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PreprintCC BY 4.0BioHackrXiv

DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms

  • Hidemasa Bono
  • Naoya Oec
  • Haruka Tanimoto
  • Tomohiro Taguchi
  • Amane Kurata
  • Ryo Nozu
Open at sourcePDFDOICite

Abstract

We report progress on Quest for Pathways with eXpression (QPX), a pathway analysis environment for non-model organisms, developed during the DBCLS BioHackathon 2026 (BH26). Building on prior BH23/BH25 work, we demonstrated PathLift, a tool that lifts WikiPathways GPML pathways to other species via ortholog mapping, using an Arabidopsis-to-rice mitochondrial complex I example. We also created annotated pathway maps in QPX integrating transcriptome/proteome data for hypoxic stress response, and transcriptome/metabolome data for the non-model organism Symplocarpus renifolius, which lacks an established gene ID system. This clarified data-formatting requirements for linking QPX maps to expression tables and surfaced a string-identifier handling issue in QPX's backend, reported upstream. Future work includes reproducible ChEBI ID assignment, automated pathway digitization, and compound-centered functional networks from PubChem/PubTator3 data.

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Cite

BibTeXRIS
BibTeX
@misc{bono2026dbcls,
  title = {{DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms}},
  author = {Hidemasa Bono and Naoya Oec and Haruka Tanimoto and Tomohiro Taguchi and Amane Kurata and Ryo Nozu},
  howpublished = {BioHackrXiv},
  year = {2026},
  month = sep,
  doi = {10.37044/osf.io/7egfm_v1},
  url = {https://osf.io/preprints/biohackrxiv/7egfm_v1/},
  note = {CC BY 4.0},
}
RIS
TY  - UNPB
TI  - DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms
AU  - Hidemasa Bono
AU  - Naoya Oec
AU  - Haruka Tanimoto
AU  - Tomohiro Taguchi
AU  - Amane Kurata
AU  - Ryo Nozu
PY  - 2026
DA  - 2026/09/19
PB  - BioHackrXiv
DO  - 10.37044/osf.io/7egfm_v1
UR  - https://osf.io/preprints/biohackrxiv/7egfm_v1/
AB  - We report progress on Quest for Pathways with eXpression (QPX), a pathway analysis environment for non-model organisms, developed during the DBCLS BioHackathon 2026 (BH26). Building on prior BH23/BH25 work, we demonstrated PathLift, a tool that lifts WikiPathways GPML pathways to other species via ortholog mapping, using an Arabidopsis-to-rice mitochondrial complex I example. We also created annotated pathway maps in QPX integrating transcriptome/proteome data for hypoxic stress response, and transcriptome/metabolome data for the non-model organism Symplocarpus renifolius, which lacks an established gene ID system. This clarified data-formatting requirements for linking QPX maps to expression tables and surfaced a string-identifier handling issue in QPX's backend, reported upstream. Future work includes reproducible ChEBI ID assignment, automated pathway digitization, and compound-centered functional networks from PubChem/PubTator3 data.
ER  -