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

3. 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

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