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

Paolo Ciccarese, PhD

Mass General Hospital Harvard Medical School

paolo.ciccarese@gmail.com

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?

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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

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

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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

APPs

for t

he S

eman

tic R

esou

rces

Pro

ject

, May

201

0

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

Reagents (reproducibility)

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

antibodyregistry.org

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

graph representation

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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

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

Annotation Ontology Network

The Living DocumentProject

Biotea

Annotations at Harvard

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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

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

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

Participants

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

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

Public Mailing List

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

Specifications (Drafts)

2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD

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

Acknowledgements

• Tim Clark, Director of MIND Informatics• Domeo Support: Maryann Martone, Anita

Bandrowski, Vadim Astakhov, Anita de Waard, Bradley Allen, Keith Gutfreund, Antony Scerri

• 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