Idea > Draft > Work started > POC > Prototype

Linked open biodiversity data


image 0_1mIH3vsNn8fGWWLO.jpg (2.5MB)

Problem


Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space.

The export module of GeoNature is currently generating a file in the SINP Standard and is not an endpoint per se.

We are currently lacking the Observations in the SemWeb cloud so we can compute queries on occurences.

Sparql Microservice could be used to provide a micro graph as an endpoint.

Idea


A SPARQL micro-service is a lightweight, task-specific SPARQL endpoint that provides access to a small, resource-centric, virtual graph, while dynamically assigning dereferenceable URIs to Web API resources that do not have URIs beforehand. The graph is delineated by the Web API service being wrapped, the arguments passed to this service, and the restricted types of RDF triples that this SPARQL micro-service is designed to spawn.

Demo here : http://sparql-micro-services.org/demo-sms?param=Delphinapterus+leucas

Team


Olivier Rovellotti
Julien Corny
Amandine ?
Franck Michel ?
Jean Marc ?

Steps

*Identify what geonature wants to be open
*Deal with "sensible data"
*Have workshop on Open and semantic data
*Modify the GeoNature API
*Plug the Sparql MicroService
*Demo the platfrom on a geographical region

Papers

Integration of Web APIs and Linked Data Using SPARQL Micro-Services—Application to Biodiversity Use Cases†
by Franck Michel
https://www.mdpi.com/2078-2489/9/12/310

Filtered-Push: A Map-Reduce Platform for Collaborative Taxonomic Data Management
Zhimin Wang2 , Hui Dong2 , Maureen Kelly3 , James A. Macklin3 , Paul J. Morris1
Robert A. Morris2
http://biowikifarm.net/v-filteredpush/w/media/a/a8/PID797506.pdf

Links

https://github.com/PnX-SI/GeoNature/issues

Data

https://www.data.gouv.fr/fr/datasets/observations-de-biodiversite-faune-flore-du-parc-national-des-ecrins/

Software

https://geonature.fr/
https://github.com/PnX-SI/GeoNature-citizen
https://github.com/PnEcrins/FollowDem

https://ozymandias-demo.herokuapp.com/
http://sparql-micro-services.org/demo-sms?param=Delphinapterus%20leucas

Software Plan