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phetsims / build-a-molecule

"Build a Molecule" is an educational simulation in HTML5, by PhET Interactive Simulations.
GNU General Public License v3.0
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Nomenclature standard #217

Closed arouinfar closed 3 years ago

arouinfar commented 3 years ago

Recently, two teachers have contacted phethelp in regards to nomenclature. In both cases, the user expected the displayed name to be the common name.

CID IUPAC traditional name Name on PubChem entry
1045 4-aminobutylamine putrescine
6584 acetic acid methyl ester methyl acetate

We're currently working on updating the data set in #158, so I reached to Isam to see if these naming discrepancies would be resolved. He confirmed that we are using the IUPAC Traditional Name provided in the SDF files. In the case of putrescine, the names provided in the SDF file are:

> <PUBCHEM_IUPAC_OPENEYE_NAME>
butane-1,4-diamine

> <PUBCHEM_IUPAC_CAS_NAME>
butane-1,4-diamine

> <PUBCHEM_IUPAC_NAME_MARKUP>
butane-1,4-diamine

> <PUBCHEM_IUPAC_NAME>
butane-1,4-diamine

> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
butane-1,4-diamine

> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
4-aminobutylamine

There isn't a field for the common/preferred name displayed on the PubChem entry. However, the prevailing name seems to be butane-1,4-diamine. Perhaps we should be using the PUBCHEM_IUPAC_NAME instead?

issamali67 commented 3 years ago

PUBCHEM_IUPAC_NAME can give "less simple" names, which may not be the preferred ones. Here is an example: CID 6585, which is peracetic acid in the current and new data bases. If we use IUPAC_NAME then it will appear as ethaneperoxoic acid, which is also the prevalent name. However, pubchem lists it under the title peracetic acid, so I guess peracetic is the preferred name (which is also PUBCHEM_IUPAC_TRADITIONAL_NAME).

arouinfar commented 3 years ago

Thanks for the information @issamali67. Let's stick with the PUBCHEM_IUPAC_TRADITIONAL_NAME. I'll be sure to make a note about the convention in the Teacher Tips.