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EUDAT Webinar "Organise, retrieve and aggregate data using annotations with B2NOTE" | |


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| | Annotate your research data with B2NOTE:
A note in the margins of a book or a scientific paper, a comment on a manuscript: we are all using annotations to add information to existing physical documents. To offer a similar experience with digital content within the EUDAT Collaborative Data Infrastructure (CDI), we developed a service that allows associating additional information to a file, in a computer-readable format, without changing the file or the data record itself. These digital annotations can thus be searched to organize, retrieve and aggregate files, datasets and documents.

Although B2NOTE is a standalone service, it has been designed to be integrated with the existing EUDAT services. In the first pilot version, B2NOTE allows to annotate files located in B2SHARE. The service is called as a “widget” within the B2SHARE User Interface. B2NOTE allows you to easily and intuitively create three types of annotations: a semantic tag coming from identified ontology repositories (only Bioportal at the moment but we are working toward integrating more vocabularies), a free-text keyword that can be used when you do not find a semantic term in particular and a free-text comment.

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EUDAT Webinar "Organise, retrieve and aggregate data using annotations with B2NOTE" | |

  1. 1. www.eudat.euEUDAT receives funding from the European Union's Horizon 2020 programme - DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate data in the EUDAT CDI Yann Le Franc - e-Science Data Factory, Paris, France March 16, 2017 This work is licensed under the Creative Commons CC-BY 4.0 licence. Version 2017-1 Attribution: Y. Le Franc (e-Science Data Factory)
  2. 2. About Helping scientists to generate FAIR data Consulting (Data Management Planning, …) Custom software development: Creating user friendly data management tools for scientists Integrating semantic web and Linked Data in scientific tools Knowledge modeling Research & Innovation (validated by French Ministry of Research) Data curation and publication Interested in working with us?
  3. 3. Outline of the webinar Short introduction about annotations - Q&A Demo session - Q&A Open discussion - Q&A Conclusions
  4. 4. What do we mean by annotation? By definition, an annotation is “a note added to a text, book, drawing, etc., as a comment or an explanation” (from Merriam Webster). In our context, it is an assertion we want to make about a digital resource i.e. a text file, an image, a recording, a movie,... .
  5. 5. The added-value of annotations Enriching digital content with your personal keyword without modifying the data record Structure data differently using annotations Support data curation before and after publication Create aggregated datasets from multi-scale or multi- domain datasets.
  6. 6. B2NOTE: the data annotation service Pilot version released: Three main types of annotations: Semantic Annotation of the data in the EUDAT CDI with domain specific ontologies Free-text keywords Comments Based on the W3C Web Annotation Data Model Using JSON-LD/RDF format Integrated with B2SHAREv2
  7. 7. Web Annotation Data Model Use W3C Web Annotation data model – ( Serialized in JSON-LD ( = JSON based representation of RDF graphs
  8. 8. B2NOTE Pilot service Crowdsourcing annotator All annotation are public Private annotation in the next release Easy-to-use Auto-completion with terms from domain specific controlled vocabularies Intuitive User Interface Easily create new datasets selected based on annotations Easy integration approach based Widget/iframe approach Integrate with EUDAT services (B2SHARE,…) Integrate with community web UI Easy to deploy Store triples as JSON-LD in MongoDB backend Uses Django as CMS
  9. 9. Outline of the demo Creating an annotation View and access your annotation Edit your annotation Searching for annotated datasets Export aggregated dataset Export annotations
  10. 10. TIME FOR A DEMO
  11. 11. Where to provide feedbacks on B2NOTE? Within the service: button "Let us know what you think” Evaluation Request for additional feature Bug report By email:
  12. 12. Additional topics to discuss Service architecture Annotation Data Model Using your ontology for annotating files Querying annotations as RDF API
  13. 13. B2NOTE architecture
  14. 14. B2NOTE Annotation Model anno1 rdf:type body1 oa:tagging oa:hasTargetoa:hasBody oa:motivatedBy oa: Annotation person1 dcterms:creator foaf:Person rdf:type “pseudo” foaf:nick client1 as:generator as:Application rdf:type “” foaf:name “B2Note v1.0” foaf:homepage “2017-01-17T09:51:02Z” “2017-01-17T09:51:02Z” dcterms:created dcterms:issued “” oa:Composite Semantic Tag rdf:type oa:TextualBody Keyword and Comment rdf:type
  15. 15. Working with ontologies
  16. 16. About the ontology index Harvested 1 ontology repository: Bioportal 434 ontologies More than 5 millions of concepts Problem of interoperability Problem of discoverability
  17. 17. The Ontology Look Up service Using your own ontology for annotating Provide access to multi-disciplinary ontological resources (discoverability) Register and describe your endpoint/API for harvesting Register and describe your ontology: propose a mapping with internal OLS data model Use B2SHARE to publish your ontology
  18. 18. EUDAT Semantic Working Group Workshop Barcelona – April 3-4 "How to improve the discoverability and the interoperability of multi-disciplinary scientific semantic resources?"
  19. 19. Querying the Annotation graph
  20. 20. Querying the Annotation graph Triple Store: OpenLink Virtuoso Script converting JSON-LD to RDF Pending issues: Configuration of the SPARQL endpoint Design of a workflow to update RDF content with new annotations
  21. 21. B2NOTE API Built using the Python REST API framework Eve Accessing annotation Accessing all annotations: Use filters to access specific annotations Use projections to retrieve specific elements of the annotations.
  22. 22. Future work Improvement of the User Interface and User functionalities Using W3C DCAT model to structure the aggregated datasets Improvement auto-complete function Integration with other EUDAT services Development of production-ready service
  23. 23. Thanks Antoine Brémaud, PhD (e-Science Data Factory) Pablo Rodenas (Barcelona Supercomputing Center)
  24. 24. Contact Info B2NOTE: Yann Le Franc, PhD : e-Science Data Factory:
  25. 25. Q&A and Concluding Remarks
  26. 26. www.eudat.euEUDAT receives funding from the European Union's Horizon 2020 programme - DG CONNECT e-Infrastructures. Contract No. 654065 EUDAT & RDM Summer School 3-7 July 2017, FORTH, Heraklion, Crete, Greece
  27. 27. What is the Summer School about? Focused on Data Management and using EUDAT services, the EUDAT Summer School aims to introduce early-career researchers to the principles and tools needed for careers in data intensive science and data management. The course will provide attendees with a better understanding of the European e-Infrastructure landscape, the different tools and services offered by them, and how they can be used to improve the quality of your research outputs. Who should apply? Early-career researchers working with big data, as well as researchers from less data-intensive communities and data managers, interested in furthering their careers in the fields of data management, data science or digital preservation.
  28. 28. What is the goal? Attendees will understand how the international e- infrastructures, which originate in different fields of research, are building blocks to allow a more integrated solution to meet their needs; they are expected to actively explore data services guided by our experts. The topics covered by the Summer School are: • The Research Data Lifecycle • The FAIR Data Concept • Writing a Data Management Plan • The EUDAT Service Suite Overview • High Performance Computing (HPC) Programming Models • Using the EGI Federated Cloud for Data Analysis • Linking HPC to Data Management • Open Data and Cross-disciplinary Research • Long Term Data Curation
  29. 29. How to apply? Visit for criteria and financial support opportunities When is the deadline for applying? Monday 17 April 2017 @ 23:59 CET