Annotation Model v. 1.0 for March/April
• They will have a new structure that we believe will help lowering the learning and implementation curves
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
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Acknowledgements
• Tim Clark, Director of MIND Informatics• Domeo Support: Maryann Martone, Anita
Bandrowski, Vadim Astakhov, Anita de Waard, Bradley Allen, Keith Gutfreund
• W3C Community Group: Robert Sanderson, Herbert van de Sompel and all the members
• Funding: National Institutes of Health, Elsevier Laboratories, and Eli Lilly & Co.
2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD