2025-02-21

This is PMAS's COMMONS Lab daily Open Notebook.

Today is 2025.02.21

Todo today

Have a look at the COMMONS research discussion forum

- https://github.com/orgs/commons-research/discussions

Daily work on the Open Science for natural products research Viewpoint

See Viewpoint

Doing

Chat wioth Javier on Scholia Possibility to establisha DB of NP isolated in Chili with their geographical occurences.

We start with the example of https://scholia.toolforge.org/chemical/Q82866929

https://scholia.toolforge.org/taxon/Q15513067#metabolome

This one is connected to the GBIF id https://www.gbif.org/species/5343387

We manually created the taxon ranmge properties for this one

https://www.wikidata.org/wiki/Q15513067

So now we can check for molecules found in the Astragalus genera for which the taxon range includes Chile. https://w.wiki/D9aT

We can observe that few taxa have in fact Chile as a taxonrang https://w.wiki/D9an

We started with Tiago's http://tiago.bio.br/gbif_range_to_wikidata/

Lets see how we can use / adapt this for our use case

https://api.gbif.org/v1/occurrence/search?taxonKey=212&continent=africa&limit=0&facet=speciesKey&facetMincount=10&facetLimit=5000

For countries, the url should be encoded

https://api.gbif.org/v1/occurrence/search?taxonKey=212&country=CL&limit=0&facet=speciesKey&facetMincount=10&facetLimit=5000

We started to investigate the possibility to map traditional uses from taxon to indegeneous peoples

https://www.wikidata.org/wiki/Q158780

Discussing about ethopharmocological KG

https://ieeexplore.ieee.org/abstract/document/10443268 https://www.nature.com/articles/s41597-023-02757-0 https://gitub.u-bordeaux.fr/erias/oregano

Directus/Qfield

We try to set up a EMI project for Javier (temporary while we have the EMI data portal up and running)

We could create both a qfieldcloud and directus username However we are stuck at the stage of Project creation (https://emi-collection.unifr.ch/qfieldcloud/admin/core/project/add/) as we cannot setup the owner. To be checked with Edouard.

This , https://emi-collection.unifr.ch/qfieldcloud/admin/auditlog/logentry/ , for example returns a 500

Paused

Done

Notes

Todo tomorrow, one day ... or never

Today I learned that

  • o