One of the blogs I really enjoy reading is Deepak Singh’s Business,Bytes,Genes and Molecules. Today there was a blog post about ChemSpider but something strange happened…I could ONLY read it in Google Reader. When I tried to navigate to the actual website it asked me to Save a file. See below.

It may be harmless but I’ve suffered enough at the hands of “bad files” to not grab it. Anyone else seeing this symptom? It’s in both browsers (IE and FF) and on two computers.

Anyhow, thankfully I can read it in Google Reader. There’s a point Deepak raises and I insert it here..

“On the web, data should be available as an addressable resource. The fact that data is available as RDF is great (and I wish more data was available as such). However, my personal preference is that data, especially open data, needs to be accompanied by APIs and bindings that allow the data to be accessed in a number of formats (not a dump per se). I think over time the acceptable formats will be established, much like XML/JSON/RSS have become the standard transport formats. The key aspect here are the business models. Is the business in providing a service on top of the data? For example for more than X number of API calls, there could be a fee associated.”

Just in case people have missed them we have a whole series of Web Services available already and they are being used. You can find details about them here:

Mass Spec Web Services

Taverna Hooks to ChemSpider Web Services for Metabolomics

Web Services Demo Pages and Example Code

Microsoft Hook Web Services into Infomesa

Waters Deliver Integration Via Web Services

There are more examples. We have thousands of calls a day using the Web Services at present and welcome more feedback on them!

Stumble it!

4 Responses to “Comments to Business,Bytes,Genes and Molecules”

  1. Deepak says:


    Didn’t realize you were at Bio-IT World. Would have loved to have breakfast with you.

    The download is just the index.php file from wordpress. I am trying to figure out what’s going on. So far my hosting company hasn’t been able to figure out it. Deleting some plugins has allowed access to individual posts, but I still can’t get to the home page. Thank goodness for RSS readers.

    Glad to see the emphasis on web services. It’s the way data is going to be consumed as we move forward. It also allows people to leverage data sources in interesting/innovative new ways. I really like the Taverna service mentioned above.

  2. David Bradley says:

    I’m pretty sure that’s an issue with your browser Tony, not the site in question. I too see that occasionally, when, for some unknown reason, the MIME type gets confused (it could be a proxy/caching thing) and a file with a php or some other extension that’s supposed to render as if it were a normal html page fires up the “save as” dialog rather than opening the page in a browser window…it’s as if the browser sees the php extension and ignores the fact that it’s not a script but an html page that just happens to have php instead of html as its extension.

    To fix choose the “Open With” option and set it to always open with Firefox (your browser)


  3. Antony Williams says:

    Deepak, Thanks for the acknowledgment regarding the web services. We have had them for a while and encourage people to use them, integrate to us and provide us feedback. Other than PubChem I think we are likely one of the few Free Access websites providing this type of integration..are you aware of others?

  4. Deepak says:


    I am not, but that could be a function of following the more biology oriented sites. There, it’s becoming more prevalent, so I suspect more chemistry oriented sites will follow. My guess is this will be driven by metabolomics and safety/tox related information.

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