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Annotopia: Open Annotation Server


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Annotopia is a universal annotation server with an Open Annotation heart. Presentation at 'I Annotate 2014', San Francisco, CA, USA on April 4th 2014.

Published in: Technology, Education

Annotopia: Open Annotation Server

  1. 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. 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 ( Paolo Ciccarese, PhD
  3. 3. Paolo Ciccarese, PhD
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  5. 5. Paolo Ciccarese, PhD
  6. 6. Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications. Clark T., Ciccarese P, Goble C.
  7. 7. graph representation Paolo Ciccarese, PhD
  8. 8. Paolo Ciccarese, PhD
  9. 9. Unstructured & structured annotation Paolo Ciccarese, PhD
  10. 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. 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 Paolo Ciccarese, PhD Harvard Annotation Hub
  12. 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. 13. Annotopia Universal Annotation Hub With an Open Annotation heart I Annotate 2014 :: April 4th :: San Francisco Paolo Ciccarese, PhD
  14. 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. 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. 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 Paolo Ciccarese, PhD
  17. 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…) Paolo Ciccarese, PhD
  18. 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. 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. 20. Follow Us • @domeo • @annotopia • @paolociccarese • Installing/customizing Domeo and Annotopia? • Contact: