Has your scientific research been wasted?

I had a good Thanksgiving weekend this year - spending time with family and friends. But as I go back to work this week I have now gotten somewhat depressed over something I did Sunday night. I decided to remove myself from the UC Davis internet proxy to see how many of my past papers that I have published I can obtain without the UC subscriptions. So I went to pubmed, and typed in my name (Eisen JA) and got most of my papers, which are listed at the bottom of this blog (some do not come up due to publication off the pubmed grid or due to co-authors screwing up my initials). (NOTE  - LISTING DELETED 4/09 BECAUSE THE FORMATTING IS ALL MESSED UP)

And then I went to see how many of my papers were freely available and how many were not. What I was most interested in was - what is the deal with papers I wrote before becoming an Open Access convert? For many it is easy to figure out if they are freely available - Pubmed has a link saying "Free in PMC" which refers to Pubmed Central. For others, it was a little trickier.

The results were both good and bad and a summary is below. A few things struck me. First, a lot of my life's work is not readily available without paying other for it. In the day and age of the internet, this means that these papers will simply be read less and less as time goes by. And that makes me very sad. If I had chosen to publish those papers in other journals, anyone in the world could get them at any time. Thankfully I did publish many papers in journals like PNAS, and ASM journals, and NAR - journals that have now decided to release them to Pubmed Central. And also thankfully (but less so) I published some papers in journals that have at least made them freely available on their web sites.

Most surprisingly to me is that a reasonable number of my papers in Nature are freely available on the Nature web site as part of their Genomics Gateway program. Nature deserves serious kudos for doing this and they stand out compared to Elsevier journals (which do not seem to ever do this) and even Science. This is disappointing as Science is published by a scientific society but apparently does not seem to care much about access to publications. Nature, a commercial publisher, is in my opinion doing more for scientific openness than Science. Now, Nature has a long way to go, but I am SO glad I listened to their editors like Chris Gunter and Tanguy Chouard who made a big deal about the Genome papers being free. I did not think it was that big a deal, but in retrospect they were ahead of me in thinking about availability. Plus Nature clearly makes more of an effort to provide free online material than they have to - and certainly make more available than Science.

So in the end - I am sad about my partially wasted past. But I am pleasantly surprised that at least some papers I thought would be more restricted are actually free (although only on the Publishers site for now - Hopefully these journals will submit them to PMC at some point). I guess - you win some and you lose some and some are somewhere in between.

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Summary of openness --- other scientists should do this exercise

In Pubmed Central and Open Access

• ASM journals (7) . Thanks ASM. Eisen et al. 1992; Liu et al. 1993; Shafer et al 1997; Fleischmann et al. 2002; Alland et al. 2003; Miller et al 2003; Nelson et al. 2004
  
• Nucleic Acids Research (3). Thanks NAR and Rich Roberts. Eisen et al. 1994; Eisen et al. 1995; Haft et al. 2001.
• PNAS (9); White et al 1998; Nierman et al. 2001; Eisen et al. 2002; Tettelin et al. 2002; Paulsen et al. 2002; Fraser et al. 2002; Seshadri et al. 2003; Seshadri et al. 2004; Schmidt et al. 2005.
• Genome Biology (1) Eisen et al. 2000
• PLoS Journals (6) Wu et al. 2004; Ward et al. 2004; Wu et al. 2005; Wu et al. 2006; Eisen et al. 2006.
• Genetics (1) Tanaka et al.2004.

Available free on publisher's sites (notideal but better than nothing)

• Genome Research (1) Eisen 1998
• MBE (1) Pollock et al 2000.
• Nature (6) Nelson et al 1999; Lin et al. 1999; Eisen 2001; Heidelberg et al. 2000; Eisen 2002; Gardner et al. 2002

Must buy paper

• FEMS Microbiol Lett. Gruber et al 1998
• Human Genetics Wei et al 1998
• Trends in Genetics Eisen 1999
• Mutation Research Eisen and Hanawalt 1999.
• Current Opinion Journals Eisen 2000a; Eisen 2000b Bevan et al. 2001 Nierman et al 2000.
• Methods in Enzymology Nelson et al. 2001.
• Genomics Coleman et al. 2000. Hamilton et al. 2006.
• Research in Microbiology Nierman et al. 2000.
• Theoretical Population Biology Eisen and Wu 2002.
• Env. Microbiol Nelson et al. 2002
• Plant Mol Biol Ermolaeva et al. 2003.
• BBRC Yang et al. 2003
• Genome Biology Review Desjardins et al. 2005.
• IJSEB Badger et al. 2005.
• OMICS Leebens-Mack et al. 2006
• Nature Journals (5) Fraser et al. 2000; Beja et al. 2002; Heidelberg et al. 2002; Read et al. 2003; Heidelberg et al. 2004.
• Science (11) White et al. 1999; Tettelin et al. 2000; Salzberg et al. 2001.; Tettelin et al. 2001; Salzberg and Eisen 2001; Wood et al. 2001; Paulsen et al. 2003; Eisen and Fraser 2003; Methe et al. 2003; Venter et al. 2004; Seshadri et al 2005.
• Photo Res Dassarma et al. 2001

Not available anywhere

• Older paper published in the Journal of Molecular Evolution Eisen 1995.
• Older paper in Methods in Molecular Biology Eisen 1997
• Older paper in Nature Medicine Eisen et al. 1997