Idea > Draft > Work started > POC > Prototype

CHALLENGE 12
TOPIC : Protect Nature
SEE YOU ON JITSI : https://meet.jit.si/Hack4nature_LINKED_OPEN_BIODIVERSITY_DATA
CHAT ON SLACK : https://app.slack.com/client/T01AW3UBLUB/C01BM34KMQX/details
AGENDA :
- Tuesday, 7 september 2021 : OPENING
-

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 occurrences.

SPARQL micro-services could be used to turn existing Web APIs into dedicated endpoints.

Idea


A SPARQL micro-service is a lightweight method to query a Web API with SPARQL It dynamically queries the Web API and translates the response into an RDF graph aligned on any target vocabulary. Plus, it can assign dereferenceable URIs to Web API resources that do not have URIs beforehand.

This can be used to align multiple Web APIs on a common model and make their integration easier within a client web application.

This can also be very effective in integrating multiple APIs using federated SPARQL queries. 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 a SPARQL micro-service on top of it
*Demo the platform on a geographical region

Papers

Integration of Web APIs and Linked Data Using SPARQL Micro-Services — Application to Biodiversity Use Cases.
Franck Michel, Catherine Faron Zucker, Olivier Gargominy, Fabien Gandon. https://doi.org/10.3390/info9120310

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://github.com/frmichel/sparql-micro-service

https://ozymandias-demo.herokuapp.com/

Software Plan