The success or failure of Web 2.0 efforts for scientists depends to a large extend on the availability of cool applications that make the everyday life of a scientist easier. Many of these applications of course already exist, but I would argue that there is a lot of room for improvement. And I would also argue that in a lot of cases we just have to take the example of the Web 2.0 world and adapt it to the needs of scientists – Nature Network itself would be an example of this approach.

Meetings and Seminars
Scientific meetings and seminars are one example were we can do better. Web 2.0 is an ideal approach for this, and Upcoming is the classic application. There are of course a number of websites that list meetings and seminars for scientists, but they either focus on the big meetings or list just the seminars of a particular institution. Look at the discussion How to find a science event in Berlin in the Nature Network Berlin Forum to see what I mean.

What can we do to improve the situation?
We can wait that either one of the big players or a clever startup has a great idea. But one of the attractive features of Web 2.0 is user participation. We need more discussions between scientists and software developers on what is needed and what can be done. These discussions are of course already taking place, but science bloggers can do more to collect interesting ideas and articulate them. We want the integration of reference managers in online writing tools such as Google Docs or Buzzword, but how do we make our voice heard?

Secondly, we can write applications ourselves. The barriers of entry have become really low, and one reason are the APIs (application programming interfaces) of both science applications or conventional Web 2.0 apps:

• Pubmed
• Scopus
• Connotea
• Google Maps
• Google Docs
• YouTube
• Flickr
• Technorati
• Facebook
• eBay
• Amazon
• Yahoo

And there were hints of a Nature Network API. With some skills in PHP, Python, Java or Ruby, anybody could create an interesting mashup with these APIs over a weekend. Maybe linking Connotea tags to YouTube videos and Flickr pictures?

Google Publish or Perish is a new science writing tool that facilitates paper submissions. The tool was field-tested at the NIH and should be particularly valuable for open access and public access journals. Accepted papers are automatically added to your Researcher ID account.

For more information, read this forum post by Matt Brown.

Last week I received email invitations from three different journals to submit a research article. I should have felt flattered, but it is unclear why it is me that received invitations to the journals Biomarker Insights, Genomics Insights and International Journal of Medical Sciences. All three journals already exist for a few years, and I wouldn’t say that the focus of my research is biomarkers or genomics.

Then I thought about a recent blog post by Gunther Eysenbach: Black sheep among Open Access Journals and Publishers. In this post he calls the sending of unsolicited emails simply spamming and argues that there are also throw-away journals out there from shady publishers trying to cash in on the current surge of interest in open access publishing.

And this is what all three journals mentioned above have in common: they are open access journals and the author pays for the (accepted) article. It is obvious that any journal that gets paid by the author is interested in soliciting articles whereas a subscriber-pays journal would be interested in attracting new readers. There is nothing wrong with this, but there are two potential problems. (1) Like most people I don’t like spam. (2) Journals with an author-pays business model have to be extremely careful about the quality of their papers.

Potential authors should first check whether the journal (if it is a biomedical journal) is indexed in Medline (Genomics Insights is not) and either has a reasonable impact factor or (for new journals) receives enough citations.

Our recent discussion on public access made me have a closer look on the options I have for my own papers. The results aren’t pretty.

Most journals allow posting post-prints on a university website
The copright agreement with the journal is the easy part. Most publishers allow posting of post-prints (after peer-review, but not the journal PDF) in a non-commercial repository, usually the repository of your institution. Below are the policies of three prominent publishers.

Elsevier
As an author, you retain rights for a large number of author uses, including use by your employing institute or company. These rights are retained and permitted without the need to obtain specific permission from Elsevier. These include (...) the right to post a revised personal version of the text of the final article (to reflect changes made in the peer review process) on the author’s personal or institutional web site or server, with a link to the journal home page

Springer
An author may self-archive an author-created version of his/her article on his/her own website. He/she may also deposit this version on his/her institution’s and funder’s (funder-designated) repository at the funder’s request or as a result of a legal obligation, including his/her final version, provided it is not made publicly available until after 12 months of official publication. He/she may not use the publisher’s PDF version which is posted on www.springerlink.com for the purpose of self-archiving or deposit. Furthermore, the author may only post his/her version provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer’s website. The link must be accompanied by the following text: “The original publication is available at www.springerlink.com”.

Nature Publishing Group
When a manuscript is accepted for publication in an NPG journal, authors are encouraged to submit the author’s version of the accepted paper (the unedited manuscript) to PubMedCentral or other appropriate funding body’s archive, for public release six months after publication. In addition, authors are encouraged to archive this version of the manuscript in their institution’s repositories and, if they wish, on their personal websites, also six months after the original publication. In all these cases, authors should cite the publication reference and DOI number on any deposited version, and provide a link from it to the URL of the published article on the journal’s website.

The policies of some of the smaller publishers can be more difficult to find. Sometimes an email exchange with the publisher will be necessary.

Many universities have institutional repositories
OpenDOAR is a directory of open access repositories. My university doesn’t yet have an institutional repository. After a short email exchange they offered to host my post-prints on a public webserver. I currently have no details on the software platform used or how many people in my university use this service.

Post-prints may no longer be available
Most publishers don’t allow posting of the journal PDF. You have to post the final manuscript after per-review (post-print). The problem: I no longer have these manuscripts for papers published more than a few years ago – thinking that the PDF would be enough.

Your post-prints are hard to find
OpenDOAR has a search function, but searching several institutional repositories at once is complicated. Your best bet is probably to find a paper in Pubmed and then try to find the institutional repository for that author. But maybe you have to check several institutional repositories if the authors are not all from the same institution.

Conclusions
Posting your paper in an institutional repository can be a challenging project. It is therefore advisable to think about this before paper submission. What is your publication strategy? Do you need open access? Does the journal offer free content after an embargo period of 6 or 12 months? What is the journal policy regarding post-prints? And most importantly, keep the manuscript version right after peer-review. A central repository such as Pubmed Central doesn’t have most of these shortcomings.

A real Web 2.0 application needs a serious mashup). At least the folks at ResearcherID thought so. You might remember that ResearcherID creates a unique author ID for each interested scientist and was launched by Thomson Scientific (recently renamed to Thomson Reuters) earlier this year.

The new ResearcherID features include a mashup with Yahoo Maps that shows the location of your collaborators. Here are some examples from fellow Nature Networkers:

• Martin Fenner
• Raf Aerts
• Bob O’Hara

Wentworthville, Australia is the furthest I can go to find a paper coauthor.

Now the really interesting question would be: when do we see mashups with Nature Networkers? For a start we have the Nature Network London Flickr Mashup created by Matt.

The legal disputes following the withdrawal from the market of two drugs for the treatment of pain (the COX-2 inhibitors rofecoxib and valdecoxib) have led to another critical examination of the paper publishing process. I have written in February about the drug company Pfizer trying to obtain confidential peer review documents from the journals JAMA and NEJM. Courts in Chicago and Boston have denied such requests.

An article and accompanying editorial in this week’s JAMA look at guest authorship and ghostwriting in publications related to rofecoxib (better known as Vioxx, produced by Merck). Guest authorship was defined as an author that does not meet authorship criteria. The Uniform Requirements for Manuscripts to Biomedical Journals from the International Commitee of Medical Journal Editors (ICMJE) define authorship as follows:

Authorship credit should be based on 1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) drafting the article or revising it critically for important intellectual content; and 3) final approval of the version to be published. Authors should meet conditions 1, 2, and 3.

Ghostwriting was defined as the failure to designate an individual that made significant contributions to the research or writing of a manuscript.

The JAMA article did a systematic analysis of the court documents obtained during litigation related to rofecoxib. Guest authorship was identified in 16% of research articles and 26% of review articles; ghostwriting was identified in 13% of research articles and 10% of review articles. The editorial in the same issue is called Impugning the Integrity of Medical Science: The Adverse Effects of Industry Influence and dicusses this article as well an another article called Reporting Mortality Findings in Trials of Rofecoxib for Alzheimer Disease or Cognitive Impairment in the same issue. The editorial proposes that drastic action is necessary and includes a list of 11 measures.

Criteria for authorship and disclosure of financial interests are clearly defined not only by the ICMJE, but also by the World Association of Medical Editors (WAME) and by most journals. And the European Medical Writers Association (EMWA) has published guidelines on the role of medical writers in peer-reviewed publications. As medical writers usually don’t fulfill the authorship criteria defined above (with the possible exception of review articles), they should rather be acknowledged. The EMWA guidelines propose the following wording:

We thank Dr Jane Doe who provided medical writing services on behalf of XYZ Pharmaceuticals Ltd.

The rules are clear and it is also clear that there will be violations of these rules. Guest authorship and ghostwriting are probably common practices, not only in publications supported by drug companies. Typical examples would be the inclusion of the department head that did little more than to provide financial support or the exclusion of the technician that did critical experiments but is not acknowledged. Cases of suspected guest authorship or ghostwriting should be taken seriously and the papers in JAMA will ignite a renewed discussion on these topics.

For different views on this topic, look at Exit ghost by Juan Carlos Lopez over at Spoonful of Medicine and Cut it out. Cut it out now. by Derek Lowe at In the Pipeline.

The new NIH Public Access policy started this past Monday. Fellow Nature Networker Graham Steel has summarized this week’s reaction of the blogosphere. I would like to highlight some of the discussions we had here on Nature Network.

Bob O’Hara wonders about the cost of publishing in Open Access: Show us the Money!. He argues that shifting the costs from reader to author can create problems. Most authors, especially those with limited resources, would be reluctant to pay submision fees if they can also submit to a journal without those fees. But the reader-pays model could give authors more bargaining power with journals. The post created an interesting discussion about the different aspects of publishing costs

Graham Steel pointed out the Second European Conference on Scientific Publishing in Biomedicine and Medicine that takes place in Oslo September 4-6 in Oslo, Norway. The conference focusses on open access and bibliometrics.

I wrote two blog posts about public access. In Germany, most research organizations have signed the Berlin Declaration, but in contrast to the new NIH policy, there is no mandatory public access. In another blog entry, I looked at public access to my own research papers – most of them are only accessible for those with institutional journal subscriptions.

What is the next step for me? That I need to learn more about self-archieving – both the policies of the journals I have published and the institutional repository at my university.

I did a little experiment to figure out whether the fulltext versions of my last 15 papers (published between 1997-2008) are available online. The result:

• 3 papers available for everybody
• 10 papers only available from within my institution (Journal subscription required)
• 2 papers only available for purchase

Interestingly, the papers in the two journals with the highest impact factor are both available as fulltext. And the third fulltext paper is my paper with the most citations (and published in 1998).

Conclusion: Not that anyone would care what I have to say, but you have to work in an institution with a good library budget to read my papers.

Starting this week, papers submitted from NIH-funded research have to be made publicly available no later than 12 months after publication. But what is the current situation in Germany, especially mandatory Open Access?

The Berlin Declaration from October 2003 was a strong statement of support for Open Access and was signed by all major research and funding organizations, including Deutsche Forschungsgemeinschaft (DFG), Max Planck Gesellschaft (MPG), Helmholtz-Gesellschaft, Fraunhofer-Gesellschaft and Leibniz-Gemeinschaft. In contrast to the new NIH public access policy (and the Welcome Trust and Howard Hughes Medical Institute), there is no mandatory Open Access in any of these organizations.

The German Publisher Springer, one of the largest STM (Science, Technology and Medicine) publishers, has a Springer Open Choice option. Authors who pay for this option will retain the copyright of their paper and the article will be made available with full Open Access.

Around christmas, mandatory open access for NIH-funded research was signed into law:

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

Starting April 7, the new NIH Public Access Policy implementing this law will take effect for most NIH grantees. The NIH is soliciting comments until May 1st for this new policy. Open Access and this new policy are complicated topics that simply can’t be covered in a single blog post. This week will certainly see a lot of discussion on this topic, both on Nature Network and elsewhere. Please state your view on the topic either in blog entries or join the discussion in the Publishing in the New Millenium Forum. I will try to summarize (some) of the discussion at the end of this Public Access Week.