freebase3There has been encouragement that we look at Freebase as an additional online resource to integrate to. In terms of chemical entities some of the Wikipedia structure collection has made its way onto Freebase and has been enhanced to include InChIs and SMILEs. It’s not clear to me whether the InChIs on Freebase are all obtained FROM Wikipedia or were layered on later onto Freebase. So, I approached the Freebase group and asked if they could provide me a dump of the InChIStrings and the SMILES strings together with the associated FreeBase IDs and the chemical names. In this way we would be able to generate SDF files for depositions and end up with the structures (converted from InChIs and SMILES) as well as the associated chemical names and Freebase IDs. Simple idea right?

freebase11So, we converted InChIs and SMILES and generated the depositions. Freebase links now show up in the Data Sources section and, if you put your cursor over the GUID you see an image of the page and can click through to the record on FreeBase. See the image above. The Freebase GUID for Benzene is here: #9202a8c04000641f800000000000ac66

All seems well. I have a question though…I look at a structure like Dapagliflozin on Wikipedia here and see full stereochemistry explicitly defined in the name and in the image. However, on Freebase I note that the stereochemistry is NOT explicitly defined in the InChI. The InChI is:  1/C21H25ClO6/c1-2-27-15-6-3-12(4-7-15)9-14-10-13(5-8-16(14)22)21-20(26)19(25)18(24)17(11-23)28-21/h3-8,10,17-21,23-26H,2,9,11H2,1H3/t17?,18?,19?,20?,21-/m0/s1

So, when we take the InChIs and the chemical names, convert the InChIs and deposit the chemical structures we end up with a “destruction” of the curation work we have done on ChemSpider. We end up with TWO structures for Dapagliflozin, not one (See below)


And now we need to start the curation efforts AGAIN to clean out misassociations of names and structures. So, what we are going to do is delete the deposition of Freebase structures and redeposit without the chemical names. In this case the outlinks to Freebase will be in place but the structures will not be found by a name search UNLESS the Freebase GUID is associated with an already curated name-structure pair that is coincident with the Freebase name.

I can say that the Freebase team were a pleasure to work with and, in theory, once the Wikipedia curation project is finished the SMILES and InChIs on Freebase will be correct and such linkages back to Freebase will be easier, and correct. In the meantime I am interetsed in where the Freebase SMILES And InChIs are coming fro (I think a lot of them are from Wikipedia but am not sure) and we are going to make certain on our side that we remove the chemical names so as to not decrease the quality of our curation efforts.

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