1. ANNOTOPIA: an OPEN
ANNOTATIONServer forScience
Applications Everybody
Paolo Ciccarese, PhD
Assistant Professor of Neurology at Harvard Medical School
Co-chair of the W3C Open Annotation Community Group
I Annotate 2014 :: April 4th :: San Francisco
Thanks to Tim Clark, Principal Investigator and MIND Informatics director

2. Domeo Annotation Toolkit
• In production since 2010
• Manual and semi-automatic (text-mining)
annotation and structured-annotation
• Exposes annotation and provenance in RDF
• Integrated with third parties platforms and
knowledge bases
• Used in Academia, Biomedical
Communities, Pharmaceutical
Industry, Publishing Industry
• Currently version 2.1 (github.com/domeo/)
http://www.annotationframework.org/ Paolo Ciccarese, PhD

3. http://www.annotationframework.org/ Paolo Ciccarese, PhD

4. http://www.annotationframework.org/ Paolo Ciccarese, PhD

5. http://www.annotationframework.org/ Paolo Ciccarese, PhD

6. http://arxiv.org/abs/1305.3506
Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in
Biomedical Communications. Clark T., Ciccarese P, Goble C.

7. graph representation
http://www.annotationframework.org/ Paolo Ciccarese, PhD

8. http://www.annotationframework.org/ Paolo Ciccarese, PhD

9. Unstructured & structured annotation
http://www.annotationframework.org/ Paolo Ciccarese, PhD

10. Some of the things we learned…
• One single UI platform can hardly serve
everybody, no matter how customizable it is…
much UI research/experimentation is needed
• Annotation needs to rely on powerful open back-
ends that might deal with multiple annotation
clients/formats/protocol/domains
• The central ‘Annotation Hub’ model is not a
good/wise approach
• As we always thought: data matters
(Force11, Data Citations, FairPort of Elixir, Data
platforms)

11. Harvard CATCH proposal
• Common Annotation,Tagging and Citation (CATC) API
is a unified public open API that will enable
storing, searching, discovering, sharing and analyzing
scholarly annotations produced on four digital media
types - text, image, audio and video - across existing
pedagogical and research tools at Harvard.
• Proposal with: Phil Desenne and Martin Schreiner
https://osc.hul.harvard.edu/liblab/proj/catch Paolo Ciccarese, PhD
Harvard Annotation Hub

12. CATCH for HarvardX
• CATCH refocused on a variant of annotator.js
• Integrated with HarvardX in January 2014
• Collected annotations on poetry
I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD

13. Annotopia
Universal Annotation Hub
With an Open Annotation heart
I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD

14. Annotopia Open Annotation Server
• For creating, persisting and managing annotation
of anything that can be identified:
documents, multi-media and data… so that we
(you) can focus on the front end
• Provides services and uniform APIs for: storage
(with access control and
authentication), search, reporting, text-
mining, image analysis, controlled vocabularies
and mashups…
• Provides extension points
• Aims at supporting easier development of open
distributed architectures for annotation
I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD

15. By using Annotopia…
• No need to use a specific annotator client or
application, you can mix and match clients
• You can install your own serveror use an
available instance
• You can even use Annotopia only for
publishing annotation in Open Annotation
format
• You will be able to connect Annotopia servers
for federated querying
I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD

16. Component: Smart Storage
• Storage using a combination of Triple Store and
Elastic Search
• The core is Open Annotation plus support for:
– Multiple input/output annotation formats (normalized
to OA for querying and indexing)
– Access control and various authentication mechanisms
– Collections of annotations
– Documents variants
– Structured (and semantic) general-purpose or domain-
specific annotations through extensions
https://github.com/Annotopia/AtSmartStorage/ Paolo Ciccarese, PhD

17. Imagine annotating…
• Documents (HTML and PDF) with multiple tools
(Domeo, Utopia, annotator.js)
• (Bibliographic) records with bibliographic
management platforms
• (Biological) Entities in databases and knowledge
bases
• Hi-res imaging (Brain imaging) and 3D models
(proteins, brain anatomy…)
• Data in various shapes and domains (genomic
data, clinical data…)
https://github.com/Annotopia/AtSmartStorage/ Paolo Ciccarese, PhD

18. I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD
Custom Annotators
Annotopia
Instance 1
Annotopia
Instance 2
APIs
(OA++)
Annotopia: Opening Up Annotation
Aggregated
query
App
App
App

19. Early Installations
• Mass General & Harvard
• Eli Lilly Research Labs, UK
• University of Manchester (in testing and
includes integration with Utopia for PDF)
• European Bioinformatics Institute (planned)
I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD

20. Follow Us
• @domeo
• @annotopia
• @paolociccarese
• Installing/customizing Domeo and Annotopia?
• Contact: paolo.ciccarese@gmail.com