2012 CNI Fall Membership Meeting

Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group

Paolo Ciccarese, PhD

Mass General Hospital Harvard Medical School

[email protected]

2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC

Annotation in Biomedicine

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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?


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


Semantic tagging

APP

News and Hypotheses

Biol

ogic

al P

roce

sses

Videos/imagesPathways Expe

rts

Antibodies 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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


http://www.jbiomedsem.com/content/3/S1/S1

http://annotationframework.org/

https://twitter.com/DomeoTool

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…’


http://purl.obolibrary.org/obo/PR_000004168

http://purl.obolibrary.org/obo/PR_000000001

APPs

for t

he S

eman

tic R

esou

rces

Pro

ject

, May

201

0


Reagents (reproducibility)


antibodyregistry.org

Annotation of Argumentation

classic publication

scientific discourse ‘semantic’ representation

http://tinyurl.com/cgyna2m

Semantic Web Applications in Neuromedicine (SWAN) project [2007]


graph representation


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


Video AnnotationTools

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


http://www.jbiomedsem.com/content/2/S2/S4

Annotation Ontology Network

The Living DocumentProject

Biotea

Annotations at Harvard


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

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


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


http://www.w3.org/community/openannotation/


Participants

54 ParticipantsFrom more than 30 institutionsAdditional users interact through the mailing list


Public Mailing List


Specifications (Drafts)


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


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.
