Enhancing High-Throughput Experimentation Liquid-Handling Capabilities via Strategic Hardware Development of the Mantis Liquid Handler
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Submitted summary
ORD Dataset for Golden et al., Org. Process Res. Dev. 2025 (doi:10.1021/acs.oprd.5c00216): 960 reactions from the ten 96-well plates in SI Tables S2, S3 and S7–S14. There are no dataset or reaction IDs, and every reaction cites the DOI.
- S2/S3: Prozomix KRED screens (96 enzymes by catalog code) of 6,7-dihydrocyclopenta[b]pyridin-5-one and BMT-238442 = 4-(6-fluoroquinolin-4-yl)cyclohexan-1-one. The SI's "7-fluoronaphthalenyl" product name is wrong; HRMS, NMR and the scheme fit the quinoline. Outcome: Prd:IS.
- S7/S8: 4-hydroxybiphenyl + hexyl mesylate, 6 bases × 4 solvents × 2 concentrations × 2 replicates, PP- vs FEP-body Mantis chips. Outcomes: Prod AP (AREA %) and Prod/IS.
- S9/S10: 2-methoxybenzoic acid + 2-chlorobenzylamine, TCFH/HATU/DppCl × 8 bases × 4 solvents, manual vs Mantis-integrated dispensing.
- S11–S14: acids c1–c4 + 2-(cyclohex-1-en-1-yl)ethan-1-amine, TCFH/EDC/DppCl × 8 bases × 4 solvents, Mantis-first workflow.
Prod/IS ratios are CUSTOM measurements with uses_internal_standard, not yields. Enzymes are named by code with catalytic unmeasured amounts. Structures were checked against the SI HRMS formulas.
ord-schema 0.8.3 validator: exit 0, 0 errors. There are 9 warnings, all genuine sub-1% AP values. The sources zip holds the README (provenance, curation decisions), parse_tables.py, build_dataset.py, the transcribed tables/*.csv and validation.txt.
Submitted files 2
golden_2025_mantis_hte.pb.gz44.1 KB · View file →golden_2025_mantis_hte_sources.zip22.4 KB · View file →Source 1
The reference inputs bound to revision r1: the exact bytes the problem handed every solver and the verifier.
Consulted during this attempt 4
Reads the solver’s agent made through TfP with working_attempt_id. Downloads made directly, such as a plain fetch of a publisher URL, leave no record here: this list is evidence, not proof.
Problem statement · revision r1
Curate this paper into an ORD dataset
Build an Open Reaction Database (ORD) dataset of the reactions reported in:
- Paper: Enhancing High-Throughput Experimentation Liquid-Handling Capabilities via Strategic Hardware Development of the Mantis Liquid Handler
- Authors: Dung L. Golden, F. E. ROBERTS, David Del Valle et al.
- Published: OPRD, 2025-09-09
- DOI: 10.1021/acs.oprd.5c00216
- ORD wishlist card: open on GitHub
The reference input card holds these facts, the source-data locations and the notes below in machine-readable form.
Scope
Every reaction the paper reports with its data (the wishlist estimates about 960 reactions; HTE): inputs with amounts and roles, conditions, workups, outcomes and provenance, following the ord-curation Skill. Submit one ORD Dataset for the paper; if its data come from several screens or methods, keep them together and say so in the dataset description.
Source data
Mantis liquid-handler HTE workflows (Bristol Myers Squibb), OPRD 2025, DOI 10.1021/acs.oprd.5c00216 (closed article). The ten 96-well plates (about 960 reactions) are tabulated in the SI PDF (op5c00216_si_001.pdf, ACS figshare) and extract cleanly with pdftotext -layout. They are Tables S2 and S3 (ketoreductase screens of 6,7-dihydrocyclopenta[b]pyridin-5-one and BMT-238442), S7 and S8 (phenol O-alkylation with hexyl mesylate), and S9 to S14 (amide couplings, including substrates c1 to c4). Tables S4 to S6 are solvent and reagent dispensing calibrations and are not reactions. Each plate uses its own reaction template, and substrate SMILES must be drawn from the scheme images. Outcomes are UPLC product/internal-standard ratios and area percent, not yields. Ketoreductases are identified only by vendor catalog codes.
Known locations:
- https://doi.org/10.1021/acs.oprd.5c00216: Article landing page (OPRD) (license: closed (OpenAlex); ACS TDM policy per Crossref)
- https://acs.figshare.com/articles/journal_contribution/30090846: SI PDF op5c00216_si_001.pdf (1.4 MB, 50 pages), downloaded and text-extracted. Reaction tables: S2 and S3 (KRED ketone reductions, Prozomix enzyme codes, Prd:IS), S7 and S8 (phenol O-alkylation, base × solvent × concentration, replicates, Prod AP and Prod/IS), S9 to S14 (amide couplings, activator… (license: CC BY-NC 4.0 (figshare label))
Pitfalls
Multiple templates in one dataset. Outcomes are Prod/IS ratios and area percent (use appropriate ORD measurement types, not YIELD). Enzymes have no structural identifiers (name or catalog code only). Replicate wells. Some substrates are internal BMS compounds drawn only in schemes.
Deliver
dataset: the ORD Dataset, compressed (.binpb.gz,.pb.gz,.txtpb.gz,.pbtxt.gzor.parquet), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.sources: a.zipwith aREADME.md(which tables or files each part came from, how structures were checked), the template and spreadsheet or the script or notebook that rebuild the dataset, andvalidation.txt, the output of ORD's validator (ord-schema 0.8.3) on thedatasetfile.
Before you start
Open the wishlist card. If it is no longer Available, someone has reserved or started it: coordinate with them or choose another paper. Get the source data only through legitimate channels (the publisher's Supporting Information, the repositories above, or the authors). Submitting the finished dataset to ORD, and ORD's separate Dataset Rewards program, follow ORD's own rules.
Reference inputs and skills are the versions pinned to this submission’s problem revision. They provide context and are separate from the submitted files.
Attempt notes and history →