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PreprintCC BYChemRxiv

ChemConnect: Making chemical identifier relationships and disagreements explicit and actionable

  • İlhan Mutlu1
  • Martin Krauss2
  • Emma L. Schymanski3
  • Jana Schor1,4,5
5 affiliations
  1. 1Department of Computational Biology and Chemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, Leipzig, Germany, 04318
  2. 2Department of Exposure Science, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, Leipzig, 04318
  3. 3Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Belvaux, Luxembourg, 4367
  4. 4Department of Computer Science, Faculty of Mathematics and Computer Science
  5. 5Leipzig University
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Abstract

Chemical identifiers serve as essential links between molecular structures, experimental measurements, biological activities, and regulatory information. Discrepancies can arise when independently curated databases assign different identifiers to the same substance, often due to curation inconsistencies or intentional differences in representing salts, solvates, protonation states, and stereochemistry. Here, we introduce ChemConnect, a provenanceaware graph framework designed to integrate chemical identifiers from NORMAN SusDat, EPA CompTox Chemicals Dashboard, and PubChem without resolving them to a single canonical chemical entity. The ChemConnect graph contains ∼8.5 million chemical identifier nodes and ∼7.5 million connections, of which ∼ 65 thousand are derived structural-parent and stereochemical relationships whose agreement with external references is systematically quantified. ChemConnect preserves the information supplied by each source and stores the derived relationships separately, so that users can see how each relationship was obtained. This allows users to compare sources, identify records whose identifiers contradict each other, and connect related records, such as a salt and its neutral form, that have no identifier in common.

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Cite

BibTeXRIS
BibTeX
@misc{mutlu2026chemconnect,
  title = {{ChemConnect: Making chemical identifier relationships and disagreements explicit and actionable}},
  author = {İlhan Mutlu and Martin Krauss and Emma L. Schymanski and Jana Schor},
  howpublished = {ChemRxiv},
  year = {2026},
  month = oct,
  doi = {10.26434/chemrxiv.15010940/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010940/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - ChemConnect: Making chemical identifier relationships and disagreements explicit and actionable
AU  - İlhan Mutlu
AU  - Martin Krauss
AU  - Emma L. Schymanski
AU  - Jana Schor
PY  - 2026
DA  - 2026/10/23
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15010940/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010940/v1
AB  - Chemical identifiers serve as essential links between molecular structures, experimental measurements, biological activities, and regulatory information. Discrepancies can arise when independently curated databases assign different identifiers to the same substance, often due to curation inconsistencies or intentional differences in representing salts, solvates, protonation states, and stereochemistry. Here, we introduce ChemConnect, a provenanceaware graph framework designed to integrate chemical identifiers from NORMAN SusDat, EPA CompTox Chemicals Dashboard, and PubChem without resolving them to a single canonical chemical entity. The ChemConnect graph contains ∼8.5 million chemical identifier nodes and ∼7.5 million connections, of which ∼ 65 thousand are derived structural-parent and stereochemical relationships whose agreement with external references is systematically quantified. ChemConnect preserves the information supplied by each source and stores the derived relationships separately, so that users can see how each relationship was obtained. This allows users to compare sources, identify records whose identifiers contradict each other, and connect related records, such as a salt and its neutral form, that have no identifier in common.
ER  -