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A Plea to Academia to Help Design a Lesson Plan Using ChemSpider

03 Aug

Over the past 48 hours there has been an interesting discussion on CHMINF. The discussion was around how to teach a large class of students to learn about literature searching, about structure searching, property searching etc. The tools are out there to perform such searches and to facilitate students learning about the types of resources they will need to access if and when they enter industry. The premise of the exchange was that some of the gold standard resources, while excellent, are commonly not affordable at the level necessary to train large classes of students. Below is a posting I placed back onto CHMINF. My question to you readers is as follows “Is there an academic who would like to work with me on a Lesson Plan involving ChemSpider?“. If so…contact me please.

The exchange…the > indicates the comments made by one of the commentators to the original post and I used it as the basis for my own feedback.

Colleagues,

I wonder whether or not it might be possible to use the ChemSpider service as one of the resources for the classes? For example, relative to some of the comments made below it is possible to perform the majority of searches at www.chemspider.com – this includes structure searches, property searches,name searches as well as LITERATURE searches of open Access articles. See details below…

>1. Ability to use a chemical drawing program to insert chemical drawing in a lab report.

AJW> On ChemSpider …refer to http://www.chemspider.com/news/?p=39

2. Ability to identify a compound by multiple methods, such as CAS registry number, IUPAC or CAS index name, common name.

AJW> For searching by numeric identifiers, systematic names or common names use the search page at http://www.chemspider.com/Search.aspx
and review the comments made at http://www.chemspider.com/news/?p=29 and http://www.chemspider.com/news/?p=23

>3. Ability to locate basic property information on a given compound in standard sources such as CRC Handbook, Lange’s, Merck, Dictionary of Organic Compounds, MSDS (whatever basic reference tools you have).

>AJW> I am not suggesting that ChemSpider is a reference tool as yet…but in terms of searching on basic property information use the Advanced Search at http://www.chemspider.com/Search.aspx?t=adv

Select the appropriate check box to perform searches by structure and substructure, via intrinsic properties, predicted properties, identifiers and data source. The nice thing about this approach is that the students will find the linkages into reference sources such as the NIST webbook, PubChem, Wikipedia and other rich sources of information

>4. Ability to locate 3-5 articles about a topic related to a specific compound.

>AJW> Use the ability to search on >50,000 Open access chemistry articles bytext. We are presently adding another 60,000 open access articles. Perform the search here:

http://www.chemspider.com/chemrefer.aspx

For example, search for dithiazoles and get this results set:
http://www.chemspider.com/ChemRefer.aspx?zoom_query=dithiazole&zoom_and=0

>5. Ability to identify the parts of a research paper and to summarize the relevance of the paper.
>6. Ability to cite articles using a standard citation style, such a ACS.

>… An assignment might be to locate information (defined by you and the lab director) about an organic compound of interest to them – why the molecule is of interest to them, some basic properties, locate 3 current articles on the compound – summarize relevance of one article in 2-3 sentences, cite all three articles according to a preferred style.

>It’s tempting to throw every possible nuance into such an assignment, but I’d stick to basics: compounds have names and properties, and you can find current literature about compounds by searching relevant article databases.

>AJW> And bring it all together using a system like ChemSpider…and I should think a PubChem and Pubmed combination would do the same, you would be able to interrogate structures, articles, properties and even spectra (scroll to the bottom of http://www.chemspider.com/RecordView.aspx?id=5557 to see an example of spectra…more examples will show up shortly).

I am VERY interested in working with someone, hopefully from this list, to potential develop a lesson plan that could be posted on ChemSpider for others to use as a skeleton to build on. If anyone has an interest in doing this please contact me directly. Thanks

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on August 3, 2007 in Vision

 

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