the Annotopia Open Annotation

Services Platform25 February 2014

Paolo Ciccarese & Tim ClarkMassachusetts General Hospital

Harvard Medical School

© 2014 Massachusetts General Hospital

Canonical information

Canonical information

Canonical information

Canonical information

Laboratory data

Canonical information

Canonical information

Laboratory data

Linear narrative

Canonical informationCanonical

informationCanonical

information

RDF

Bob: They used PDAPP mice to show this.

Alice: Not sure model is good - seizures.

Bob: Reproduce on another model.

RDF

Bob: They used PDAPP mice to show this.

Alice: Not sure model is good - seizures.

Bob: Reproduce on another model.

Annotopia• Annotopia is an open source, multimedia annotation repository.

• It holds structured and unstructured annotation in a formal standardized model…

• Using the W3C Open Annotation model (W3C OA), serialized as JSON-LD.

+

=

Goals• Web & PDF annotation

• comments, semantic tags, claim-evidence

• private, group, & institution permissions

• image-specific annotation

• Bibliographic entity resolution

Open APIs• Client side

• Utopia, Domeo, annotator.js, …

• Services side

• Standard textmining connectors

• Vocabulary services

• Mashup injection

+Literature Services

+

+Textmining Services…

Early installations

• Harvard/MassGeneral ✔

• Eli Lilly Research Labs, UK ✔

• University of Manchester ✔

• European Bioinformatics Institute (planned)

Load and preprocess document

All references become objects

Make comments localized on text

Annotate in Utopia or Domeo

visible in both

Annotate images

Annotate images

Call textmining services

& approve relevant tags

Create micropublications

Annotate & share micropublications

Some Current Collaborators

• Harvard Medical School / MGH (Tim Clark, Paolo Ciccarese)

• Eli Lilly Research UK (Derek Marren, Director Bio IT)

• Elsevier (Brad Allen, Chief Architect)

• OpenPHACTS (Lee Harland, Paul Groth)

• EMBL / EBI / Europe PubMed Central (Jo McEntyre)

• Force11 Resource Identification Initiative (Maryann Martone)

• Harvard IQSS / Dataverse (Merce Crosas, Gary King)

Annotopia Version Deployment

• Version 0: Domeo web repository.

• Version 1: EOQ1 2014. Domeo + Utopia basic annotation services.

• Version 2: EOQ2 2014. Annotator.js API. Semantic tagging, micropublications, textmining integration.

• Version 3: EOQ3 2014. Mashup services. FAIRPORT integration.

Technical WorkshopEuropean Bioinformatics

Institute

April 29, 2014

contact: Jo McEntyre, mcentyre@ebi.ac.uk

pharma participants invited

• Science-based Open Annotation services

• Metadata storage and discovery for documents, data, and other resources

• Integrate textmining and vocabulary services

• Web annotation & metadata as first-class objects

• Open source under Apache 2.0 license