Monday, July 11, 2011

Ahh ... Pubmed Central. I love you. In many ways. But alas, not today. #openaccess

Been having some challenges with Pubmed Central recently.  What is Pubmed Central?  If you don't know, and you have anything to do with the life sciences in any way, you should learn.  A good place to learn is on their info page here.   Here is the summary:
PubMed Central (PMC) is a free archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). In keeping with NLM’s legislative mandate to collect and preserve the biomedical literature, PMC serves as a digital counterpart to NLM’s extensive print journal collection. Launched in February 2000, PMC was developed and is managed by NLM’s National Center for Biotechnology Information (NCBI).
It is a fantastic resource.  Alas, there is one major limitation.  Mostly it is an archive of papers submitted by publishers.  Some publishers do not submit their material there.  Fortunately, there is now a way around this.  Author's can submit their own papers to PMC.  However, there is some caveats to this -- there are severe restrictions on what one can submit.  In the past I was aware of one of these caveats - the work in the manuscript has to have been at least partially supported by NIH funds (well, there is a way to submit if supported by the Wellcome Trust to).  To submit NIH supported work, you have to use the NIH manuscript submission system.  Why they won't take papers supported by other funding agencies I do not know.  Imagine if Genbank only took sequences inferred with NIH funds?  Imagine if libraries only took books supported by rich Europeans.  I am sure Pubmed does this because other agencies don't pay for the archive but still --- I think this is shortsighted.

And today I discovered a new caveat.  A few days ago I used the NIH manuscript submission form to submit author versions of a few of my past papers supported by NIH funds.  And one of them was rejected today because

Your submission to the NIHMS system cannot be processed because the NIH Public Access Policy does not apply to this material. The NIH Public Access Policy does not apply to book chapters, editorials, letters, or conference proceedings. As such, we are sorry that we cannot process your submission.
And though my paper was not one of these things, it is marked in such a way that it seems to be an editorial.  And thus apparently they won't take it.  I find this a bit surprising since PMC is actually filled with things like editorials including ones by me like PLoS Biology 2.0 and Genomics of Emerging Infectious Disease: A PLoS Collection and meeting reports like Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. 
and letters (none of mine but I found many of others including even responses to letters to the editor). I have run this through my brain over and over and I cannot figure out why (or in fact how) they would exclude these types of materials.   I am going to ask around and see if anyone knows more detail about this but I am not convinced there will be a simple explanation.  Most likely it will have something to do with trying to cover "research" but not opinion.  But in my opinion, research and opinion are not always distinct.

Anyway - I am a bit annoyed by all of this because really, all I want to do is find these best way to share all of my past publications and this seemed like a useful addition to posting them on my website and/or in Mendeley as well as in UC sponsored archives.  And it would be great to have all my papers in PMC.  I note - the vast vast majority of my recent work is in PMC because I basically only publish in Open Access journals that deposit their material there.  But a lot of my old work is not in PMC.  And that is too bad.  Someone, somewhere might find it useful ...


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  2. Worse yet, author deposited manuscripts are not put in the Open Access subset of PMC, even though this is the whole point of the NIH mandate. This incredible fact has been verified by the NIH/NLM/NCBI helpdesk (18 Mau 2010). Try the following query yourself and see that it returns 0 results....[filter]+

  3. I suppose they are not put in the OA section b/c they do not want to spend time figuring out what the copyright issues are for each paper, or something like that. I will ask around about this too.