The document discusses some of the unintended consequences of including patent-extracted and deuterated drug compounds in PubChem, including increased complexity and confusion for users. Specifically, it notes that the same marketed drug like Rosuvastatin is represented by over 15 compound IDs in PubChem due to different deuterated forms extracted from patents. This "multiplexing" of compound IDs can mess up search results and integration with other databases. While filtering out such compounds may be ideal, it is difficult to distinguish experimental from hypothetical structures in patents. Better flags or clustering of related compounds could help address the issues.

1. The Unforseen Consequences of Opportunistic Deuterated Drug Claims, Patent Extraction Feeds and the PubChem Chemistry Rules When data integration gets fuzzy Chris Southan ChrisDS Consulting, Göteborg, Sweden BioIT World, Hannover, Oct 2010

3. Discordance of Drug Collections

4. Will the real Rosuvastatin stand up ?

5. But 15 CIDs ?

6. “ Heavy” Rosuvastatin (+28) CID 25241235

7. Patent Filings on Deuterated Drugs “ Protia's patents appear to be a blunderbuss approach, with a mass of US filings 237 published to date but only 11 PCT applications. None of these provide exemplification or any biological description. Concert has 39 PCTs and 26 US applications published, Auspex 57 PCTS and 39 US applications” (Comment from “In the Pipeline” blog, June 2009)

8. A Pipeline With Unintended Consequences

9. Some of them Might Just Work ? But we don’t know which one of the 25 !

10. Picking Off the Best-sellers Connectivity Deuteros 1) 38 32 2) 4 88 0 85 3) 15 12 7) 7 4 8) 8 7 9) 11 9 10) 68 66 13) 29 26 14 ) 51 48 15) 16 11

11. Sorting

12. Extent of the Problem

15. Questions ?