Data producers deserve citation credit, says Nature Genetics

Posted on 05 Oct 2009 by Maxine Clarke

Datasets released to public databases in advance of (or with) research publications should be given digital object identifiers to allow databases and journals to give quantitative citation credit to the data producers and curators, according to the October Editorial of Nature Genetics (41, 1045; 2009) .

After reviewing the arguments for assigning a citable credit to data, particularly those which are released publicly before formal publication in a journal, as is increasingly the case in some fields (and required by some funders), the Editorial asks: "What form should citable data identifiers take? They must work with existing unique resource identifier conventions and with the existing well-funded stable repositories used by research communities. However, these identifiers are not just for locating data but are for stably identifying the data units and versions with particular data producers, curators, funders and affiliations in a citable form. Because publications are currently the main source of scientific credit and because publishers have already developed citable digital object identifiers (DOI), it would seem to be their opportunity to grasp or to fumble. We propose citing DOIs that tag a combination of repository, database, accession, version, contributor and funder.

Of course, precise citation of all research output represents the bare minimum of respect for colleagues and competitors. This journal also endorses communication between data producers and data users. Whereas it is impossible for journals to restrict the use of data already in the public domain, we can show evidence of communication between producers and users to referees. Many funders of large resource projects now require a data release policy and plan for global analysis by the data producers. These parts of the successfully refereed grant should be published as a ‘marker paper’ or deposited in a citable preprint archive such as Nature Precedings. At very least, the details of the producers’ work and intents should be available to users in a citable form in the database holding the data. Data users can submit an email demonstrating that they have contacted the data producers with their plan for use of the data and showing that they have read the producers’ data release policy, conditions and plan for analysis."

Please see also the continuing Nature Network online discussions about pre-publication and post-publication data release. We welcome your views there.

Nature Chemical Biology on assigning responsibility and credit

Posted on 29 Sep 2009 by Maxine Clarke

The journal’s October Editorial outlines new policies that refine the responsibilities of authors and require author contribution statements in Nature Chemical Biology research papers ( Nat. Chem. Bio. 5, 697; 2009):

“When a manuscript is submitted to Nature Chemical Biology, one author assumes the role of corresponding author. This individual, typically a principal investigator of the study, serves as the central point of contact for the manuscript and manages communication with the journal while the paper is under consideration. Corresponding authors also take responsibility for coordinating communication among the paper’s authors and for certifying that all authors have agreed to the contents of the manuscript prior to submission. Our ”https://www.nature.com/authors/editorial_policies/authorship.html">updated authorship policy now clarifies the corresponding author’s role in managing the manuscript’s author list: prior to submission, the corresponding author “ensures that all authors are included in the author list, its order has been agreed by all authors, and that all authors are aware that the paper was submitted”.

Why are these changes needed? Because publication records remain an important metric for assessing the research productivity of individual scientists, it is essential that author lists are accurate and are determined in an objective and open manner. Most authorship disputes result from lack of clarity on two main points: (i) defining whether an individual’s scientific contributions warrant authorship and (ii) determining the order of the author list. Obtaining agreement on these points is made more challenging by differences in authorship models among disciplines and individual laboratories, and by the fact that collaborative papers in interdisciplinary areas often include data from multiple research groups."

The Editorial goes on to describe further details of these policies, including the introduction of authors’ contributions statements in published articles.

Nature journals’ authorship policies.

Nature Chemical Biology guide to authors.

About the Nature Chemical Biology editors.

June highlights from Nature Biotechnology

Posted on 25 Jun 2009 by Maxine Clarke

Nature Biotechnology’s June issue contains several articles of particular interest to scientists as communicators, authors and entrepreneurs. Here are a few highlights:

Nature Biotechnology 27, 514 – 518 (2009).

Science communication reconsidered.

Tania Bubela et al.

As new media proliferate and the public’s trust and engagement in science are influenced by industry involvement in academic research, an interdisciplinary workshop provides some recommendations to enhance science communication. Among these are that graduate students need to be taught about the social and political context of science and how to communicate with the media and a diversity of publics; that the factors contributing to media hype and errors (largely of omission) are explicitly recognized to allow science institutions and media organizations informed communication policies; research on science communication should be expanded to include online and digital media; more investment in the systematic tracking of news and cultural indicators, including traditional news outlets but also radio, entertainment TV, religious media, the web and new documentary genres; and a new ‘science policy’ beat in journalism courses to fill in the gaps between the technical backgrounders preferred by science writers and the conflict emphasis of political reporters. Finally, the authors argue, if there is a major threat to science journalism, it is that science journalists are losing their jobs at for-profit news organizations; new models of support for science journalism are needed, in which online digital formats blend professional reporting with user-generated content and discussion.

Nature Biotechnology 27, 528-530 (2009):

Maters of their universe.

Genentech—the biotech venture that launched a thousand companies—is no longer its own master. In March, majority stakeholder Roche reached an agreement with the South San Francisco, California–based company under which the Swiss drug maker would take over the biotech for $46.8 billion. But many remember those first years when a small team of bright, intellectually disciplined young scientists—often rowdy and personally eccentric people—got the company up and running. Randy Osborne and Laura DeFrancesco caught up with a few of those pioneers to talk about that era, their time and how they felt leading the charge.

Nature Biotechnology 27, 531 – 537 (2009).

Wasting cash—the decline of the British biotech sector.

Graham Smith, Muhammad Safwan Akram, Keith Redpath & William Bains

Undercapitalization and overgenerous boardroom compensation for management have been major contributors to the poor performance of UK biotech. Despite historic leadership in European biotech, the UK’s industry has suffered a near collapse in the past two years and now has little private or public investment and no candidates for world-class companies. Why do shareholders allow UK public biotech companies to accumulate top management that pays itself so much, is unmotivated to drive shareholder value and as a consequence apparently drains the company of resources, notably cash? These questions, and others, are addressed in the feature.

Nature Biotechnology website.

Nature Biotechnology guide to authors.

Nature Biotechnology conference programme.

Nature Biotechnology focuses and supplements.

New rules for presentation of statistics in cell biology

Posted on 18 Jun 2009 by Maxine Clarke

New rules for the presentation of statistics in the Nature journals are described in the June Editorial of Nature Cell Biology (11, 667; 2009). From the Editorial:

Thanks to advanced imaging technologies and better integration with molecular and systems approaches, cell biology is undergoing something of a renaissance as a quantitative science. Robust conclusions from quantitative data require a measure of their variability. Cell biology experiments are often intricate and measure complex processes. Consequently the number of independent repeats of a measurement can be limited for practical reasons, yet the variability of the measurements can be rather high. Cell biologists have developed good intuition to guide their analysis of such constrained datasets. Biological complexity and the reliance on intuition can cause culture shock to physical scientists crossing over into cell biology (a kind of extension of the celebrated ‘two cultures’ concept of C. P. Snow).

With the arrival of quantitative information and ‘-omic’ datasets, statistical analysis becomes a necessity to complement instinct. The problem is that statistical tools are built on basic assumptions such as the independence of replicate measurements and the normality of data distribution. Usually, sizeable datasets are prerequisite for statistical analysis. Alas, these can be as hard come by as a biostatistician (n is typically well below 5). The result is that all too often statistics (frequently undefined ‘error bars’) are applied to data where they are simply not warranted.

There are no easy solutions to rectify the prevalence of poor statistics in cell biology studies. However, an obvious recommendation is to consult a statistician when planning quantitative experiments. Consider whether n represents independent experiments (you may actually be publishing a measure of the quality of your pipette!) and whether it is large enough for the test applied. Avoid showing statistics when they are not justified; instead, show ‘typical’ data or, better still, all the measurements. Importantly, displaying unwarranted statistics attributes a misleading level of significance to the data. Always describe and justify any statistical analysis applied. We have updated our guidelines to reflect these recommendations. One key rule: if the number of independent repeats is less than the fingers of one hand, show the actual measurements rather than error bars. If you wish to present error bars, include the actual measurements alongside them.

Finally, please remember that you are interrogating a complex system — be careful not to discard ‘outlier’ data points on a whim, as they may well be as relevant as clustered measurements. One is naturally inclined to ignore data that does not match the hypothesis tested, but biology is rarely as black and white as we would like. Do not make ‘hypothesis driven’ research become ‘hypothesis forced’!

Nature Immunology on authorship policy

Posted on 26 May 2009 by Maxine Clarke

Nature Immunology (10, 553; 2009), in its June Editorial, summarizes the new responsibilities Nature Publishing Group has established for authors.

‘Author contributions’ statements were introduced by the Nature journals in 2006 to encourate authors to identify the efforts of each coauthor. In a Nature Editorial last month (Nature 458, 1978; 30 April 2009), it was announced that all Nature journals now require that an ‘author contributions’ statement accompany all original research papers. Authors can decide how detailed these descriptions can be, but no author should be left out.

From the Nature Immunology Editorial:

The purpose of authorship statements is to give coauthors due credit for their relative contributions. This concern is not insignificant to a ‘middle author’, who may be seeking promotion or a new position. Such an investigator may not have a ‘first author’ publication to their record but nevertheless has provided a substantial contribution to the development or execution of certain studies. Likewise, for studies that result from the collaboration of multiple laboratories, authorship order can sometimes be difficult to ascribe. Identifying who did what provides greater transparency to the process of assigning authorship.

In the same Nature Editorial, new responsibilities were announced for ‘senior authors’. These responsibilities include ensuring that the original data described in the study are preserved and retrievable for reanalysis, confirming that the data presented in the manuscript are representative of the original data collected, and anticipating and minimizing any obstacles to the sharing of data, reagents, materials or algorithms described in the published work. For collaborative studies, at least one senior author who represents their group must assume these responsibilities for their contributions to the study. Often the ‘corresponding author’ is the laboratory chief and is thus in a position of authority to speak for others in their group. But this is not always the case. Sometimes the laboratory head, acting as a mentor, will assign ‘corresponding authorship’ to another author as training toward the development of independent research career skills. However, the responsibilities outlined above would remain with the most senior researcher of the group, who is not necessarily the corresponding author.

NPG policies on authorship.

Nature Photonics on combating plagiarism

Posted on 04 May 2009 by Maxine Clarke

In its May Editorial, Nature Photonics (3, 237; 2009) describes some of the ways in which the Nature journals combat scientific misconduct and practices such as ‘guest’ authorship. Part of the Editorial concerns plagiarism:

“Many forms of plagiarism exist, but the goal is generally the same — to garner false or undue credit. Plagiarism sometimes involves reuse of another author’s published work, but it is commonly thought that the most typical tool of the plagiarist is self-plagiarism: the reuse of substantial parts of an author’s own published work, particularly without appropriate referencing, and less commonly, duplicate publication, in which the results are recycled in their entirety.

The peer-review process provides a net for catching offenders, but it cannot provide a fail-safe barrier. As a result, Nature Photonics is now starting to use the plagiarism-detection software ”https://www.crossref.org/crosscheck.html">CrossCheck, which makes comparative checks between provided manuscripts and those previously published and in an existing database. Any manuscript that seems to show an abnormally high match will be immediately investigated. Unfortunately, plagiarism can also occur without verbatim duplication of words or data. And it is here that the lines between normal and acceptable activity and plagiarism become smeared, and the likelihood of detection and punitive repercussions is diminished.

Using another researcher’s arguments and logic, even if the text is not identical, without due reference is intellectual plagiarism. This type of plagiarism can be subtle and as simple as not including a reference to a highly relevant previous paper. Citation-related plagiarism, whether it is intentional, or due to gross negligence, can give an untruthful impression of precedence, reassigning credit from the original discoverer to another person.

When reporting scientific messages, it is an author’s responsibility to find and acknowledge the critically relevant literature, or at least to have endeavoured to do so with rigour. Failing this can result in falsely apportioned claims, albeit caused by negligence.

If plagiarism is suspected in research results published by us, it is our policy to conduct an immediate investigation and if deemed appropriate to contact the author’s institute and funding agencies and consider a formal retraction of the paper. Although it is often the first authors who have historically borne the brunt of confirmed misconduct allegations, our editorial policies highlight the serious responsibilities of all coauthors: “submission to a Nature journal is taken by the journal to mean that all the listed authors have agreed to the content”. It is unreasonable to expect each author to be responsible for every aspect of the paper, but it is the responsibility of the corresponding author to manage the understanding that all authors are expected to have made reasonable attempts to check the findings submitted to a journal for publication."

The full text of this Nature Photonics Editorial.

Nature Photonics guide to authors.

About the Nature Photonics editors.

Nature journals policy on plagiarism.

Nature journals policy on authorship.

Clarifying authors’ duties and making “contributions statements” mandatory

Posted on 30 Apr 2009 by Maxine Clarke

Here is the text of an Editorial in the 30 April issue of Nature (458, 1078; 2009 – free to access online):

The Nature journals encourage authors to treat their data and their collaborators with the respect that their communities demand. High-profile journals have a duty to reinforce the trends towards greater transparency and to help scientists to fulfil their responsibilities as researchers and authors. We are therefore introducing small but important changes in our policies to reflect these goals.

In a previous Editorial (Nature 450, 1; 2007), we asked for feedback about whether we should require senior or corresponding authors to sign a statement that they had taken some specific ‘integrity insurance’ steps before the manuscript was submitted. Some applauded this idea, but most were not in favour. (Some of the feedback can be seen here.) Major doubts were expressed about the ability of corresponding authors to take on such responsibility given the diversity of collaborations. The belief was also expressed that such signed statements would too often be worthless box-ticking exercises. Although we regretfully accept these realities, we believe that we should go further in spelling out the responsibilities of co-authors, and in requiring an implicit acceptance of them.

Accordingly, we have modified the Nature journal policy on authorship, which is detailed on our website. For papers submitted by collaborations, we now delineate the responsibilities of the senior members of each collaboration group on the paper. Before submitting the paper, at least one senior member from each collaborating group must take responsibility for their group’s contribution. Three major responsibilities are covered: preservation of the original data on which the paper is based, verification that the figures and conclusions accurately reflect the data collected and that manipulations to images are in accordance with Nature journal guidelines, and minimization of obstacles to sharing materials, data and algorithms through appropriate planning.

Corresponding authors have multiple responsibilities, but we now make it clearer that the author list should include all appropriate researchers and no others, and that the order has been agreed to by all authors. They are expected to have notified all authors when the manuscript was submitted, they are the point of contact with the editor and they must communicate any matters that arise after publication to their co-authors.

Another change is that we have strengthened our policy for statements of authors’ contributions. This policy was first introduced nearly 10 years ago (Nature 399, 393; 1999) to make the credit due to individual co-authors more explicit. Since then, authors of Nature papers have had the opportunity to include in their papers a statement that details each author’s role in the published work. Over the past 10 years, the proportion of authors who choose to include this has risen dramatically.

This acceptance, and discussions with authors who have chosen not to include such a statement, has led us to change our policy. Rather than ‘strongly encouraging’ such statements, we now require them for publication of original research papers in Nature and the Nature research journals. The detail provided can vary tremendously and authors are left to structure them as they see fit. We insist only that no author be left out.

To ensure that authors are familiar with these changes, we will shortly require the corresponding author to confirm that he or she has read the Nature journal policies on author responsibilities and is submitting the manuscript in accordance with those policies.

Nature journals’ authorship policies.

John Dick interview at Nature Reports Stem Cells

Posted on 22 Apr 2009 by Maxine Clarke

John Dick, the subject of this month’s Q&A at Nature Reports Stem Cells (April 2009), identified the first cancer stem cell, in leukaemia. The widely used xenotransplantation assay that he developed can confirm the identity of prospective haematopoietic stem cells by demonstrating their ability to re-establish a human blood system in the mouse. He is a professor at the University of Toronto and its affiliated Princess Margaret Hospital and Director of the Program in Cancer Stem Cells at the Ontario Institute for Cancer Research. Monya Baker, Editor of Nature Reports Stem Cells investigates his call for more controversy.

Q: What’s the best advice you’ve ever received as a scientist?

A: Everyone in science has to have an ego. You have to think: Here’s a question that nobody knows an answer to, and I think I can come up with a way to answer that question. Of course you always want to answer the questions that nobody has answered before, but if an experiment is worth doing, it’s worth doing even if there are a number of people also trying to get the answer. If someone else gets there first, it just means that you can go on faster to the next question.

Nature Reports Stem Cells home page.

The Niche, the blog of Nature Reports Stem Cells.

About Nature Reports Stem Cells.

Nature Genetics on representing authorship in PubMed

Posted on 08 Apr 2009 by Maxine Clarke

In its April Editorial, Nature Genetics (41, 383; 2009) addresses the issue of contributor attribution in PubMed, the index provided by the US National Library of Medicine (NLM) and used by many researchers to navigate tens of millions of biomedical publications dating back to 1948.

Nature Genetics, in common with many other journals, regularly receives queries from authors about how to format their manuscripts so that authors are correctly credited. As stated in the Editorial, “The short answer is that authors must be listed in the paper’s byline (the author list under the title) or identified elsewhere in the paper as authors to appear as authors in PubMed. PubMed curators can also identify and index consortium collaborators identified as such within the paper. If contributors are listed as consortium members, but not identified as authors, they will appear in PubMed only as collaborators.”

But the questions don’t stop there. Journals are increasingly being asked about how authors can ensure “equal authorship” is represented in PubMed or why the email address for the corresponding author does not always appear in PubMed, for example. Journals provide this type of information as XML tags (‘metadata’), but what happens to it when it reaches its destination?

Authors need to be able to provide documentation of their roles in their consortium papers to funders for grants and to committees for career advancement. So that journals can provide this information consistently, unique author-controlled identifiers will need to be universally adopted and linked in publisher metadata. Nature Genetics suggests that instead of being controlled by any organization, “even one as central to everyday research as NLM’s invaluable indexing service”, there needs to be “agreed conventions that allow authors and third-party indices to offer distributed solutions for different applications. All of these solutions would be fed by the metadata provided by authors with their word processors and by publishers with their tagging schemas.”

The Editorial continues: “Our recommendation is that PubMed should leave the publisher-supplied metadata as it is supplied if it has ambitions to provide the more detailed author affiliations that authors frequently ask us about. Authors, please think whether you would welcome the wider adoption of existing technical conventions that allow universal and distributed appreciation of your growing reputation, or whether you would rather continue to muddle along trying to extract a reputation from the slowly-evolving customs of a national central library. Whatever solution we end up with, we should keep clear the distinctions between research data collection, analysis and writing.”

Nature Chemical Biology answers authors’ questions

Posted on 27 Jan 2009 by Maxine Clarke

Nature Chemical Biology is offering new content and functionality to authors. Online enhancements to the chemistry functionality are described here, with examples. And the journal is also introducing Primers, a series of peer-reviewed, one-page summaries of chemical or biological topics designed to jump-start readers’ ability to comprehend research in a particular area. Green fluorescent protein is the topic of this Primer, if you would like to take a look at the format. (See here for further information about this particular Primer.)

In the February 2009 issue (Nature Chem. Biol. 5, 61; 2009), the editors offer further guidelines and tips for authors submitting their research to the journal, following on from previous Editorials (Nature Chem. Biol. 4, 715; 2008 and 5, 1; 2009). In the February Editorial, the editors answer common questions:

Do you actually read cover letters?

Should I submit a Brief Communication or an Article?

What do I need to submit?

Must my manuscript be perfectly formatted?

Are presubmission inquiries useful?

How are papers assigned to editors?