Curate this paper into an ORD dataset

Build an Open Reaction Database (ORD) dataset of the reactions reported in:

• Paper: ‘Chemistry at the speed of sound’: automated 1536-well nanoscale synthesis of 16 scaffolds in parallel
• Authors: Li Ting Gao, Shabnam Shaabani, Atilio Reyes Romero et al.
• Published: Green Chemistry, 2023-01-17
• DOI: 10.1039/D2GC04312B
• 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 1,536 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

Green Chemistry 2023, 25, 1380 (DOI 10.1039/D2GC04312B). The article is CC BY 3.0 and its PMC open-access copy (PMC9940305) is CC BY. It reports automated acoustic-dispensing nanoscale synthesis in a 1536-well plate across 16 multicomponent-reaction scaffolds. The only SI is one PDF (GC-025-D2GC04312B-s001.pdf), and its outcomes are plate maps with qualitative calls (high / medium / none). No machine-readable dataset or repository deposit was found. To curate it, map every well to its building blocks and scaffold, then write the qualitative outcome as a product measurement. Structured well-level data from the authors would make this far more reliable than reading plate-map images.

Known locations:

• https://pmc-oa-opendata.s3.amazonaws.com/PMC9940305.1/GC-025-D2GC04312B-s001.pdf: The only SI file: a PDF with the 1536-well plate maps and qualitative outcome calls. Listed in the PMC OA metadata but not downloaded. (license: CC BY (PMC OA subset license_code; Crossref gives CC BY 3.0 for the article))
• https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9940305/fullTextXML: Full-text XML (PMC9940305). It lists one supplementary PDF and no data deposit. (license: CC BY 3.0 (article))
• https://pubs.rsc.org/en/content/articlelanding/2023/gc/d2gc04312b: Publisher landing page. It returned a Cloudflare bot challenge, so it was not inspected. (license: CC BY 3.0 (article, per Crossref))

Pitfalls

Outcomes are qualitative (high/medium/none, probably from MS detection), not yields. The 16 multicomponent scaffolds mean several reaction templates. Individual products are probably not characterised. Each well has to be matched to its building blocks and dispense volumes from the plate layout, which is hard to check automatically without the authors' plate map files.

Deliver

• dataset: the ORD Dataset, compressed (.binpb.gz, .pb.gz, .txtpb.gz, .pbtxt.gz or .parquet), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.
• sources: a .zip with a README.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, and validation.txt, the output of ORD's validator (ord-schema 0.8.3) on the dataset file.

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.