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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.
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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
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+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, [email protected]
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
