Overview
Enzyme information from the BRENDA database is accessible through both a SOAP interface. Currently, the SOAP interface requires an extensive knowledge of the provided methods. Repeated queries of the text file, which are costly in terms of time and efficiency, are needed to gather enzymatic information for machine learning applications.
PER BRENDA converts the provided BRENDA text file into a JSON which mirrors BRENDA's structural organization. This intuitive design allows a user to quickly and easily perform queries for desired information across various enzymes. The parsed output JSON can then be traversed for EC numbers, categories, subcategories, and fields of the JSON. an Aptional parameter allows for extracting the file in a comma sepa-rated textfile.
Feel free to use this code! But if you do, please provide reference to the following publciation: TBA
Python 3.8
pandas
Python perBRENDAParser.py --ifile brenda_download.txt --ofile parsed.json optionally --efile error.json
Python perBRENDAExtract.py --ifile parsed.json --templatefile template.json --ofile extract.json
optionally --csvfile brenda.csv --compoundfile comps.txt
Extractions may be executed provided with a parsed JSON file name, output file name, and extraction parameters. These parameters include EC numbers, subcategories, and fields of interest. For command line extractions, a templatefile should be included to extract these parameters, an example template may be found in entryTemplate.json and categoryTemplate.json.
For the extraction of a single subcategory, a csvfile may be provided for a csv output of the subcategory. For extractions with Substrate/Product and Natural Substrates a compoundfile which will contain a list of all the compound names in the extraction result without duplicates. The file may be processed on MetaboAnalyst for KEGG, PubChem, and other database ID numbers.
Category: Labels shown in BRENDA sidebar (example Enzyme-Ligand Interactions)
Subcategory: Labels shown under each category (example Activating Compounds)
Fields: Columns in each subcategory (example (under Activating Compounds) ACTIVATING COMPOUND, UNIPROT, or COMMENTARY)
To extract multiple EC numbers under the same branch, use '.' at the end of the stem (example '1.1.')
Avaliable fields are as follows:
Activating Compound (AC): COMMENTARY, LITERATURE, ORGANISM, ACTIVATING COMPOUND, UNIPROT
Applications (AP): COMMENTARY, LITERATURE, ORGANISM, APPLICATION, UNIPROT
Cofactors (CF): COMMENTARY, LITERATURE, ORGANISM, COFACTOR, UNIPROT
Cloned (CL): CLONED (Commentary), LITERATURE, ORGANISM, UNIPROT
Crystallization (CR): CRYSTALLIZATION (Commentary), LITERATURE, ORGANISM, UNIPROT
Protein Variants (EN): COMMENTARY, LITERATURE, ORGANISM, PROTEIN VARIANTS, UNIPROT
Expression (EXP): LITERATURE, ORGANISM, EXPRESSION, COMMENTARY, UNIPROT
General Information (GI): COMMENTARY, LITERATURE, ORGANISM, GENERAL INFORMATION, UNIPROT
General Stability (GS): GENERAL STABILITY, LITERATURE, ORGANISM, UNIPROT
IC50 Values (IC50): COMMENTARY, LITERATURE, ORGANISM, INHIBITOR, IC50 VALUE, UNIPROT
Inhibitors (IN): COMMENTARY, LITERATURE, ORGANISM, INHIBITOR, UNIPROT
Ki Values (KI): COMMENTARY, LITERATURE, ORGANISM, INHIBITOR, Ki VALUE, UNIPROT
kcat/KM Values (KKM): COMMENTARY, LITERATURE, ORGANISM, SUBSTRATE, kcat/KM VALUE, UNIPROT
KM Values (KM): COMMENTARY, LITERATURE, ORGANISM, SUBSTRATE, KM VALUE, UNIPROT
Localizations (LO): COMMENTARY, LITERATURE, ORGANISM, LOCALIZATION, UNIPROT
Metals and Ions (ME): COMMENTARY, LITERATURE, ORGANISM, METALS and IONS, UNIPROT
Molecular Weight (MW): COMMENTARY, LITERATURE, ORGANISM, MOLECULAR WEIGHT, UNIPROT
Natural Substrates (NSP): COMMENTARY (Substrate), COMMENTARY (Product), LITERATURE, ORGANISM, NATURAL PRODUCT, REVERSIBILITY, NATURAL SUBSTRATE, UNIPROT
Oxidation Stability (OS): OXIDATION STABILITY, LITERATURE, ORGANISM, UNIPROT
Organic Solvent Stability (OSS): COMMENTARY, LITERATURE, ORGANISM, ORGANIC SOLVENT, UNIPROT
pH Optima (PHO): COMMENTARY, LITERATURE, ORGANISM, pH OPTIMUM, UNIPROT
pH Range (PHR): COMMENTARY, LITERATURE, ORGANISM, pH RANGE, UNIPROT
pH Stability (PHS): COMMENTARY, LITERATURE, ORGANISM, pH STABILITY, UNIPROT
pI Values (PI): COMMENTARY, LITERATURE, ORGANISM, pI VALUE, UNIPROT
Posttranslational Modification (PM): COMMENTARY, LITERATURE, ORGANISM, POSTTRANSLATIONAL MODIFICATION, UNIPROT
Organisms (PR): COMMENTARY, SEQUENCE DB, LITERATURE, ORGANISM, ORGANISM, UNIPROT
Purification (PU): PURIFICATION (Commentary), LITERATURE, ORGANISM, UNIPROT
Reactions (RE): COMMENTARY, LITERATURE, ORGANISM, REACTION, UNIPROT **bad**
Renatured (REN): RENATURED/Commentary, LITERATURE, ORGANISM, UNIPROT
References (RF): COMMENTARY, LITERATURE, REFERENCES
IUPAC Name (RN): ACCEPTED NAME (IUPAC)
Reaction Types (RT): REACTION TYPE
Specific Activity (SA): COMMENTARY, LITERATURE, ORGANISM, SPECIFIC ACTIVITY, UNIPROT
Systematic Name (SN): SYSTEMATIC NAME
Substrates/Products (SP): COMMENTARY (Substrate), COMMENTARY (Product), LITERATURE, ORGANISM, PRODUCT, REVERSIBILITY, SUBSTRATE, UNIPROT
Storage Stability (SS): STORAGE STABILITY, LITERATURE, ORGANISM, UNIPROT
Source Tissues (ST): COMMENTARY, LITERATURE, ORGANISM, SOURCE TISSUE, UNIPROT
Subunits (SU): COMMENTARY, LITERATURE, ORGANISM, SUBUNIT, UNIPROT
Synonyms (SY): COMMENTARY, LITERATURE, ORGANISM, SYNONYM, UNIPROT
Turnover Numbers (TN): COMMENTARY, LITERATURE, ORGANISM, SUBSTRATE, TURNOVER NUMBER, UNIPROT
Temperature Optima (TO): COMMENTARY, LITERATURE, ORGANISM, TEMPERATURE OPTIMUM, UNIPROT
Temperature Range (TR): COMMENTARY, LITERATURE, ORGANISM, TEMPERATURE RANGE, UNIPROT
Temperature Stability (TS): COMMENTARY, LITERATURE, ORGANISM, TEMPERATURE STABILITY, UNIPROT