Archive for the Uncategorized Category

For the past 8 months I’ve been running two blogs associated with ChemSpider…the ChemSpider blog and this blog, ChemSpider News. These had different intents – the ChemSpider blog was to cover the general directions, vision, activities, challenges and community conversations about the ChemSpider service. ChemSpider News was to cover details of new functionality as it was rolled out. What has happened is that the postings on this blog regarding new functionality have been missed by the readers of the other blog as a result of the readership being different (and different subscriptions to Feedburner being in place). This has not been good for the ChemSpider users since they have not been getting the latest and greatest news about new functionality. It’s a great shame to deliver new functionality and not have people use it for weeks on end because they don’t know about it.What I’ve also been posting on the ChemSpider blog are my own personal views regarding a whole variety of issues…none of them ChemSpider related. For example, my views on vaccines, on fluoride, on drugs, and on my views of various research undertakings. Recently John Doe took me to task in a recent response on the ChemSpider blog. While I vehemently disagree with his comment regarding the reasons behind my posting I have decided to separate news regarding ChemSpider and its mission, direction and new functionality from my own personal commentaries, pleas, musings and, once in a while, thigh-slapping fun exchanges (especially the ones about erectile dysfunction drugs and how the drug industry can learn from the golfing industry).

So, this site, while it will remain online for past references , will be discontinued in terms of new postings and all new functionality comments will be posted to the ChemSpider Blog. The ChemSpider blog will become just that…all about ChemSpider.

chemconnector-logo.pngRegarding ChemConnector and it’s associated Blog. That blog will be a communication vehicle for the website, to go online shortly. As many of you will know me from the ChemSpider blog you will likely be aware that I took a sabbatical after 10 years working a company and have taken a few months down. For the time-being my intention is to spend some time consulting for groups and organizations interested in utilizing my skills and growing the business of ChemConnector – Connecting Scientists to Problem Solvers. This, of course, in parallel to the ongoing work on ChemSpider. More on this will come shortly and will be exposed on the site.

At the prompting of one of our users, and a clever idea it was too, we have implemented the ability to use the “split-nature” of the InChIKey to facilitate searches by connectivity only, and thereby ignoring the stereo layer for example. Wikipedia declares: InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 8 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, followed by a single checksum character.


Now, if you click on the first part of the string you will get a connectivity structure search of Google.

and………… if you click on the second part of the string you will get an exact structure search of Google.

We will add the ability to search within ChemSpider or via Google or other search engines shortly.

I have reported previously on the integration between the ChemSpider site and the SureChem online patent database (1,2,3). What is unique about the SureChem patent database is that it is searchable by structure and substructure as well as text. By indexing the structures from SureChem on ChemSpider we can allow search results on ChemSpider to link directly to the related patent on SureChem. One click away.

We have now added the ability to search ONLY structures with associated patents. In the Advanced Search Mode simply click on the appropriate option “Filter only those having patents link”. Enjoy!

Some of you might have been affected by ChemSpider service outages over the weekend. We are used to experiencing outages as a result of power cuts or internet service provider outages. Unfortunately this one is our of our making. There were numerous things going on over the weekend and we were hoping for only slight interruptions. We have had to add another terabyte of storage to the system and needed to pull down the system to put the drives in place. Also, we are in the process of rebuilding our index for the Chemrefer service and this is putting a strain on our servers. Add to this the fact that Google appear to be indexing all of our InChIKeys (we estimate about 10,000 transactions per day on the server just from this indexing process). As commented previously ChemSpider runs skinny and we don’t have an enormous rack of servers, we are limited to 3. We apologize for the outages but until we can afford to have ChemSpider run as a hosted service this may happen from time to time.