Added the two datasets from the surf publication (#195)

[bdeadman]

Borylation and minisci datasets from the SURF publication (ChemRxiv, 2024, 10.26434/chemrxiv-2023-nfq7h-v2 D O I: 10.26434/chemrxiv-2023-nfq7h-v2 [opens in a new tab]). These are reactions which have been collected from the literature and summarised in SURF format by @alexarnimueller.

The Jupyter Notebook used to convert the datasets is located at bdeadman/surf/surf2ord_troubleshooting.ipynb. The surf2ord.py script has been modified to output data into the latest ord-schema version and preferred style.

Notes:

• Provenance data was not found in the Minisci dataset so this is assumed to also be @alexarnimueller
• In the borylation dataset several rows had catalyst_1 only defined by the CAS number. In all but 1 of these I have found a SMILES string to approximate the catalyst.
• surf2ord now assigns each reagent/catalyst/reactant/solvent to a separate input instead of collecting together them by role. Inputs with multiple components would be used when they are known to be added as a solution or mixture.
• rxn_type has been converted to REACTION_TYPE instead of NAME (makes it compatible with ord-schema >0.3.38)
• cas numbers have been converted to the CAS_NUMBER type instead of NAME
• Isolated analysis type in SURF has been defined as WEIGHT analysis type in ORD.
• datast_name and dataset_description options added to surf2ord function. This ensures the output dataset passes validations in ord-schema >0.3.86. Placeholder text is included by default so the text can be edited afterwards.
• Fixed the code so it no longer multiples fractional yields by 100 * 100.

[github-actions[bot]]

Change summary:	Filename	Added	Removed	Changed
data/borylation_ord.pbtxt	0	0	0
data/minisci_ord.pbtxt	0	0	0
	0	0	0

[github-actions[bot]]

Change summary:	Filename	Added	Removed	Changed
data/99/ord_dataset-99c23cf435dc42f1af884053bc8b11c7.pb.gz	1111	0	0
data/c1/ord_dataset-c1e2bd4243aa49448b1e61636463c7cf.pb.gz	130	0	0
	1241	0	0

[bdeadman]

@connorcoley @skearnes I was able to pull this through into open-reaction-database/ord-data:#195 without getting approval. It should probably be checked at this stage before it is approved to go into main.

[skearnes]

@connorcoley @skearnes I was able to pull this through into open-reaction-database/ord-data:#195 without getting approval. It should probably be checked at this stage before it is approved to go into main.

Yes, that's expected; we don't protect any branches except for main by requiring approvals.

[github-actions[bot]]

Change summary:	Filename	Added	Removed	Changed
data/99/ord_dataset-99c23cf435dc42f1af884053bc8b11c7.pb.gz	1111	0	0
data/c1/ord_dataset-c1e2bd4243aa49448b1e61636463c7cf.pb.gz	130	0	0
	1241	0	0

[skearnes]

@qai222 do you have time to take a look at these for correctness?

[github-actions[bot]]

Change summary:	Filename	Added	Removed	Changed
data/99/ord_dataset-99c23cf435dc42f1af884053bc8b11c7.pb.gz	1111	0	0
data/c1/ord_dataset-c1e2bd4243aa49448b1e61636463c7cf.pb.gz	130	0	0
	1241	0	0

[github-actions[bot]]

Change summary:	Filename	Added	Removed	Changed
data/99/ord_dataset-99c23cf435dc42f1af884053bc8b11c7.pb.gz	1111	0	0
data/c1/ord_dataset-c1e2bd4243aa49448b1e61636463c7cf.pb.gz	130	0	0
	1241	0	0

[bdeadman]

For item 2, this is how it is recorded in the SURF table file. Since it is a GC yield I suspect it is just a calibration error. While not ideal, I think we need to report it as it is written. There are already >100% yields in the ORD from the USPTO data.

This particular reaction has come from this paper: https://pubs.acs.org/doi/10.1021/acscatal.0c00152. Unfortunately the rxn does not appear in the SI, and I don't have access to the paper.

[qai222]

For item 2, this is how it is recorded in the SURF table file. Since it is a GC yield I suspect it is just a calibration error. While not ideal, I think we need to report it as it is written. There are already >100% yields in the ORD from the USPTO data.

This particular reaction has come from this paper: https://pubs.acs.org/doi/10.1021/acscatal.0c00152. Unfortunately the rxn does not appear in the SI, and I don't have access to the paper.

Yeah the paper says "Yields were determined by gas chromatography and are based on moles of B 2 pin 2." in table 2 caption. I agree we should report as it is.