A list of antibiotics compiled by Nikiforos Alygizakis (EI/Uni Athens) as part of the Marie Curie-Sklodowska Action Initial Training Network (MSCA ITN) ANSWER (http://www.answer-itn.eu/). See Paulus et al 2019 DOI: 10.1016/j.ijheh.2019.01.004. An additional suspect list of human phase-I antibiotic metabolites, created with BioTransformer (v3.0.0) was provided by Tim Jonkers (VU, NL); Jonkers et al 2023 DOI: 10.1016/j.chemosphere.2023.138093 and is available on the SLE website. Dataset DOI: 10.5281/zenodo.2621956.

v0.2.0: added the CYP Metabolites Step 1 files.

University of Athens Surfactants and Suspects List from Gago-Ferrero et al. 2015. DOI: 10.1021/acs.est.5b03454. Dataset DOI: 10.5281/zenodo.2621979

A list of Swiss insecticides, fungicides and TPs, included as Table S1 from Moschet et al. 2013. DOI: 10.1021/ac4021598. Dataset DOI: 10.5281/zenodo.2623740.

Parent-Transformation Product Pairs of various micropollutants from Eawag: Swiss Federal Institute for Aquatic Science and Technology (https://www.eawag.ch/en/), described in Schollee et al 2017 DOI:10.1007/s13361-017-1797-6 . Dataset DOI: 10.5281/zenodo.3754448.

Update 23/04/2020: fixed names, added synonym columns and classification information.
Update 15/05/2020: adjusted classification information following feedback from Juliane.
Update 13/01/2023: adjusted selected BT entries based on feedback from Emma Palm.
Update 07/02/2023: adjusted selected BT entries to fix 4-Me-BT issues. 

HSDBTPS is a list of metabolites / transformation products extracted from the "Metabolites/Metabolism" section from HSDB (Hazardous Substance Data Bank) in PubChem (https://pubchem.ncbi.nlm.nih.gov/source/11933). Dataset DOI: 10.5281/zenodo.3827487.

Entries automatically extracted from HSDB are manually validated to remove mismatching CIDs, and add additional CIDs not captured using the descriptions provided. Files are created with a default to not import any data until this has been checked. Please report any mismatches, despite best efforts it is possible that errors are present, all files are under version control so that entries can be corrected/updated/enhanced over time and recommitted.

Recent uploads (2022 and later) are handled with ShinyTPs (code + article from Palm et al 2023 DOI:10.1021/acs.estlett.3c00537). The original code associated with this deposit is located here. 

Updates:

16 May 2020: Added the source file (extract of all HSDB Metabolites/Metabolism entries as is from JSON file), plus an updated S68_HSDBTPS_StructInfoOnly.csv with one new structure and renamed to include S68, plus the first draft of the Transformations table. 28 May 2020: added InChIKey and DIXSID files. 11 June 2020: added updated Transformations and Structure files to contain new CIDs and resulting reactions from new PubChem registrations. Dec 23, 2022: first dataset from Emma Palm added, using her TP curation app. DTXSID file dropped. 23 Mar 2023: added Biosystem and Enzyme columns, filling in biosystem where appropriate. 24 Mar 2023: new azo dye reactions from Emma Palm added. 1 Apr 2023: more azo dye reactions from Emma Palm. 4 Apr 2023: added new CIDs. 27 June 2023: added many new substances, including new CIDs. 28 June 2023 added transformations, 30 June 2023 added new CIDs. 11 July added missing CIDs to transformations table. 18 Nov 2023: added new reactions from Jolly Komolo (no new CIDs). 1 Dec 2023: new reactions from Marie, incl. two new CIDs. 19 Dec 2023: new reactions from Marie, incl. 1 new CID, updated CIDs from Dec 1. 29 April 2024: new reactions from Marie, CID updated. 16 July 2024: added reactions from Olga. 26 July 2024: added BPA=>MBP. 6 Aug 2024: adjusted many triazine names, added one new reaction. 27 Nov 2024: added Griseofulvin reactions. 8 Feb 2025: added Sertraline TP. 14 Mar 2025: added missing CID for O-Demethyl phosphamidon.

HBM4EU CECscreen is a suspect screening list for Chemicals of Emerging Concern (CECs) plus metadata and predicted Phase 1 metabolites. CECScreen is part of the HBM4EU project (coord. UBA) > WP16 "emerging chemicals" (lead INRA, JP Antignac/L Debrauwer) > Task 16.1 (lead IRAS, J Vlanderen / R Vermeulen) > Main contributor (J Meijer) > Involved Partners (M Lamoree, T Hamers, S Hutinet, A, Covaci, C Huber, M Krauss, DI Walker, EL Schymanski). Further details in Meijer et al (2021) DOI: 10.1016/j.envint.2021.106511. Dataset DOI: 10.5281/zenodo.3956586.

Update 23/7/2020 (v0.1.1): updated MetFrag files to remove elements causing errors (Os, Pd, Ag, Be). Update 8 Nov 2022 (v0.1.2) removed new lines in several synonyms as detected at BioHackEU22.

The Metabolite Reaction Database, MetXBioDB, is a biotransformation database used to improve the knowledge- and machine learning-based systems of BioTransformer (http://biotransformer.ca/) by Djoumbou-Feunang et al (2019), DOI: 10.1186/s13321-018-0324-5. Dataset DOI: 10.5281/zenodo.4056560.

This dataset is extracted from the database behind BioTransformer (http://biotransformer.ca/) by Yannick Djoumbou-Feunang, David S. Wishart and colleagues, for addition to the PubChem Transformations section. Change logs and version tracking at the ECI GitLab site.

Change log: 13 Oct: added InChIKey file. 16 Oct: updated substances with missing CIDs and transformations. 5/11 many bug fixes finally committed, added DTXSIDs. 22/6/2023 adjusted one CID that changed upon PubChem standardization. 15 Nov 2023: fixed typo in reaction description. 26 Feb 2024: corrected name for CID 65564. 6 Aug 2024: fixed many triazine synonyms.

This dataset is designed to provide an entry point for users to contribute transformation products and reactions documented in the literature for addition to the NORMAN SLE and PubChem Transformations section. Dataset DOI: 10.5281/zenodo.4318838.

Change logs and version tracking at the ECI GitLab site.

Change log: v0.0.2 added InChIKey file. v0.1.0 added new reactions from Anca Baesu and DTXSIDs. v0.2.0 added PFAS TPs from Parviel Chirsir. v0.2.1 more PFAS TPs from Parviel. v0.3.0 Emma added HMMM TPs; v0.3.1 updated references and added new CIDs; added new MS/MS file. v0.4.0 new PFAS TPs plus MS/MS and NMR. v0.4.1 new CID added, plus CID 67543 updated to 14571268. v0.5.0 new 8:2 FT TPs plus annotation data; new structures. v0.5.1 added new CIDs. v0.5.2 added 2:2 to 6:2 FT TPs, updated ref for Bugsel. v0.5.3: added new CIDs. v0.6.0 added new structures. v0.7.0 added more new structures. v 0.7.1: updated CIDs in substances, fixed PFHpA mapping in transformations (some were mismapped to CID 67819). v 0.7.2: updated Biosystem description for many records. v0.8.0: updated CID 163201609 => 166001338, adjusted last 4 MS/MS, added Barisci AOP transformations. v0.9.0 added new structures. v0.9.1 updated CIDs and added radical structures from deposition. v0.10.0 added new irgarol reaction; v0.10.1 added new CID. v0.11.0 added Avendano and Mabury transformations from Parviel. v0.12.0 added Washington MS/MS and Marjanovic MS/MS and reactions. v0.13.0 added Galaxolide transformation. v0.14.0 added Zweigle PFAS TPs with MSMS. v0.14.1 added new CIDs. v0.15.0 added antibiotic TPs from Paul Löffler, SLU, incl. entries with no CID. v0.15.1 added new CIDs. v0.16.0 added benzothiazole reactions. v0.17.0 added TooCOLD TPs from Rick. v0.18.0 added new TFA reactions. v0.19.0 added pak choi reactions, several with no CID. v0.19.1 added new CIDs. v0.20.0 added dimers from Li Ji. v0.20.1 added new CIDs. v0.21.0 added the EJ Weber PFAS libraries "EnvLib" and "MetaLib", curation by Parviel and Emma. Some new CIDs to come. v0.21.1: fixed char issues in substance & transformation files. v0.21.2 added new CIDs. v0.22.0 added "Class_parent" column to the substance deposition file to aid annotation. v0.23.0: added Parviel's zebrafish entries. v0.24.0: added Lingmin Jin, Shiyang Chen & Li Ji's atrazine data. v0.24.1: added new CIDs. v0.24.2 added new SMILES, IK and CID for simetryn-sulfanuride=> simetryn-thioperoxol.

Suspect list of pesticides and pesticide transformation products (TPs) from SLU, created based on Sweden's national monitoring program and the pesticide properties database (PPDB) described in Frank Menger et al (2021) DOI: 10.1021/acs.est.1c00466. Dataset DOI: 10.5281/zenodo.4687924.

Updates: 27 Apr. 2021 - added new CIDs, replaced InChIKey file with *.txt version not *.inchikey. 10 May: added missing reference fields to transformations file. May 2023: updated 4 entries with new SMILES/CIDs according to feedback from PubChem. April 2025: reverted 1 CID back to a new (old) preferred form due to annotation disappearing. 2 Jun 2025: adjusted TFA synonym.

A library containing the collision cross section (CCS) values of 311 adducts of 148 contaminants of emerging concern (CECs) and their metabolites measured with drift tube ion mobility high resolution mass spectrometry (in positive and negative ionization modes with N2 as drift gas) as described in Belova et al. (2021) DOI: 10.1021/acs.analchem.1c00142. Dataset DOI: 10.5281/zenodo.4704648.

Changes: 27/04/2021 added new CIDs from deposition. 10/5/2021: added transformations table. 30/8/2022: corrected [M+H]+ for BDCIPP (CID 188119) to 157.35 A^2 (from 178.72) upon request of the authors (see Belova et al. (2022) DOI: 10.1016/j.aca.2022.340361).