Everything Old is New Again: WLN in PubChem

February 10, 2010

An older article I did on Wiswesser Line Notation (WLN) seems to have interested a few people over the years. For the unfamiliar, WLN was a line notation system that at one point was the way to name organic compounds. Among its most remarkable attributes was how easy it was to learn - supporters claimed that high school graduates with minimal chemistry knowledge could be taught WLN in a matter of days. WLN was used both as a unique identifier (exactly the role InChI plays today), and as a display mechanism before the advent of chemical graphics systems.

Now it turns out that WLN is popping up in a most modern place: PubChem.

As part of a structure/synonym interconversion service Metamolecular has started offering to its customers, we've been analyzing the mountain of synonyms contained in PubChem. One of the things we found: a number of WLNs.

For example, the PubChem record for Fluoral hydrate gives the WLNs "QYQXFFF" (connected structure) and "VHXFFF &QH" (disconnected hydrate) as synonyms.

Many of these WLN synonyms have been deposited as part of the DTP/NCI Dataset. It's not clear at this point to what extent WLNs are still being generated and deposited into PubChem. I have it on good authority that no modern implementations of a WLN encoder exists, so these PubChem WLNs may simply be relics of a bygone era. Then again, maybe not.