The document discusses Annotopia, an open annotation server that aims to support the creation, persistence, and management of annotations on any identifiable documents, multimedia, and data. It provides services and APIs for storage, search, reporting, text mining, image analysis, and integrating with controlled vocabularies and other systems. Annotopia seeks to make annotation easier by allowing the use of multiple annotation tools and clients without being tied to a specific one.

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