the Annotopia
Open Annotation Services
Platform
25 February 2014
Paolo Ciccarese & Tim Clark
Massachusetts General Hospita...
Canonical information
Canonical information
Canonical information
Canonical information Laboratory data
Canonical information
Canonical information Laboratory data
Linear narrative
Canonical informationCanonical informationCan...
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 annotati...
+
=
Goals
• Web & PDF annotation
• comments, semantic tags, claim-evidence
• private, group, & institution permissions
• image...
Open APIs
• Client side
• Utopia, Domeo, annotator.js, …
• Services side
• Standard textmining connectors
• Vocabulary ser...
+
Literature Services
+
+
Textmining
Services
…
Early installations
• Harvard/MassGeneral ✔
• Eli Lilly Research Labs, UK ✔
• University of Manchester ✔
• European Bioinf...
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 Marr...
Annotopia Version
Deployment
• Version 0: Domeo web repository.
• Version 1: EOQ1 2014. Domeo + Utopia basic
annotation se...
Technical Workshop
European Bioinformatics Institute
April 29, 2014
contact: Jo McEntyre, mcentyre@ebi.ac.uk
pharma partic...
• Science-based Open Annotation services
• Metadata storage and discovery for documents,
data, and other resources
• Integ...
Annotopia open annotation services platform
Annotopia open annotation services platform
Annotopia open annotation services platform
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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 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.

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Annotopia open annotation services platform

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