Wp2

Henry, Catarina, Bernd, Ming, Maelle, Edouard

What do we have ?

Physical objects

- living specimens (look trough the window !)
- dried tissues collections (bring Tubes)
- extracts (Tubes)
- fridges

Digital objects

- Species list. We had a quick talk with https://botalista.community/ people.
- iNat. The DBGI iNat project https://www.inaturalist.org/projects/digital-botanical-gardens-initiative

We cant use the iNat API (because we have non-research grade observation - cultivated specimens)

See examples of DBGI iNat entries curated by others :

Think of a way to capture these community curated entries and forward then to the implicated botanical gardens.

- Directus (http://directus.dbgi.org/) Have a quick tour.
- MassIVE (several set uploaded e.g. https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=bd2a519b678e4f92aeca6434166ea548, https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=589f0793f15d4b87aebd699900ad468e)
For long term consider other MasSpec repositories. (Metabolights https://www.ebi.ac.uk/metabolights/) Others ?


- Physical samples tracking: none at the moment.

What do we want ?

Physical objects

- living specimens (look trough the window) - Could this improve ? How ?
- dried tissues collections (Falcon Tubes) - Could this improve ? How ?
- extracts (Tubes) - Could this improve ? How ?
- fridges () - Could this improve ? How ?

Digital objects

- Species list
- iNat
- Directus
- MassIVE. Are they new developments /recommendations on this side ? GNPS2 ?
- Physical samples tracking

Frictionless Software toolkit (https://frictionlessdata.io/) Bioregistry (https://bioregistry.io/) (Also in WP3)

If we take the directus example, it is hosted on a computer of the COMMONS Lab at UniFr and can only be accessed through the UniFr VPN. Should we buy / rent another machine to ease external access ? If so where ? Which specifications ?

OpenBIS

A workshop is to be planned in the next month. In the first 15 days of March. Doodle to be send by Henry and Caterina Physical / remote Half a day to get started. Objectives :

get familiar with openBIS (https://openbis.ch/)
Fill in the empty openBIS templates

OpenBIS instance could be hosted on switchengines (https://www.switch.ch/engines/) For around 1000$/year Docker image existing.

Possibilities of lightweight implementation ? Is this really necessary ?!

Backlinks

Program