changed data structure

assays/Data/metabolites_key.csv

+metbolomics_metabolite	kegg_metabolite
+Alanine	None
+Arabinose	None
+Arginine	L-Arginine
+Ascorbic acid	Ascorbate
+Asparagine	None
+Aspartic acid	L-Aspartate
+Cellobiose	None
+Citrate	Citrate
+Cysteine	L-Cysteine
+Fructose	None
+Fumarate	Fumarate
+Galactinol	None
+Galactitol	None
+Galactose	D-Galactose
+Glucose	alpha-D-Glucose
+Glutamic acid	L-Glutamate
+Glutamine	L-Glutamine
+Glyceric acid	D-Glycerate
+Glycerol	Glycerol
+Glycine	Glycine
+Glycolic acid	Glycolate
+Histidine	L-Histidine
+Isoleucine	L-Isoleucine
+Ketoglutaric acid	None
+Lactic Acid	None
+Leucine	L-Leucine
+Lysine	None
+Malate	(S)-Malate
+Maltose	None
+Melibiose	None
+Methionine	L-Methionine
+Myo-Inositol	myo-Inositol
+Nitrate	Nitrate
+Ornithine	L-Ornithine
+Palmitic Acid	Hexadecanoic acid
+Phenylalanine	L-Phenylalanine
+Phosphate	None
+Proline	L-Proline
+Pyruvate	Pyruvate
+Raffinose	None
+Serine	L-Serine
+Shikimic acid	Shikimate
+Spermine	None
+Stearic acid	None
+Succinic acid	Succinate
+Sucrose	None
+Sulfate	Sulfate
+Threonine	L-Threonine
+Tryptophan	L-Tryptophan
+Tyrosine	L-Tyrosine
+Urea	Urea
+Valine	L-Valine
+Xylose	None

assays/README.txt

+# Omics_db
+Adds omics data plus additional info into a database. In addition provids API and GUI for interacting with DB
+
+Project sturcture as follows
+
+Omics_db
+|   README.md
+|   .git
+|
+└───Code
+|   |   __init__.py
+|   |   get_omics_data.py
+|   |   init_db.ipynb
+|   |   metabolomics_preprocessing.py
+|   |   Omics_API.py
+|   |   proteomics_preprocessing.py
+|   |   remove_duplicate_omics.py
+|   |   transcript_preprocessing.py
+|
+└───Data
+|   |   metabolite_data_all.csv
+|   |   metabolite_key.csv
+|   |   metabolomics_data.parquet
+|   |   Omics_db.db
+|   |   Proteomics_data.csv
+|   |   Proteomics_data.parquet
+|   |   transcript_data.csv
+|   |   transcript_data.parquet
+|
+└───Test
+|   |   DB_Query.ipynb
+|   |   Test_API.ipynb
+

assays/TODO.txt

+Add module 'sucorse metabolism'
+
+Analyse photosynthesis -> celvin cylce -> photorespiration -> sucorse metabolsim -> starch metabolim
+
+Add module for cisteine
\ No newline at end of file