Frequently Asked Questions
Quick answers about the data, the graph, and how to use the site.
What is FAIR-TPs?
FAIR-TPs is a web interface to browse transformation products (TPs) and metabolites collated from open resources. It emphasizes transparent provenance, reuse, and exportability.
Where does the data come from?
From the “Transformations in PubChem” dataset on Zenodo (CC BY 4.0). We use Transformations_CID_Info_all.csv (compounds) and PubChem_all_transformations_wExtraInfo.csv (reactions).
Which identifiers can I search by?
Name, SMILES, InChI, InChIKey, CID. Substructure search accepts SMARTS (server-side RDKit).
How are reaction directions defined?
Edges are directed as predecessor → successor. Explore direct neighbours or load the full subgraph; use “Shortest Pathway” to find the minimal number of steps.
Can I download subsets?
Yes. Export compounds and reactions as CSV/XLSX, plus MetFrag-ready CSVs. Headers are stable for reproducibility.
How are compound names chosen?
Per-CID display names use a majority-frequency rule with a tie-break (shorter label, then alphabetical). Other names remain as aliases (e.g., 6:2 FTOH for PFAS entries).
How often is FAIR-TPs updated?
Whenever a new Zenodo release is available, the ETL pipeline can be re-run and the site refreshed. Counts and charts on the Stats page update accordingly.
How should I cite FAIR-TPs?
Please cite the FAIR-TPs preprint (B. Mayahi, EH Palm & EL Schymanski, Browsing FAIR Transformation Product Information with FAIR-TPs, 2025, Chemrxiv, DOI: 10.26434/chemrxiv-2025-lgbnq) and the FAIR-TPs website (B. Mayahi, EH Palm & EL Schymanski, FAIR-TPs website, 2026, https://fairtps.lcsb.uni.lu/. Accessed DD-MM-YYYY.). The manuscript is currently under revision.
How should I cite FAIR-TPs datasets?
To cite individual datasets in FAIR-TPs, please cite the Zenodo dataset (see "Dataset DOI" in the reaction display) and the related publication indicated in the "Evidence DOI" field. Additional source information (see the source files in the downloads) can be cited if appropriate. Please also cite the FAIR-TPs article if this website was the entry point to the data (see other citation FAQ entry).
What is the license?
Datasets are released under a CC-BY-4.0 license, unless indicated otherwise. EAWAG-BBD is CC-BY-NC-SA-4.0. License information can be found on individual datasets in Zenodo, on display in FAIR-TPs and is also listed on the Stats page.
Can I contribute corrections or new reactions?
Yes. Use the FAIR CSV template linked on the About page and contact us. We welcome community datasets and corrections.