2024-03-06
PAMREIN's daily Open Notebook (COMMONS Lab)
Todo - Check Github
-[] API with Pick-Axe
Meetings
- short feedback for my first line of codes
I should make a readme for other people to know how to use it. good practice good readme
Daily report (What did I learn?)
About Pick-axe
- Metacyc has information about metabolic pathways database. It provides the "JN1224min ruleset" (1224 reaction rulset) for pick axe. For each reaction exist an UniProt entry for the specific Enzyms.
- It has two compound property filters. One for molecularweight (MV) and one for atomic composition of an individual compound to determine if it should be removed from the network.
- Pickaxe generates cemical fingerprints (bit vectores with the RDKit) for see similarities. It has a cutoff filter and sampling filter (weighted Tanimoto distribution)
- With the Metabolomics filter needs as input a list of experimental mass-to-charge (m/z) values and a list of possible adducts.
- Thermodynamics-based filter uses the Gibbs free energy.
- Feasibility filter: Deep learning-based Reaction Feasibility Checker (Deep_RFC). It is incorporated into Pickaxe.
- Outputs: generated networks in three different formats. Each format has information about the compounds: reactions, reactionrules and target molecules. Results can be stored in a MongoDB as a JSON format. It also supports Systems Biology Markup Language (SBML).