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 to simply 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

Founder of ChemZoo Inc., the host of ChemSpider ( ChemSpider is an open access online database of chemical structures and property transaction based services to enable chemists around the world to data mine chemistry databases. The Royal Society of Chemistry acquired ChemSpider in May 2009. Presently working as a consortium member of the OpenPHACTS IMI project ( This focuses on how drug discovery can utilize semantic technologies to improve decision making and brings together 22 European team members to develop an infrastructure to link together public and private data for the drug discovery community. I am also involved with the PharmaSea FP7 project ( trying to identify new classes of marine natural products with potential pharmacological activity. I am also one of the hosts for three wikis for Science: ScientistsDB, SciMobileApps and SciDBs. Over the past decade I held many responsibilities including the direction of the development of scientific software applications for spectroscopy and general chemistry, directing marketing efforts, sales and business development collaborations for the company. Eight years experience of analytical laboratory leadership and management. Experienced in experimental techniques, implementation of new NMR technologies, walk-up facility management, research and development, manufacturing support and teaching. Ability to provide situation analysis, creative solutions and establish good working relationships. Prolific author with over a 150 peer-reviewed scientific publications, 3 patents and over 300 public presentations. Specialties Leadership in the domain of free access Chemistry, Product and project management, Organizational and Leadership development, Competitive analysis and Business Development, Entrepreneurial.
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Posted by on April 20, 2011 in General Communications


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