![Page 1: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/1.jpg)
www.eudat.euEUDAT receives funding from the European Union's Horizon 2020 programme - DG CONNECT e-Infrastructures. Contract No. 654065
WebinarAnnotate data in the EUDAT CDI
Yann Le Franc - e-Science Data Factory, Paris, FranceMarch 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)
![Page 2: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/2.jpg)
About
Helping scientists to generate FAIR dataConsulting (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 inworking with [email protected]
![Page 3: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/3.jpg)
Outline of the webinar
Short introduction about annotations - Q&A
Demo session - Q&A
Open discussion - Q&A
Conclusions
![Page 4: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/4.jpg)
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,... .
![Page 5: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/5.jpg)
The added-value of annotations
Enriching digital content with your personalkeyword 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.
![Page 6: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/6.jpg)
B2NOTE: the data annotation service
Pilot version released: http://b2note.bsc.es
Three main types of annotations:
Semantic Annotation of the data in the EUDAT CDI withdomain specific ontologies
Free-text keywords
Comments
Based on the W3C Web Annotation Data Model
Using JSON-LD/RDF format
Integrated with B2SHAREv2
![Page 7: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/7.jpg)
Web Annotation Data Model
Use W3C Web Annotation data model –(https://www.w3.org/TR/annotation-model/)
Serialized in JSON-LD (https://www.w3.org/TR/json-ld/) = JSON based representation of RDF graphs
![Page 8: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/8.jpg)
B2NOTE Pilot service
Crowdsourcing annotatorAll annotation are publicPrivate annotation in the next release
Easy-to-useAuto-completion with terms from domain specific controlledvocabulariesIntuitive User Interface
Easily create new datasets selected based on annotations
Easy integration approach based Widget/iframe approachIntegrate with EUDAT services (B2SHARE,…)Integrate with community web UI
Easy to deployStore triples as JSON-LD in MongoDB backendUses Django as CMS
![Page 9: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/9.jpg)
Outline of the demo
Creating an annotation
View and access your annotation
Edit your annotation
Searching for annotated datasets
Export aggregated dataset
Export annotations
![Page 10: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/10.jpg)
TIME FOR A DEMO
https://b2note.bsc.es
![Page 11: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/11.jpg)
Where to provide feedbacks on B2NOTE?
Within the service: button "Let us know what you think”
EvaluationRequest for additional featureBug report
By email: [email protected]
![Page 12: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/12.jpg)
Additional topics to discuss
Service architecture
Annotation Data Model
Using your ontology for annotating files
Querying annotations as RDF
API
![Page 13: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/13.jpg)
B2NOTE architecture
![Page 14: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/14.jpg)
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
“http://b2note.bsc.es”
foaf:name
“B2Notev1.0”
foaf:homepage
“2017-01-17T09:51:02Z”“2017-01-17T09:51:02Z”
dcterms:created dcterms:issued
“http://b2share.eudat.eu/record/30”
oa:CompositeSemantic Tag
rdf:type
oa:TextualBodyKeywordandComment
rdf:type
![Page 15: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/15.jpg)
Working with ontologies
![Page 16: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/16.jpg)
About the ontology index
Harvested 1 ontology repository: Bioportal
434 ontologies
More than 5 millions of concepts
Problem of interoperability
Problem of discoverability
![Page 17: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/17.jpg)
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
![Page 18: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/18.jpg)
EUDAT Semantic Working Group Workshop
Barcelona – April 3-4
"How to improve the discoverability and the interoperability of multi-disciplinary scientific semantic resources?"
![Page 19: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/19.jpg)
Querying the Annotation graph
![Page 20: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/20.jpg)
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
![Page 21: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/21.jpg)
B2NOTE API
Built using the Python REST API framework Eve
Accessing annotation
Accessing all annotations: https://b2note.bsc.es/api/annotations
Use filters to access specific annotations
Use projections to retrieve specific elements of the annotations.
![Page 22: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/22.jpg)
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
![Page 23: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/23.jpg)
Thanks
Antoine Brémaud, PhD (e-Science Data Factory)
Pablo Rodenas (Barcelona SupercomputingCenter)
![Page 24: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/24.jpg)
Contact Info
B2NOTE: Yann Le Franc, PhD : [email protected]
e-Science Data Factory: [email protected]
![Page 25: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/25.jpg)
Q&A and
Concluding Remarks
![Page 26: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/26.jpg)
www.eudat.euEUDAT receives funding from the European Union's Horizon 2020 programme - DG CONNECT e-Infrastructures. Contract No. 654065
EUDAT & RDM Summer School3-7 July 2017, FORTH, Heraklion, Crete, Greece
eudat.eu/eudat-summer-school
![Page 27: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/27.jpg)
What is the Summer School about?Focused on Data Management and using EUDAT services, theEUDAT Summer School aims to introduce early-careerresearchers to the principles and tools needed for careers indata intensive science and data management.The course will provide attendees with a better understanding ofthe European e-Infrastructure landscape, the different tools andservices offered by them, and how they can be used to improvethe quality of your research outputs.
Who should apply?Early-career researchers working with big data, as well asresearchers from less data-intensive communities and datamanagers, interested in furthering their careers in the fields ofdata management, data science or digital preservation.
![Page 28: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/28.jpg)
What is the goal?Attendees will understand how the international e-infrastructures, which originate in different fields ofresearch, are building blocks to allow a more integratedsolution to meet their needs; they are expected toactively 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
![Page 29: Webinar Annotate data in the EUDAT CDI · EUDAT receives funding from the European Union's Horizon 2020 programme -DG CONNECT e-Infrastructures. Contract No. 654065 Webinar Annotate](https://reader033.vdocument.in/reader033/viewer/2022042919/5f60aecb3b7f394ee93aedc9/html5/thumbnails/29.jpg)
How to apply?Visit
eudat.eu/eudat-summer-schoolfor criteria and financial support opportunitiesWhen is the deadline for applying?
Monday 17 April 2017 @ 23:59 CET