2023-11-08
This is PMA's DBGI daily open-notebook.
Today is 2023.11.08
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Meeting DBGI Wednesday 08 November 2023
Luca's present EMIKG pipeline
Available at https://zenodo.org/records/10089363
- difference between modular code and monolithic code
One of the steps we certainly need to work on is the alignment of all EMI-related projects. We need to define the set of APIs that need to be available in the EMI backend, to better focus our efforts and aim to have a well-defined product to deliver.
I have prepared a Google Docs document that we may use to jot down notes. Please add objects to the object section using the "Header 2", and methods to each object using "Header 3". Feel free to include https://draw.io/ schemas to clarify potentially difficult points.
Please proceed with edits using the 'suggestion' mode, to make clear the author of each contribution and be able to chat before integrating any edit. Find the link with edit access here: https://docs.google.com/document/d/1qe4RawQZSaklTiOTgPah0EtVJZap8GIOnL6bFAjufcU/edit?usp=sharing.
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Jail shell : to protect the server from the users (they can be nasty ... you know ... users)
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Kubernetes : overkill in our case. We'll go for Docker swarms
/TODO/
- Fill the API documentation which has for objective to describe what the EMI portal functions are. For now a google doc https://docs.google.com/document/d/1qe4RawQZSaklTiOTgPah0EtVJZap8GIOnL6bFAjufcU/edit?usp=sharing Will be moved to a git versioned files when it stabilizes.
- Establish a shared Draw.io for the overall schema of the EMI actions
- Order HPC config for the EMIKG backend (mirror of the current COMMONS lab HPC)
- Order GPU https://www.digitec.ch/de/s1/product/gainward-rtx-4090-phantom-gs-24-gb-grafikkarte-22671040
Tarcisio's presentation of the EMIKG semantic model
Available at https://zenodo.org/records/10089497
Two services now available
https://dbgi.vital-it.ch/login https://dbgi.vital-it.ch/bioquery
SOSA ontology see Emi Semantic Model https://github.com/digital-botanical-gardens-initiative/earth_metabolome_ontology
/TODO/
- Have a script for conversion form SPARQL to JSON format suitable for Bio-Query
- Generate a Query survey form to be added to Bio-Query
- Add link to the protege shared EMI semantic model
Edouard's presentation of the collection process
Available at https://zenodo.org/records/10089416
- Collect Open Weather data
- List which additional data can be collected by observers in the field
- List which additional data can be collected by observers in the lab
Henry's presentation of the sample tracking process
Available at https://zenodo.org/records/10091485
PID Sample tracking and OpenBis
https://openbis-dbgi.labnotebook.ch/openbis/webapp/eln-lims/
/TODO/ Get in touch with UNiFr library. https://www.unifr.ch/biblio/en/ Maybe HENKEL Thomas thomas.henkel@unifr.ch Datacite Get in touch with IGSN people. https://www.igsn.org/ Get in touch with the DISSCO people. https://www.dissco.eu/
Understand what is the real added value of IGSN for the DBGI project. In which sense is it particularly designed to track Physical Objects ? (what the diff with a classical DOI) Discussion :
- use Zenodo ?
- use the kg.earthmetabolome.org/samples/dbgi_0000001 for ex ? Not OK in case this website dies : interest of the DOI
Anne-Laure proposes to start a Nagoya protocol discussion group.