3 ms·
I know it's a picayune comment, but bad references bug me. The preprint mentions: "Molecular similarity calculator The primary function of this tool is to eval
by dalke 3y ago
I know it's a picayune comment, but bad references bug me. The preprint mentions:
"Molecular similarity calculator The primary function of this tool is to evaluate the similarity between two molecules, utilizing the Tanimoto similarity measure 76 based on the ECFP2 molecular fingerprints 77 of both input molecules."
Molecular similarity is a particular area of expertise for me. I was curious what they cited. It's:
[76] TT, T. An elementary mathematical theory of classification and prediction; 1958
His full name is "Taffee Tadashi Tanimoto", with surname "Tanimoto". The 1958 paper says "T. T. Tanimoto", so that should be "Tanimoto, T. T." to match the citation style.
Also, it's highly unlikely they've read that paper. It's an internal IBM Technical Report which requires an ILL request, which is how I got it. Worldcat lists only 8 libraries with a copy.
If they have read it they would be unusual. In talking with people I found that most people cite it not because they read it but because other people cite it, so they see it as the appropriate citation.
The citation for the version published in the scientific literature is Rogers D.J., Tanimoto T.T. (October 1960). "A Computer Program for Classifying Plants". Science. 132 (3434): 1115–8. https://www.science.org/doi/10.1126/science.132.3434.1115 https://www.science.org/doi/10.1126/science.132.3434.1115
For a bit of science, task 4 in A.1.3 starts by telling "CN1CCC(CC1)=C1C2=C(SC=C2)C(=O)CC2=CC=CC=C12" is toxic.
PubChem tells me that structure is ketotifen, https://pubchem.ncbi.nlm.nih.gov/#query=CN1CCC(CC1)%3DC1C2%3DC(SC%3DC2)C(%3DO)CC2%3DCC%3DCC%3DC12 https://pubchem.ncbi.nlm.nih.gov/#query=CN1CCC(CC1)%3DC1C2%3... , and quotes DrugBank "In the US, it is now used in an over-the-counter ophthalmic formulation for the treatment of itchy eyes associated with allergies" . See also https://en.wikipedia.org/wiki/Ketotifen https://en.wikipedia.org/wiki/Ketotifen .
How is a program supposed to make it less toxic when it's already a widely used medicine?
There's perhaps an important issue - what does "toxic" mean? Something applied to your skin might be safe, but toxic if eaten in a large amount.
Task 5 in A.1.4 has the software respond that 20 grams of grain alcohol can be purchased from A2B Chem for 143 USD.
First, I found I couldn't find that entry in A2B Chem, but more importantly, that price seems rather high, yes?
Neither of which was caught in the student evaluations.