2023-02-07
This is PMA's DBGI daily open-notebook.
Today is 2023.02.07
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Meeting witrh Maelle
Some notes on the Data visualization project
https://microbeatlas.org/ https://masst.gnps2.org/microbemasst
Have a look into the functionning of the GNPS families of dashboards https://www.nature.com/articles/s41592-021-01339-5 https://github.com/mwang87/GNPS_LCMSDashboard
For molecules display
https://github.com/wjm41/molplotly
Loacaly you can use DataWarrior https://openmolecules.org/datawarrior/
Sources of large molecular datatables. https://zenodo.org/communities/the-lotus-initiative/?page=1&size=20
Data Sources
LOTUS with metadata https://zenodo.org/record/7534071#.Y-IRNJOZP8Y
main libraries for chemoinfo
https://www.rdkit.org/ https://cdk.github.io/
Chemical classifiers
https://pubmed.ncbi.nlm.nih.gov/34662515/ https://github.com/mwang87/NP-Classifier https://npclassifier.ucsd.edu/ http://classyfire.wishartlab.com/
TMAP and fingerprints
https://gdb.unibe.ch/ https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00445-4
Chemical spaces
https://pubs.acs.org/doi/full/10.1021/acs.jnatprod.8b00767
The PF dataset paper https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac124/6980761 And the associated GraphDB interface https://enpkg.commons-lab.org/graphdb/sparql
Paused
Done
Notes
- Suggestion to improve the Welcome is to add a link to Markdown tutorials