Annotopia: Open Annotation Server

Paolo Ciccarese
Paolo CiccaresePrincipal Informatics & Knoweldge Engineer at Innovation Lab
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
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
http://www.annotationframework.org/ Paolo Ciccarese, PhD
http://www.annotationframework.org/ Paolo Ciccarese, PhD
http://www.annotationframework.org/ Paolo Ciccarese, PhD
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.
graph representation
http://www.annotationframework.org/ Paolo Ciccarese, PhD
http://www.annotationframework.org/ Paolo Ciccarese, PhD
Unstructured & structured annotation
http://www.annotationframework.org/ Paolo Ciccarese, PhD
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)
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
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
Annotopia
Universal Annotation Hub
With an Open Annotation heart
I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD
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
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
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
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
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
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
Follow Us
• @domeo
• @annotopia
• @paolociccarese
• Installing/customizing Domeo and Annotopia?
• Contact: paolo.ciccarese@gmail.com
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Annotopia: Open Annotation Server

  • 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
  • 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.
  • 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