Copyright©2007 Antony Williams
In a recent blog PMR commented on the quality of ChemSpider while focusing appropriately on the issue of quality in aggregated datasets. He commented specifically on a search performed on Sodium Chloride and the records located shown here. His comment was that the third of these , the structure of Na2Cl2, was “rubbish”. PMR commented “There is little point in collecting 10 million structures if you cannot rely on any of them”.Â We’re struggling with the issue.
So here’s the question…is it rubbish? PMR commented that for data collections thatÂ “…there is junk in the historical record. And there is junk in some of the links donated. That may be where the Na2Cl2 for sodium chloride came from.” But it’s not junk. It’s chemistry. The existence of Na2Cl2 microclusters has been reported (1).Â The sodium chloride dimer is also on the NIST webbook Â and indexed into PubChem as record cid=6914545.
PMR went on to comment “But Pubchem is not, and should not be, a data repository except for NIH data. But nor should any other organisation try to aggregate all the data. Whar we should do is pool the metadata (InChIs, names, etc.( in pubchem and develop links and searches to distributed repositories and datasets elsewhere.”. I love the vision!
Here’s the definition of what ChemSpider is trying to do from the What is ChemSpider page “There are tens if not hundreds of chemical structure databases and no single way to search across them. There are databases of curated literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data and on and on. The only way to know whether a specific piece of information is available for a chemical structure is to have simultaneous access to all of these databases. Since many of these databases are for profit there is no way to easily determine the availability of information within these commercial or even in the open access databases. With ChemSpider the intention is to aggregate into a single database all chemical structures available within open access and commercial databases and to provide the necessary pointers from the ChemSpider search engine to the information of interest. This service will allow users to either access the data immediately via open access links or have the information necessary to continue their searches into commercially available systems. The question â€œis there specific information about my chemicalâ€ will be answered. Accessing the information may require a commercial transaction with the appropriate provider.”
Our intention is to do exactly as suggested “pool the metadata (InChIs, names, etc and develop links and searches to distributed repositories and datasets elsewhere.” It’s already started.
One comment…the molecular weight for Na2Cl2 in the record on ChemSpider IS incorrect. This is listed as a known bug . It’s fixed…we just need to calculate properties for 10 million compounds. It’s underway.Stumble it!