Open Science

Daniel, Egon

Open Science questions and Communication within the DBGI as well as communication with the community and public.

See slides at the end of

Lightning Dendron workshop

❗ News : Dendron is apparently no longer actively developed. Here is Kevin's (Dendron main dev) message https://discord.com/channels/717965437182410783/737323300967022732/1072563304289030164

Generalities

Have a look in : https://wiki.dendron.so/

For DBGI

Have a look in Welcome

Setup of individual Open Notebooks according to Setup

RIO Topical collection:

https://riojournal.com/topical_collections

- Publication of the ChordB ORD proposal ?

Would allow to have a first research outcome published. How should we proceed regarding the budget ? How heavy should be the reformating ?

• Zulip, Github Discussions

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

A slide explaining the relation of :

• email
• Zulip
• Dendron
• Github Discussions
• Github issues

When to use what and why ?

See last slide at

All these means are encouraged but should not be a brake to implication and development

Botanical Gardens, collection of specimens & legal aspects

Botanical Gardens

• Anne-Laure, Donat, Nadir, Blaise, Gregor

What do we have ?

For now UniFr / UniNe

What do we want ?

Should we contact other Botanical gardens in CH ? International ?

Maybe yes at least for questions regarding Nagoya and CBD. (e.g Geneva BG, Vienna Botanical Gardens, IPEN exchange group) BGCI (BG conservation iNternational) HBH (Hortus Botanicus Helveticus )

Meeting in Neuchâtel in August 30-31 Manu will present DBGI

Private Partner Orchids Green House (EMI/DBGI ?) Legal & ethics ? Nagoya status.

We want to track provenance and licences regarding reuse of data.

Litterature information collection

This part should eventually be linked with the anticipated LOTUS project. However discussing it we could think about the best way to integrate Taxonomic treatments in the DBGI-KG from the very beginning of the project and not afterwards

From Donat's part

Thanks for the invitation. I had a look at the program and wonder whether you want to have a few slides about the linking of metabolomes to specimens to literature, essentially what you asked for in the BiCIKL TNA proposal. On our side we are interested to process Phytochemistry so you could then create the links and we could work with Patrick Ruch to see how we could annotate chemical substances in SIBiLS once we have the Phytochemistry articles in SIBiLS

https://docs.google.com/presentation/d/1Uhfk8HFNLtoMRpwkJcADOv1IVEki2hHoisWvMBXBA1o/edit#slide=id.g6e365e6214_2_75

They are two aspects here.

• how do we track specimens and not only species ?
• how do we exploit previous knowledge

Both are very important, but the first one is of utmost importance in the DBGI and EMI.

Purl.org or similar to mirror url such as inat observations ids PIDs (Persistent Data Id) EPIC SSCC https://www.pidconsortium.net/

Which are the metadata that we want to collect ?

Can we uniquely identify a specimen ?

We basically have

• observations (tracked on iNat)
• specimens (How ? can this be tracked ?) if they dont exist we create it.
• species (tracked on iNat)

❗ This point turned out to be not so simple as we have discussed. It's however an important an interesting one to tackle.

DISSCO (https://www.dissco.eu/) and Taxonomic Data WG TDWG (https://www.tdwg.org/)

Working group on legal and ethics aspects of acces to genetic / metabolic diversity

Anne-Laure

Data are linked to genetical resssource. Nagoya protocol. We need legal guarantees. What can be published under which conditions ?

CITES plants. Applied after 2014. Nagoya concern use of traditional knowledge.

Ethical guidelines. Prior Informed Consent.

• ask to juridical in university. Legal services. To be check in UniF and UniNe HBH (Hortus Botonicus Helveticus )

Present DBGI/EMI

Valérie Wyssbrod

👉 Set up a small working group on legal and ethics aspects.

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 :

• https://www.inaturalist.org/observations/139418418
• https://www.inaturalist.org/observations/139418397
• https://www.inaturalist.org/observations/139418389

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 ?!

Ana, Tarcisio, Christophe, Daniel (can't be there due to teaching duties), Egon, Jakub, Philippe

What do we have ?

• ENPKG

https://enpkg.commons-lab.org/graphdb/ https://enpkg.commons-lab.org/

The idea for now is to fork the ENPKG repos on the DBGI organisation. We will build on these, at least for the MS > RDF part.

What do we want ?

• DBGI-KG

• EMI-KG

• Wikibase. Is this an option ? How complicated ? Does someone has experience in setting these up ? https://wikiba.se/

Daniel's opinion : it's worth exploring.

Could serve as a backup for iNat Could facilitate integration with iNat ? Wikibase <-> WD is straightforward.

1. start by Using existing WikiBase

Scholia could work with any Wikibase (cg Egon hackaton proposal at SWAT) See at

Daniel runs his own instance Wikibase instance.

Downside : additional efforts to set up
Why not do it on WD directly ?

WD doesn't want specimens informations. We have data at higher granularity. Several ways to test this https://www.wikibase.cloud/ Need a Wikimedia account

Will set up a small meeting with Daniel.

(PMA) I just signed up for a wikibase.cloud account. They are apparently in closed beta for now https://www.wikibase.cloud/

Ana, Maelle

What do we have ?

For now the https://enpkg.commons-lab.org/graphdb/ endpoint.

Example data exploration tools and publications from the BioSODA SNF project: https://biosoda.expasy.org/

What do we want ?

An intuitive, easy to use, data access platform allowing domain experts to explore the available data.

See Scholia proposal at the SWAT4HCLS hackaton by Egon

Hacking Scholia for custom SPARQL endpoints

https://github.com/SWAT4HCLS/Biohackathon-SWAT4HCLS-2023/issues/4 This hack project is following up efforts of other to repurpose the Scholia platform for other SPARQL endpoints, like custom Wikibase installations or Wikidata subsets. In this project we will explore how we can make the Scholia code base configurable for the aspects to show, and which panels to show. If the project is successful, we have a custom Scholia instance around any of the existing public SPARQL endpoints (e.g. ChEMBL, UniProt/NextProt, etc).

Daniel, Manu

What do we have ?

What do we want ?

Litterature information collection

https://docs.google.com/presentation/d/1Uhfk8HFNLtoMRpwkJcADOv1IVEki2hHoisWvMBXBA1o/edit#slide=id.g6e365e6214_2_75

Next meeting ?!

• Where ?
• Who ?

Outcomes and future tasks

We have set up 2 upcoming meetings (more targeted than today's) Anyone is welcome to join them. And also envisioned starting a small taskgroup.

• one small working group on legal and ethics aspects of sample collection (Anne Laure in JBN) Daniel is interested in ethics aspects and will possibly participate.
• one workshop on opneBIS (Henry, Caterina)
• one wikibase workshop (Daniel) In CH end of March 29-30 possibly few days earlier maybe in person.

Last notes by Daniel. He is involved in Soil for Europe (intersect with DBGI) PhenOps phenotypic observation, citizen science observation Botanical Gardens and citizen gardens They gather temp data.

Found back previous email of Daniel on these projects

I am involved with the EU Project "Soils for Europe" https://cordis.europa.eu/project/id/101091115 that may be of interest to you, and I talked to two projects here in Germany that I think would be good to connect with in some way, e.g. in terms of their model beddings and citizen involvement: "Pflanze KlimaSchutz" https://www.pflanzeklimakultur.de/index.php/de/ "PhenObs" https://www.idiv.de/en/phenobs.html Both involve collaborations between botanical gardens, with the first focusing on citizen science and public engagement in four German cities (Jena, Halle, Leipzig, Berlin), while the latter is more international (including Davos, whose Fabian Reppel will give a talk here in about an hour - [1]).

I also would like us to think about https://commons.wikimedia.org/wiki/Commons:Wiki_Loves_Plants and similar initiatives involving iNaturalist and Wikimedia. For instance, I would like to explore infrared imaging to highlight thermogenic plants.