2024-03-05
PAMREIN's daily Open Notebook (COMMONS Lab)
Todo - Check Github
-[]
Meetings
None
Daily report (What did I learn?)
- finished version one of the script for the toydataset.
Ctrl. + D : exit environment in Terminal
Autoformating for code
Visual studio provides a package "Black formatter" for python, which will automatically reformat when you press Ctrl. + Shift + I (for Linux) or Ctrl. + Shift + F (for Windows).
If you change the file "Open Users Settings (JSON)" and you add the line "editor.formatOnSave": true into the barely brackets, it will format if you save the file.
Sparkl's
Wikidata questions qlever website for searching wikidata (much faster than wikidata)
MINEs
The Website provides an API for searching the Metabolic In Silico Network Expansion Database.
LOTUS dataset
The columns will have following content:
chemical information
structure_wikidata,structure_inchikey,structure_inchi,structure_smiles,structure_molecular_formula,structure_exact_mass,
structure_xlogp,structure_smiles_2D,structure_cid,structure_nameIupac,structure_nameTraditional,structure_stereocenters_total,
structure_stereocenters_unspecified,
npclassifier structure_taxonomy_npclassifier_01pathway,structure_taxonomy_npclassifier_02superclass,structure_taxonomy_npclassifier_03class,
classyfire - chemical taxonomy structure_taxonomy_classyfire_chemontid,structure_taxonomy_classyfire_01kingdom,structure_taxonomy_classyfire_02superclass,structure_taxonomy_classyfire_03class,structure_taxonomy_classyfire_04directparent,
organism information organism_wikidata,organism_name,organism_taxonomy_gbifid,organism_taxonomy_ncbiid,
organism taxonomy organism_taxonomy_ottid,organism_taxonomy_01domain,organism_taxonomy_02kingdom,organism_taxonomy_03phylum,organism_taxonomy_04class,organism_taxonomy_05order,organism_taxonomy_06family,organism_taxonomy_07tribe,organism_taxonomy_08genus,organism_taxonomy_09species,organism_taxonomy_10varietas,
reference_wikidata,reference_doi,manual_validation