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How Dominant is Pubmed for Chemistry

20 Apr

Recently I moved this blog to WordPress hosting and started using a new Theme. This is work in progress. Many of the original image associations still need to be remade as the blog went from www.chemconnector.com/chemunicating to simply www.chemconnector.com. With the new theme I decided to start managing my CV, presentations and publications online too. I’ve had it staggered across various sites such as Mendeley but having it managed on my own blog just made more sense. In particular, what I have been doing is spending half an hour per night creating links between the papers on the My Curriculum Vitae page using the DOI and associated CrossRef Resolver to do the linking. It makes sense to go this path.

In order to do the linking I first have to find the DOI. To do the DOI I search the paper title on google, or the reference where necessary. It’s had some interesting results already as I detailed here. While linking up the papers…75 done and about 30 to go…I observed an increasingly obvious trend. It was an unexpected trend based on what I had been told. The trend? PubMed is not just about the Medicine and the Life Sciences.

Wikipedia declares “PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez information retrieval system.”

However, time after time, as I searched for the titles of my articles PubMed kept coming out on top, ABOVE the actual publisher. Let’s take an example. On my CV is a paper referenced as:

G. E. Martin, B. D. Hilton, K. A. Blinov, and A. J. Williams, Multistep correlations via covariance processing of COSY/GCOSY spectra: opportunities and artifacts. Magn. Reson. Chem. 46, 997-1002, (2008). The title “Multistep correlations via covariance processing of COSY/GCOSY spectra: opportunities and artifacts.” Here’s PART of the abstract..the entire abstract is marked as copyrighted but I was involved in writing it…

“Long-range homonuclear coupling pathways can be observed in COSY or GCOSY spectra by the acquisition of spectra with larger numbers of increments of the evolution period, t1, than would normally be used.  Alternatively, covariance processing of COSY-type spectra acquired with modest numbers of t1 increments, allows the observation of multistage correlations. In this work results obtained from covariance-processed GCOSY spectra are fully analyzed and compared to normally processed COSY and 80 ms TOCSY spectra. ”

I’m sure you’d agree it’s NOT very “medical”, “biomedical” or “life sciences”. Yet…if I do a Google search we find:

 

 

 

 

 

 

 

 

 

 

The full reference is here on Pubmed.

As can be seen, PubMed returns the reference above Wiley, the publisher of the article. I saw this for many, many of the publications listed on my CV. Most of them are based on NMR spectroscopy data processing approaches so why would they be in Pubmed? I am assuming this is simply because the journal itself has been identified as a journal that is “acceptable” to Pubmed? Now, I’m a chemist…and it would be super if there was a Pubmed for the whole of chemistry…of course we cannot call it PubChem…that’s already taken. But I wonder what is standing in the way of PubMed simply becoming all-encompassing…why can’t it accept all chemistry papers, for example. It’s clearly accepting some (many!) that I have authored/co-authored. Why not more? Is it policy? Is it resources? Can anyone comment?

 

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 April 20, 2011 in General Communications

 

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