1. 2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC
Annotations in Biomedicine
&Ongoing Work of the W3C Open
Annotation Community Group
Paolo Ciccarese, PhD
paolo.ciccarese@gmail.com
Mass General Hospital Harvard Medical School

2. Annotation in Biomedicine
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

3. As (biomedical) scientists…
• We deal with an increasing amount of digital
resources:
documents, images, videos, datasets, vocabul
aries, databases, software…
– About 150-200 articles a week
– 10mins/article ≈ 34 hours/week
– How can we manage it?
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

4. 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
ifdifferent terminologies are used and the information
is incomplete, or buried in images and videos
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

5. News and Hypotheses
Semantic tagging
APP
Biological Processes
Experts
Pathways Videos/images Antibodies
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

6. 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, 2012
Open 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 Meeting
Paolo Ciccarese, PhD

7. Semantic tagging through ontologies
http://purl.obolibrary.org/obo/PR_000004168
Label ‘amyloid beta A4 protein’
Exact synonyms ‘APP’, ‘amyloidogenic glycoprotein’, …
Related Synonyms ‘A4’, ‘ABPP’,
Is a
http://purl.obolibrary.org/obo/PR_000000001
Label ‘protein’
Definition ‘An amino acid chain that…’
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

8. APPs for the Semantic Resources Project, May 2010
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

9. Reagents (reproducibility)
antibodyregistry.org
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

10. Annotation of Argumentation
Semantic Web Applications in Neuromedicine
(SWAN) project [2007]
classic publication
scientific discourse ‘semantic’ representation
http://tinyurl.com/cgyna2m
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

11. graph representation
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

12. Annotation Sharing
Dynamic inventory of Web-based
neuroscience resources Video Annotation
http://www.neuinfo.org/ Tools
Viz. ann. systems
Drupal Framework for building
online scientific communities
http://sciencecollaboration.org/ Analysis
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

13. 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, 2011
An open annotation ontology for science on web 3.0
http://www.jbiomedsem.com/content/2/S2/S4
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

14. Annotation Ontology Network
Biotea
Annotations
at Harvard
The Living Document
Project
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

15. 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 Meeting
Paolo Ciccarese, PhD

16. 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 Meeting
Paolo Ciccarese, PhD Take Note Site Visit, November 1st 2012

17. 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 Meeting
Paolo Ciccarese, PhD

18. http://www.w3.org/community/openannotation/
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

19. Participants
54 Participants
From more than 30 institutions
Additional users interact through the mailing list
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

20. Public Mailing List
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

21. Specifications (Drafts)
2012 CNI Fall Membership Meeting
Paolo Ciccarese, PhD

22. 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 Meeting
Paolo Ciccarese, PhD

23. Acknowledgements
• Tim Clark, Director of MIND Informatics
• Domeo Support: Maryann Martone, Anita
Bandrowski, VadimAstakhov, 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 Meeting
Paolo Ciccarese, PhD