Archive for May 16th, 2008

16 05 2008

Blog Postings on the ChemConnector Blog

Posted by: Antony Williams in ChemConnector, ChemSpider Chemistry

Over on my other blog I have recently posted some comments that may be of interest to ChemSpider Blog readers

Spaces, Dashes and Issues with Nomenclature Conversion

It appears that members of the text-mining for chemistry community are using one or more of the commercial name to structure software programs to convert chemical names to structures and, prior to feeding the algorithms, they are removing all white spaces from the names. They are also doing the same, in some cases, with dashes. How well is that going to work? Is it safe to remove spaces from chemical names and assume this has no effect? Is consideration being given more to the accuracy of the text-mining than to the nature of systematic nomenclature?

Let’s look at some examples of the result of removing spaces from chemical names. Consider the different results just from moving a space. READ MORE

Hamburger PDFs and Making Them Structure Searchable

This is just an fyi comment for the community really since this is a general assumption that Word Documents and PDFs cannot be made structure-searchable. The truth is that both can be made structure searchable. How? Well, you need to write the correct information into the file to enable it but it’s possible. There are a number of solutions out there allowing structure-based searching of Word document files. I believe the first one was originally from Oxford Molecular before being acquired by Accelrys. I think there are now multiple including, I believe, Cambridgesoft, ACD/Labs and probably others. READ MORE

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16 05 2008

ChemSpider Deepens Integration with Wikipedia

Posted by: Antony Williams in Community Building, How ChemSpider Runs

We announced WiChempedia previously in terms of using our new dedicated website approach as a subset of ChemSpider. What we did there is show the leading part of the Wikipedia article and then ask people to click over to read the entire article on Wikipedia. We can support the entire article on ChemSpider if that is of interest to people but it’s easier, for now, to keep it as is. Comments?

What we are doing is trying to provide better integration to Wikipedia since I am working with Wikipedia on the curation of Wikipedia chemical structures and deeper integration seems appropriate. So, tonight we added the ability to Edit the Wikipedia article. In this way you can directly edit errors you might see in the lead of the article but you also get to edit the entire article if you are interested.

As an example see Taxol here. You will see the following Taxol lead for the article. Look at the END where you will see: Read more… or Edit at Wikipedia…

Paclitaxel is a mitotic inhibitor used in cancer chemotherapy. It was discovered in a National Cancer Institute program at the Research Triangle Institute in 1967 when Monroe E. Wall and Mansukh C. Wani isolated it from the bark of the Pacific yew tree, ”Taxus brevifolia” and named it ‘taxol’. When it was developed commercially by Bristol-Myers Squibb (BMS) the generic name was changed to ‘paclitaxel’ and the BMS compound is sold under the trademark ‘Taxol’. In this formulation paclitaxel is dissolved in Cremophor EL, a polyoxyethylated castor oil, as a delivery agent since paclitaxel is not soluble in water. A newer formulation, in which paclitaxel is bound to albumin as the delivery agent (Protein-bound paclitaxel), is sold commercially by [http://www.abraxisbio.com Abraxis BioScience] under the trademark [http://www.abraxane.com Abraxane].”[http://www.fda.gov/cder/foi/label/2005/021660lbl.pdf Abraxane Drug Information].” ”Food and Drug Administration.” January 7, 2005. Retrieved on March 9, 2007. Paclitaxel is now used to treat patients with lung, ovarian, breast cancer, head and neck cancer, and advanced forms of Kaposi’s sarcoma. Paclitaxel is also used for the prevention of restenosis. Paclitaxel works by interfering with normal microtubule breakdown during cell division. Together with docetaxel, it forms the drug category of the taxanes. It was the subject of a notable total synthesis by Robert A. Holton. As well as offering substantial improvement in patient care, paclitaxel has been a relatively controversial drug. There was originally concern because of the environmental impact of its original sourcing, no longer used, from the Pacific yew. The assignment of rights, and even the name itself, to BMS were the subject of public debate and Congressional hearings. Read more… or Edit at Wikipedia…
There you have it…this type of integration is a joy to do. Literally a couple of minutes to make the connection and a few minutes to set the style et voila. Editing articles in Wikipedia.

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