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2023-06-20

This is PMA's DBGI daily open-notebook.

Today is 2023.06.20

Todo today

Have a look at the DBGI discussion forum

- https://github.com/orgs/digital-botanical-gardens-initiative/discussions

Doing

Meeting with GBIF people

  • Sofia Wyler
  • Pascal Tschudin
  • Donat Agosti
  • Emmanuel Deffossez
  • Pierre-Marie Allard

Presentation

Treatment dataset Material citations

Brief DBGI and EMI presentation.

Donat Agosti14:12

https://tb.plazi.org/GgServer/html/3547A05159400538FF5AE756A8D1F9AD

and the same in GBIF Lien https://www.gbif... par Donat Agosti Donat Agosti 14:12

and the same in GBIF https://www.gbif.org/dataset/f081ba27-575f-41b5-b203-83b87db2aadf

Cytotoxic sesquiterpene lactones from Campuloclinium macrocephalum (= Eupatorium macrocephalum)

Donat introduced the possibility to dicuemnt a Physical Object using a Zenodo repo. Uses keywords and controlled vocabulary from Darwin core. Can be customized https://zenodo.org/record/6083924

https://github.com/gbif/portal-feedback/issues

https://www.gbif.org/new-data-model

Some points discussed

linking iNaturalist observations and GBIF

  • examples ?
  • Issues because observations for botanical gardens specimens correspond to "cultivated" categorie, hence no "research grade" quality in iNat, so not taken up by GBIF

how do we label an individual ?

A priori we can identify an observation (e.g. an iNat observation id https://www.inaturalist.org/observations/160942639) A priori we can label a species corresponding to this observation (e.g iNat taxa id https://www.inaturalist.org/taxa/168422-Sansevieria-cylindrica or GBIF https://www.gbif.org/species/2770617) A priori we can label the physical objects (dried powder, extracts etc) linked to an observation (in this case the emi_external_id dbgi_000512, present on the iNat observation page + inhouse)

However we do not know how to efficiently identify the individual corresponding to an observation.

  • is it required to do so ?
  • If we can, we should

Some specific problems :

  • How do we deal with organism where tthe identification of an "individual" is complicated if not impossible ?
    • carpophore of an undergrounds fungi
    • plants, lichens, animals or soil and water samples containing multiple other species (endop'hytes, associated microbiome etc.)

Some issues posted following the discussion

Examples of an observation of multiple species / organism simultaneously #4823 https://github.com/gbif/portal-feedback/issues/4823

example of organism with multiple occurrences #4822 https://github.com/gbif/portal-feedback/issues/4822

To be followed up possibly in 7-10 days.

Paused

Done

Notes

  • For next OpenBis meeting:

  • can we display picture from hyperlinks

  • can we display maps from lat/lon coordinates

  • we cannot use the API (both as user or admin) see issue on Rostyk

    • the creation of a PAT apparently didn't solve the issue

  • have a one2one and a one2many links examples

  • see for upload of a simple csv from the UI

  • try to pass current Directus tables to OpenBis

  • updates on QRcodes

Todo tomorrow

Today I learned that