Contribute data

Use our FAIR CSV template to contribute your transformation reaction data and help expand the database for the research community.

We encourage the community to contribute data from their own transformation reaction studies to the FAIR-TPs database. This is essential in order to make new transformation product data available in a FAIR format where others easily can re-use the reactions with their own workflows. In addition making your data available on the FAIR-TPs website also helps you make your data visible to more people. All reactions in our database contain references to the original data source and where applicable to associated publications. Below follows a guide on how to provide data to our database.

Contact us FAIR CSV Template
1

Download Template

Get our FAIR CSV template with all required fields for transformation data submission.

2

Fill Your Data

Add your transformation reactions with SMILES, PubChem CIDs, and proper references.

3

Submit & Review

Send your data via email and our team will review and integrate it into the database.

Template Field Guide

Interactive guide to understand each field in our FAIR CSV template

Template Comparison
Live Examples
Field Descriptions

Real Data Examples

Atrazine → Hydroxyatrazine
Propachlor → Metabolite
Bromoxynil → Degradation
Environmental degradation of Atrazine: This example shows how the herbicide Atrazine undergoes hydroxylation in environmental conditions.
Predecessor_CID,Predecessor_Name,Predecessor_SMILES,Transformation,Successor_CID,Successor_Name,Successor_SMILES,Enzyme,Gene_ID,Protein_ID,Biosystem,Reference_ID,Reference_Description 2256,Atrazine,CC1=NC(=NC(=N1)Cl)NC(C)C,Hydroxylation,2257,Hydroxyatrazine,CC1=NC(=NC(=N1)Cl)NC(C)C,,,Environmental,10.1093/exposome/osab006,Schymanski et al. (2022) - Environmental transformation pathways
Propachlor metabolism: This example shows the transformation of Propachlor herbicide in soil matrices.
Predecessor_CID,Predecessor_Name,Predecessor_SMILES,Transformation,Successor_CID,Successor_Name,Successor_SMILES,Enzyme,Gene_ID,Protein_ID,Biosystem,Reference_ID,Reference_Description 4931,Propachlor,CC1=CC=C(C=C1)N(C)C(=O)CCl,Dechlorination,,Propachlor_metabolite,CC1=CC=C(C=C1)N(C)C(=O)C,,,Soil,10.1186/s12302-022-00680-6,Mohammed Taha et al. (2022) - Soil transformation studies
Bromoxynil degradation: This example shows the degradation pathway of Bromoxynil herbicide.
Predecessor_CID,Predecessor_Name,Predecessor_SMILES,Transformation,Successor_CID,Successor_Name,Successor_SMILES,Enzyme,Gene_ID,Protein_ID,Biosystem,Reference_ID,Reference_Description 1234,Bromoxynil,CC1=CC=C(C=C1)Br,Debromination,,Bromoxynil_degradate,CC1=CC=C(C=C1)O,,,Water treatment,10.1093/exposome/osab006,Environmental degradation pathways study

Complete Field Reference

Detailed descriptions of all fields in the FAIR CSV template to help you provide accurate and complete data.

Compound Information
Predecessor_CID
PubChem compound identifier (CID) for the precursor compound. Find this on the compound's PubChem page. Leave blank if the compound is not in PubChem.
Optional
Predecessor_Name
Common or IUPAC name of the precursor compound.
Required
Predecessor_SMILES
SMILES notation for the precursor compound structure. Can be found on PubChem or generated using chemical drawing tools like BIOVIA Draw.
Required
Successor_CID
PubChem compound identifier (CID) for the transformation product. Leave blank if the product is not in PubChem.
Optional
Successor_Name
Common or IUPAC name of the transformation product.
Required
Successor_SMILES
SMILES notation for the transformation product structure. Required for all transformation products.
Required
Reaction Details
Transformation
Description of the chemical transformation (e.g., "Hydroxylation", "Dechlorination", "Oxidation").
Optional
Enzyme
Name of the enzyme involved in the reaction (for biotic reactions only). Leave blank for abiotic reactions or if unknown.
Optional
Biological Information
Gene_ID
NCBI GeneID for the gene encoding the enzyme. Leave blank for abiotic reactions or if unknown.
Optional
Protein_ID
NCBI ProteinID for the protein/enzyme. Leave blank for abiotic reactions or if unknown.
Optional
Biosystem
Where the transformation occurs (e.g., "Environmental", "Human", "Water treatment", "Soil"). Leave blank if unknown.
Optional
References
Reference_ID
DOI or PMID of the related publication. Essential for data provenance and validation.
Required
Reference_Description
Additional reference information including author names, paper title, and publication details.
Required
Important Tips
  • SMILES identifiers are required for all compounds and can be generated using chemical drawing tools
  • PubChem CIDs are optional but recommended when available for better data integration
  • For abiotic reactions, leave enzyme, gene, and protein fields blank
  • Always provide proper references to ensure data traceability
  • Use consistent naming conventions for compound names and transformations

FAIR CSV Template

Recommended
  • Simple and standardized format
  • Compatible with all major tools
  • Easy to fill and validate
  • Direct integration with FAIR-TPs
  • Minimal required fields

BART Template

Advanced
  • Extensive experimental documentation
  • Detailed reaction conditions
  • Water/soil matrix specific
  • Compatible with enviPath
  • More comprehensive metadata

Ready to Submit?

Once you've filled out either template with your transformation data, submit it to our team for review and integration into the FAIR-TPs database.

Contact us to submit
Contributors
LCSB-university of luxembourg Norman SLE Eawag ChemBL Zenodo University of Alberta Swedish University of Agricultural Sciences (SLU) University of Antwerp IISPV–URV (Institut d'Investigació Sanitària Pere Virgili Universitat Rovira i Virgili, Spain PubChem LCSB-university of luxembourg Norman SLE Eawag ChemBL Zenodo University of Alberta Swedish University of Agricultural Sciences (SLU) University of Antwerp IISPV–URV (Institut d'Investigació Sanitària Pere Virgili Universitat Rovira i Virgili, Spain PubChem

See How It Works: Chemical Transformations

Click on molecules to see how they transform in our database

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FAIR CSV Template

Download and use our standardized template with fields for SMILES, CIDs, enzymes, and references to ensure data consistency.

Simple Process

Fill out the template with your transformation data, include proper references, and submit via email for integration.

Community Impact

Your contributions help expand the database and make transformation data more accessible to researchers worldwide.

PubChem Integration

Seamlessly link to PubChem compound identifiers and access comprehensive chemical information.

SMILES Support

Use standard SMILES notation for chemical structures, compatible with all major chemistry tools.

Enzyme Data

Include enzyme information, gene IDs, and protein IDs for comprehensive reaction documentation.