UPSTREAM: evidence-led, ledgered contribution to open metabolomics software, and what a corpus-wide name screen of MassBank found
4 affiliations
- 1Independent Researcher
- 2Department of Pharmaceutical and Medicinal Chemistry
- 3Veritas University Abuja
- 4University of Abuja
Abstract
Metabolomics depends on a small set of open projects—spectral libraries such as MassBank and GNPS, and processing software such as matchms and the RforMassSpectrometry packages—maintained largely by volunteers. Outside contributions can strengthen them or consume their maintainers’ time, and claims about how much someone has contributed are rarely verifiable. We describe UPSTREAM, a program that makes both problems explicit: every contribution must start from reproducible evidence and pass a ten-rule protocol, and the program’s headline count is computed from GitHub as merged pull requests only, never typed. We report the program’s first phase in full. A name-shape screen of all 139,006 records in MassBank 2026.03 flagged 1,480 names, of which 120 were defects (precision 8.1%), nearly all of them one collection’s internal identifiers. A name–structure screen that parsed 41,822 distinct names with OPSIN found 83,737 of 86,808 assessable records consistent (96.46%) and 3,071 candidate mismatches. Hand adjudication of 60 cases sampled from the two most suspicious strata found 58.3% to be screen artefacts, and confirmed 13 records (8 compounds) whose structure is a different compound from the one named; for six of the eight, the precursor m/z or the EI ions support the name. The same screen exposed a defect in matchms itself: clean_compound_name truncates 5 of 41,822 MassBank names, and a one-line fix truncates none. Phase 1 closed with 5 complete contribution packets (duplicate searches and author review still to do before filing), one item reopened when the target’s own documentation contradicted our premise, and two items closed because no failing case could be shown. The ledger stands at n = 0 merged contributions, because filing is the author’s step and had not yet happened. All screens, packets and derivations are openly available.
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BibTeX
@misc{erumiseli2026upstream,
title = {{UPSTREAM: evidence-led, ledgered contribution to open metabolomics software, and what a corpus-wide name screen of MassBank found}},
author = {Oshoma Erumiseli and Bila Hassan Ali and Dauda Garba},
howpublished = {ChemRxiv},
year = {2026},
month = oct,
doi = {10.26434/chemrxiv.15010451/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010451/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - UPSTREAM: evidence-led, ledgered contribution to open metabolomics software, and what a corpus-wide name screen of MassBank found
AU - Oshoma Erumiseli
AU - Bila Hassan Ali
AU - Dauda Garba
PY - 2026
DA - 2026/10/14
PB - ChemRxiv
DO - 10.26434/chemrxiv.15010451/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010451/v1
AB - Metabolomics depends on a small set of open projects—spectral libraries such as MassBank and GNPS, and processing software such as matchms and the RforMassSpectrometry packages—maintained largely by volunteers. Outside contributions can strengthen them or consume their maintainers’ time, and claims about how much someone has contributed are rarely verifiable. We describe UPSTREAM, a program that makes both problems explicit: every contribution must start from reproducible evidence and pass a ten-rule protocol, and the program’s headline count is computed from GitHub as merged pull requests only, never typed. We report the program’s first phase in full. A name-shape screen of all 139,006 records in MassBank 2026.03 flagged 1,480 names, of which 120 were defects (precision 8.1%), nearly all of them one collection’s internal identifiers. A name–structure screen that parsed 41,822 distinct names with OPSIN found 83,737 of 86,808 assessable records consistent (96.46%) and 3,071 candidate mismatches. Hand adjudication of 60 cases sampled from the two most suspicious strata found 58.3% to be screen artefacts, and confirmed 13 records (8 compounds) whose structure is a different compound from the one named; for six of the eight, the precursor m/z or the EI ions support the name. The same screen exposed a defect in matchms itself: clean_compound_name truncates 5 of 41,822 MassBank names, and a one-line fix truncates none. Phase 1 closed with 5 complete contribution packets (duplicate searches and author review still to do before filing), one item reopened when the target’s own documentation contradicted our premise, and two items closed because no failing case could be shown. The ledger stands at n = 0 merged contributions, because filing is the author’s step and had not yet happened. All screens, packets and derivations are openly available.
ER -