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Annotopia open annotation services platform

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Annotopia is an open-access, open-source, open annotation services platform developed for scientific annotation of documents and datasets on the web using the W3C Open Annotation model …

Annotopia is an open-access, open-source, open annotation services platform developed for scientific annotation of documents and datasets on the web using the W3C Open Annotation model http://www.openannotation.org/spec/core/.
Using Annotopia, virtually any client application including lightweight web clients, can create, selectively share, and access annotation of web documents and data. This can be done regardless of the ownership of the base objects being annotated.
Annotopia supports unstructured, semi-structured and fully-structured (semantic) annotation; manual and automated (textmining) annotation; permissions, groups, and sharing. It also provides access to specialized vocabulary and text analytics services.
Annotopia is an open source platform licensed under Apache 2.0.

Published in: Science

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  • 1. the Annotopia Open Annotation Services Platform 25 February 2014 Paolo Ciccarese & Tim Clark Massachusetts General Hospital Harvard Medical School © 2014 Massachusetts General Hospital
  • 2. Canonical information Canonical information
  • 3. Canonical information Canonical information Laboratory data
  • 4. Canonical information Canonical information Laboratory data Linear narrative Canonical informationCanonical informationCanonical information
  • 5. RDF Bob: They used PDAPP mice to show this. Alice: Not sure model is good - seizures. Bob: Reproduce on another model.
  • 6. RDF Bob: They used PDAPP mice to show this. Alice: Not sure model is good - seizures. Bob: Reproduce on another model.
  • 7. 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.
  • 8. + =
  • 9. Goals • Web & PDF annotation • comments, semantic tags, claim-evidence • private, group, & institution permissions • image-specific annotation • Bibliographic entity resolution
  • 10. Open APIs • Client side • Utopia, Domeo, annotator.js, … • Services side • Standard textmining connectors • Vocabulary services • Mashup injection
  • 11. + Literature Services + + Textmining Services …
  • 12. Early installations • Harvard/MassGeneral ✔ • Eli Lilly Research Labs, UK ✔ • University of Manchester ✔ • European Bioinformatics Institute (planned)
  • 13. Load and preprocess document
  • 14. All references become objects
  • 15. Make comments localized on text
  • 16. Annotate in Utopia or Domeo visible in both
  • 17. Annotate images
  • 18. Annotate images
  • 19. Call textmining services & approve relevant tags
  • 20. Create micropublications
  • 21. Annotate & share micropublications
  • 22. 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)
  • 23. 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.
  • 24. Technical Workshop European Bioinformatics Institute April 29, 2014 contact: Jo McEntyre, mcentyre@ebi.ac.uk pharma participants invited
  • 25. • 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