MetXBioDB Metabolite Biotransformations by Kaggle | Other

About this Dataset

MetXBioDB Metabolite Biotransformations

Enzyme-Catalyzed Metabolism Insights

About this dataset

Welcome to the MetXBioDB, a comprehensive collection of biotransformation reactions and metabolite information from the BioTransformer database. With this data set, researchers can gain insight into the incredibly complex biochemical processes involved in the transformation and metabolism of metabolites.

The MetXBioDB comprises three separate files: metxbiodb.csv, substances.csv, and authorslists.csv. The metxbiodb file contains data regarding both substrate and product names or identifications, enzymes present in the biotransformations, types of reaction (e.g oxidation-reduction), types of biotransformation (eğhydroxylation etc.), biosystem in which it occurs ,product&substrate inchikey tags and name/reference citations used for individual experiments & results derived from them . On the other hand substances file contains metabolite properties such as molfile (& molblock), InchIKey/Inchi/, Pubchem cid numbers., along with there molecular structure represented by SMILES , Synonym1 & Synonym2 string values Also Authors list File simply contains author names associated with different reactions In general this meta: bio-chemical data provides a much sought after peek into natural information processing systems found in organisms

Researching metabollites is an incredibly complex field– Never fear! With MetXBioDB you can feel confident that you have access to all necessary data for researching everything from bio-transformations enzyme catalyzed oxidations/ reductions to metabolic pathway maps along with corresponding reference facts like powerpoints or tedx talks or academic articles!. Go forth armed with insight – unleash your potential today!

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How to use the dataset

This dataset contains biotransformation reactions and metabolite information extracted from the BioTransformer database, designed to aid researchers in gaining insight into the enzymes and biochemical processes responsible for the transformation and metabolism of metabolites. In this dataset, you have several columns that provide information about each metabolic reaction:

Substrate Name: This column contains the name of the substrate (the starting material) undergoing biotransformation.

Substrate InChIKey: This column provides a unique identifier for each substrate - its InChIKey value.

Enzyme: The enzyme associated with the reaction is given here.

Reaction Type: The type of reaction occurring is specified, such as oxidation or reduction.

Biotransformation Type: Types of biotransformations include hydroxylation, methylation etc.

Biosystems: This will provide indication what type of cell or organism is responsible for carrying out this particular transformation process.

Product Name/InChIKey/SMILES/Synonym1/Synonym2 : Information on product (end result) including its name ,InChikey value ,SMILES string etc are provided in respective columns .

Reference : A reference to study providing information about this chemical transformation .

To use this dataset effectively one can take help from following resources which are available online -

1.)PubChem(https://pubchem.ncbi.nlm.nih.gov/) - Here one can search by common name or by InchiKey ,smiles string to get structures related results like drug names having same structures and other similar metabolites .This will be helpful to distinguish between substrates used in this synthesis processes as some substrates may just differ slightly but would alter end result completely depending upon their structure so it's important to look at their basic molecule structure while performing synthesis experimentation .

2.)Uchida Database(http://uchida-biotranzfileset02e03a03a01a00x00x0003k012feo6f0_fullset_corr_map2str1str2str3str4mmolprd01cafr01fr02extvini04redivini05classspec06stereo07altrep09atommap10htl12hlacp13iserocdis1500opbt1550space1700arylsys1800int

Research Ideas

Identifying Sources of Metabolic Variability: This dataset can be used to examine genes and enzymes that are responsible for metabolite biotransformation reactions and analyze the link between genetic polymorphisms and metabolic adaptations.

Understanding Drug Interactions: This dataset can be used to explore how different drugs interact with metabolites in the human body by examining their biotransformation reactions as catalyzed by enzymes.

Informatics-Assisted Identification of Bioactive Metabolites: By extracting information on metabolites present in a certain organism or system, this dataset could aid in identifying drug-targetable biomolecules or biologically active compounds which could further be validated by laboratory experiments or clinical trials

Acknowledgements

If you use this dataset in your research, please credit the original authors.
Data Source

License

License: CC0 1.0 Universal (CC0 1.0) - Public Domain Dedication
No Copyright - You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. See Other Information.

Columns

File: metxbiodb.csv

Column name	Description
substrate_name	Name of the substrate involved in the biotransformation reaction. (String)
substrate_inchikey	InChIKey of the substrate involved in the biotransformation reaction. (String)
enzyme	Enzyme responsible for the biotransformation reaction. (String)
reaction_type	Type of reaction (e.g., oxidation or reduction). (String)
biotransformation_type	Type of biotransformation (such as hydroxylation or methylation). (String)
biosystem	Biosystem in which the biotransformation reaction occurs. (String)
prod_name	Name of the product of the biotransformation reaction. (String)
prod_inchikey	InChIKey of the product of the biotransformation reaction. (String)
reference	Reference source for the specific reaction. (String)

File: MetXBioDB_substances.csv

Column name	Description
Name	The name of the metabolite. (String)
InChIKey	The InChIKey of the metabolite, which is a unique identifier for the metabolite. (String)
SMILES	The SMILES code of the metabolite, which is a unique identifier for the metabolite. (String)
Synonym1	An alternate name for the metabolite. (String)
Synonym2	An alternate name for the metabolite. (String)

Acknowledgements

If you use this dataset in your research, please credit the original authors.
If you use this dataset in your research, please credit .

Tables

Metxbiodb

@kaggle.thedevastator_metxbiodb_metabolite_biotransformations.metxbiodb

436.35 KB
2133 rows
14 columns


CREATE TABLE metxbiodb (
  "biotid" VARCHAR,
  "substrate_name" VARCHAR,
  "substrate_cid" VARCHAR,
  "substrate_inchikey" VARCHAR,
  "substrate_inchi" VARCHAR,
  "enzyme" VARCHAR,
  "reaction_type" VARCHAR,
  "biotransformation_type" VARCHAR,
  "biosystem" VARCHAR,
  "prod_name" VARCHAR,
  "prod_cid" VARCHAR,
  "prod_inchikey" VARCHAR,
  "prod_inchi" VARCHAR,
  "reference" VARCHAR
);