Users of ChemSpider might have noticed some performance isseus in the past 2-3 weeks with our web services, service availability and speed of searches. I put my hand in the air and say “Yup, acknowledged”. Hopefully they have not been too disruptive BUT it is for the overall benefit of the service ultimately. We have been streaming in 8 MILLION links to Pubmed in order to make Pubmed structure and substructure searchable. We are NOT rolling this out with full fanfare yet but I do want to explain the performance issues you might be experiencing. We work on Microsoft technology and while we are advocates for the platforms of .NET, IIS and SQL Server we definitely are putting them under pressure as we keep expanding the database and adding more value. We have thoughts about how to resolve this but want to finishg populating the tables first.

The upside….the majority of links are already in place. For an example visit a structure and look for PubMed as a data source and click on one of the links. For example, for Valium here you will see in the datasource table a series of Pubmed IDs next to the PubMed datasource…

  16971504, 17673, 874970, 406430, 17881, 327854, 879884, 577681, 560225, 195649, …

These will link you out to PubMed directly. Try it out…

Now, do we have implementation issues? YES. The lists of external IDs can be long so right now we show only the first 10. We wiil deal with display of others shortly. We need to provide a way to curate out “junk” entries. For example, “methyl” is on Chemspider as a fragment and has links to PubMed IDs…you’ll see why if you click them..it was done with text mining. These issues will be resolved but for now we announce that PubMed is structure and substructure searchable via ChemSpider. We will explain how we did it shortly but for now we will acknowledge the massive contribution of our colleagues at SureChem. More to come…

Stumble it!

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