Daniel Lowe

[Daniel Lowe @dan2097]

@cdsouthan No, there is not. I think the most common cause of "Too many radicals for esters" would be erroneous additional whitespace

[Daniel Lowe @dan2097]

@iChemLabs Incidentally (Optical) Chemical Structure Recognition, abbreviated OCSR or CSR, is another common way of describing this without calling the process "OCR"

[Daniel Lowe @dan2097]

@houndcl In a real-world setting you could potentially also get improvements by processing all images from a given document and preferring the interpretation that gave more groups in common with the other images, as often a series of related compounds is synthesized

[Daniel Lowe @dan2097]

@houndcl Many compounds will be in PubChem, so there are real-world benefits, but I still wonder whether a fragment-based approach could be more general e.g. for documents with novel compounds; likely no advantage for the Kaggle comp, but probably within their new restrictions.

[Daniel Lowe @dan2097]

@jwmay @uspto @ReedTechLifeSci They appear to now have switched their naming scheme of _oldest.tar _old.tar, no suffix to no suffix, _r1.tar and _r2.tar. In the case I looked at the re-released files had a supplementary information zip that was missing from the original

[Daniel Lowe @dan2097]

@cdsouthan @markussitzmann @vfscalfani @theNCI The issue is the forward slash. Many web servers don't allow them as part of the URL, even when encoded, ostensibly for security reasons. As well as OSRA, there's also Imago from Epam, and MOLVEC from NCATS: https://t.co/trspC9Rl2P

[Daniel Lowe @dan2097]

@ChemConnector @markussitzmann @baoilleach I'm sure @baoilleach will correct me if I'm wrong, but I think LeadMine's current code for NMR extraction for the most part comes from that project. It's unfortunate that the next step with MestreLab, to do the NMR prediction to verify the spectra, didn't come to fruition.

[Daniel Lowe @dan2097]

@egonwillighagen @baoilleach Are you eluding to the Experimental Data Checker which tried to check whether a textual spectrum was plausible by comparison with the structure?

[Daniel Lowe @dan2097]

@cdsouthan The issue is actually the forward slash, quite a few web servers (including this one) don't correct handle encoded slashes, ostensibly for security reasons. I should probably send requests in a different way to workaround this issue.

[Daniel Lowe @dan2097]

@baoilleach You can also encounter mentions of Tyr(O-Me), which possibly makes the reason for the O clearer, I think it's to indicate which atom on the tyrosine is the substitution point, but given the normal meaning of an O in a formula this just ends up being even more unclear

[Daniel Lowe @dan2097]

@baoilleach @marwinsegler @ChemProfCramer @ACSCOMP @phisch124 @nmsoftware It is technically in the CML version of the dataset. It can be found by searching for reactions with a reactionAction where the action is "Irradiate". This action however doesn't distinguish between sonication and EM radiation (but the text can be checked)

[Daniel Lowe @dan2097]

@rmcgibbo @baoilleach If there are specific cases where ChemAxon works, but OPSIN doesn't I'm happy to look into them.

[Daniel Lowe @dan2097]

@i_vishalll @cdsouthan Apologies for the issue, OPSIN was moved to a new server earlier this week that was not configured quite right for JNI-InChI. This is now resolved.

[Daniel Lowe @dan2097]

@eawRDM InChI is the answer to the question...but if I wanted to use the chemical structure I would also want a format that more precisely captured the structure. As @baoilleach commented, the InChI/InChIKey can be generated precisely from the SMILES, but not vice versa.

[Daniel Lowe @dan2097]

@JanStanstrup @egonwillighagen I'll make it more obvious next week. I think flashing would be a step too far ;-)

[Daniel Lowe @dan2097]

@aclarkxyz @dr_greg_landrum Sometimes there is no sketch eg text-mining. The main alt. is problematic esp. OD stereo https://t.co/LJL1Q8uwQo

[Daniel Lowe @dan2097]

@cdsouthan Will try to fix as it's not even an experimental section! Tricky in general as you don't want want to find fragments of name

[Daniel Lowe @dan2097]

@MatToddChem @cdsouthan @jessicabaiget @OpenSourceTB You can paste the reaction SMILES into MarvinSketch (if you replace > with >)

[Daniel Lowe @dan2097]

@MatToddChem @cdsouthan @jessicabaiget @OpenSourceTB Each compound in the XML has SMILES/InChI (when name to structurable) +Reaction SMILES