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.

1. the Annotopia
Open Annotation Services
Platform
25 February 2014
Paolo Ciccarese & Tim Clark
Massachusetts General Hospital
Harvard Medical School
© 2014 Massachusetts General Hospital

3. Canonical information
Canonical information

4. Canonical information
Canonical information Laboratory data

5. Canonical information
Canonical information Laboratory data
Linear narrative
Canonical informationCanonical informationCanonical information

6. RDF
Bob: They used PDAPP mice to show this.
Alice: Not sure model is good - seizures.
Bob: Reproduce on another model.

7. RDF
Bob: They used PDAPP mice to show this.
Alice: Not sure model is good - seizures.
Bob: Reproduce on another model.

8. 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.

9. +
=

10. Goals
• Web & PDF annotation
• comments, semantic tags, claim-evidence
• private, group, & institution permissions
• image-specific annotation
• Bibliographic entity resolution

11. Open APIs
• Client side
• Utopia, Domeo, annotator.js, …
• Services side
• Standard textmining connectors
• Vocabulary services
• Mashup injection

12. +
Literature Services
+
+
Textmining
Services
…

13. Early installations
• Harvard/MassGeneral ✔
• Eli Lilly Research Labs, UK ✔
• University of Manchester ✔
• European Bioinformatics Institute (planned)

14. Load and preprocess document

15. All references become objects

16. Make comments localized on text

17. Annotate in Utopia or Domeo
visible in both

18. Annotate images

19. Annotate images

20. Call textmining services
& approve relevant tags

21. Create micropublications

22. Annotate & share micropublications

24. 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)

25. 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.

26. Technical Workshop
European Bioinformatics Institute
April 29, 2014
contact: Jo McEntyre, mcentyre@ebi.ac.uk
pharma participants invited

27. • 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