2023-06-12

This is PMA's DBGI daily open-notebook.

Today is 2023.06.12

Todo today

Have a look at the DBGI discussion forum

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

Doing

Notes from the Text Mining and Biodiversity workshop https://docs.google.com/document/d/1rLCXLYCNi5NyitXUkOfNkNPAjuzjQTsm1tiZSfnk0Dg/edit#

Patrick mentioned getting in touch with Botanical Gardens in Geneva.

Participants

Donat Agosti, Plazi, agosti@plazi.org Patrick Ruch, HES-SO & SIB, patrick.ruch@hes-so.ch Fabio Rinaldi, IDSIA & SIB, fabio.rinaldi@idsia.ch Joseph Cornelius, IDSIA & SIB, joseph.cornelius@idsia.ch Oscar Lithgow, IDSIA & SIB , oscarwilliam.lithgow@idsia.ch Robert Waterhouse, UNIL & SIB, robert.waterhouse@gmail.com Harald Detering, UNIL & SIB, harald.detering@unil.ch Pierre-Marie Allard, UNIFR, pierre-marie.allard@unifr.ch Christophe Dessimoz, UNIL & SIB, christophe.dessimoz@unil.ch Rainer Krug, UZH & IPBES Task Force on Knowledge and Data, Rainer.Krug@uzh.ch Nils Arrigo, Infofauna, nils.arrigo@infofauna.ch Cécile Lebrand, Cecile.Lebrand@chuv.ch Daniele Silvestro, Daniele.Silvestro@unifr.ch Clara Zemp, UNINE, clara.zemp@unine.ch Emmanuel Defossez, UNINE, emmanuel.defossez@unine.ch Jeevanthi Pathirana, HES-SO & SIB, jeevanthi.liyana-pathirana@sib.ch

Programme

Introduction from Patrick Ruch and Fabio Rinaldi

Presentation from Christophe Dessimoz

~10 min presentations of projects/tools for text mining of biodiversity data Plazi & Synospecies: Donat (slides) eBioDiv & Biodiversity PMC: Patrick (slides) ArthroMine: Joseph & Harald (slides)

Round table / panel discussions on challenges and solutions

Coffee/tea - hopefully!

Panel Questions

Are you using text mining tools in your pipeline?

Which services would you wish to have from a text mining pipeline?
Do you use literature in your respective research?
What other data do you use: specimen/GBIF, sequences/ENA, mass spec/LOTUS, … ?
How do you access literature contents: open or closed?
How to put together different communities into a joint effort?
Data stewardship: who produces which data, and who maintains it? Which open repositories are key?
What part of your research pipeline could benefit from a new tech or new database?
How to grow a dedicated biodiversity chapter within the Swiss BioData ecosystem?