A path towards the extinction of "Impact Factor"

From Ewen Callaway in Nature News:

Beat it, impact factor! Publishing elite turns against controversial metric : Nature News & Comment

Best part – the news from ASM

“And in an editorial that will appear on 11 July in eight of its journals, the American Society for Microbiology in Washington DC will announce plans to remove the impact factor from its journals and website, as well as from marketing and advertising. 

“To me, what’s essential is to purge the conversation of the impact factor,” says ASM chief executive Stefano Bertuzzi, a prominent critic of the metric. “We want to make it so tacky that people will be embarrassed just to mention it.”

This is in relation to the recent preprint I posted about a few minutes ago …

Worth a read: A simple proposal for the publication of journal citation distributions

A very strange & annoying Google Scholar / Biomed Central "glitch" #GamingMetrics

So I discovered a few days ago I had dozens of new publications in 2015.  Cool right?  Here is a screengrab:

And here is another


Until I realized, well, those were published years ago.  WTF are they doing being listed as 2015?  Clearly some glitch. And then I saw a few Tweets that pointed me to figuring out what was going on.

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So I responded

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And some discussion followed

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Fascinating. But I knew my papers were not published as preprints. And that they were published years before Google Scholar was not listing them as being published.

So – what happened? I think I now. These papers were all published in one journal – Standards in Genomic Sciences. The journal used to be published semi-independently by the Genomics Standards Consortium. Then they were transferred to / bout.
ht by / merged with Biomed Central and even the web address was forwarded to BMC where they host the archive of articles from before the transfer.  Then there is a new site with articles from after the transfer.

So when I click on the articles from the Google Scholar site I get to a strange thing.  The articles published before the transfer are also listed on the new site http://standardsingenomics.biomedcentral.com/.

For example – the Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T) is shown here with a 2015 publication date:

Although note the Copyright 2010 little bit.  Which is interesting since this paper was in fact published in 2010.  And you can find it on the other site http://standardsingenomics.org with a 2010 publication data here.

And also in Pubmed and Pubmed Central.

So – even though Biomed Central says the new papers will be in the new site and the old papers will be ket in a separate site that is not what is happening.

For some reasons some of the older papers are now being listed in the new site with a new publication date.  And I assume because Google Scholar scrapes from the journal sites, it found the “new” papers and has now added them to it’s clustering collection and has fed them into my publication list.  And despite trying I am not sure how to fix this.

I tried to “unmerge” the new publications to see if somehow the old publications showed up.  But they did not.  So .. am not sure what to do here other than to send this to BMC and Google Scholar, which I will do.  Ahh – the perils of automated systems …

I note –  this does seem to have possibly temporarily increased my total number of citations since it seems like some of these papers are now being considered twice by Google Scholar but not sure about that.  More digging.

Today’s Open Science Reading: the Open Science Reviewer’s Oath

Well this certainly is interesting: The Open Science Peer Review Oath – F1000Research.  This emerged apparently from the AllBio: Open Science & Reproducibility Best Practice Workshop.  The “Oath” is summarized in the following text from a box in their paper:

Box 1. While reviewing this manuscript:

  1. I will sign my review in order to be able to have an open dialogue with you
  2. I will be honest at all times
  3. I will state my limits
  4. I will turn down reviews I am not qualified to provide
  5. I will not unduly delay the review process
  6. I will not scoop research that I had not planned to do before reading the manuscript
  7. I will be constructive in my criticism
  8. I will treat reviews as scientific discourses
  9. I will encourage discussion, and respond to your and/or editors’ questions
  10. I will try to assist in every way I ethically can to provide criticism and praise that is valid, relevant and cognisant of community norms
  11. I will encourage the application of any other open science best practices relevant to my field that would support transparency, reproducibility, re-use and integrity of your research
  12. If your results contradict earlier findings, I will allow them to stand, provided the methodology is sound and you have discussed them in context
  13. I will check that the data, software code and digital object identifiers are correct, and the models presented are archived, referenced, and accessible
  14. I will comment on how well you have achieved transparency, in terms of materials and methodology, data and code access, versioning, algorithms, software parameters and standards, such that your experiments can be repeated independently
  15. I will encourage deposition with long-term unrestricted access to the data that underpin the published concept, towards transparency and re-use
  16. I will encourage central long-term unrestricted access to any software code and support documentation that underpin the published concept, both for reproducibility of results and software availability
  17. I will remind myself to adhere to this oath by providing a clear statement and link to it in each review I write, hence helping to perpetuate good practice to the authors whose work I review.

I note – I reformatted the presentation a tiny bit here.   The Roman numerals in the paper annoyed me.  Regardless of the formatting, this is a pretty long oath.  I think it is probably too long.  Some of this could be reduced.  I am reposting the Oath below with some comments:

  1. I will sign my review in order to be able to have an open dialogue with you.  I think this is OK to have in the oath. 
  2. I will be honest at all times. Seems unnecessary.
  3. I will state my limits. Not sure what this means or how it differs from #4.  I would suggest deleting or merging with #4.
  4. I will turn down reviews I am not qualified to provide.  This is good though not sure how it differs from #3. 
  5. I will not unduly delay the review process. Good. 
  6. I will not scoop research that I had not planned to do before reading the manuscript. Good. 
  7. I will be constructive in my criticism. Good. 
  8. I will treat reviews as scientific discourses.  Not sure what this means or how it is diffeent from #9. 
  9. I will encourage discussion, and respond to your and/or editors’ questions.  Good though not sure how it differs from #8. 
  10. I will try to assist in every way I ethically can to provide criticism and praise that is valid, relevant and cognisant of community norms. OK though this seems to cancel the need for #7. 
  11. I will encourage the application of any other open science best practices relevant to my field that would support transparency, reproducibility, re-use and integrity of your research.  Good.  Seems to cancel the need for #13, #14, #15, #16. 
  12. If your results contradict earlier findings, I will allow them to stand, provided the methodology is sound and you have discussed them in context. OK though I am not sure why this raises to the level of a part of the oath over other things that should be part of a review. 
  13. I will check that the data, software code and digital object identifiers are correct, and the models presented are archived, referenced, and accessible.  Seems to be covered in #11. 
  14. I will comment on how well you have achieved transparency, in terms of materials and methodology, data and code access, versioning, algorithms, software parameters and standards, such that your experiments can be repeated independently. Seems to be covered in #11. 
  15. I will encourage deposition with long-term unrestricted access to the data that underpin the published concept, towards transparency and re-use. Seems to be covered in #11. 
  16. I will encourage central long-term unrestricted access to any software code and support documentation that underpin the published concept, both for reproducibility of results and software availability. Seems to be covered in #11. 
  17. I will remind myself to adhere to this oath by providing a clear statement and link to it in each review I write, hence helping to perpetuate good practice to the authors whose work I review.  Not sure this is needed.

The paper then goes on to provide what they call a manifesto.  I very much prefer the items in the manifesto over those in the oath:

  • Principle 1: I will sign my name to my review – I will write under my own name
  • Principle 2: I will review with integrity
  • Principle 3: I will treat the review as a discourse with you; in particular, I will provide constructive criticism
  • Principle 4: I will be an ambassador for good science practice
  • Principle 5: Support other reviewers

In fact I propose here that the authors considering reversing the Oath and the Manifesto.  What they call the Manifesto shoud be the Oath.  It is short.  And works as an Oath.  The longer, somewhat repetitive list of specific details would work better as the basis for a Manifesto.

Anyway – the paper is worth taking a look at.  I support the push for more consideration of Open Science in review though I am not sure if this Oath is done right at this point.

Some readings on Gender Disparities in Scientific Publishing

Just a little post here with a collection of links to what I have been reading recently on Gender disparities in scientific publishing

Bibliometrics: Global gender disparities in science : Nature News & Comment

which I found out about from

How to calculate #MyGenderGap for publishing scientists

which I found out about from

My Gender Gap: Is there value in calculating the gender ratio of coauthors?

which I found out about from

Gina Baucom on Facebook

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Some other reading of interest:

I am highly skeptical of the CHORUS system proposed by scientific publishers as an end run around PubMed Central

Just read this news story … Scientific Publishers Offer Solution to White House’s Public Access Mandate – ScienceInsider

It reports on an effort by various scientific publishers to create something they call “CHORUS” which stands for “Clearinghouse for the Open Research of the United States.” They claim this will be used to meet the guidelines issued by the White House OSTP for making papers for which the work was supported by federal grants available for free within 12 months of being published.

This appears to be an attempt to kill databases like Pubmed Central which is where such freely available publications now are archived.  I am very skeptical of the claims made by publishers that papers that are supposed to be freely available will in fact be made freely available on their own websites.  Why you may ask am I skeptical of this?  I suggest you read my prior posts on how Nature Publishing Group continuously failed to fulfill their promises to make genome papers freely available on their website.

See for example:

We need to make sure such papers are freely available permanently and the only way to do this is via making them available outside of the publishers own sites.  Pubmed Central seems to be a good solution for this.  I would be happy to hear other possible solutions – but leaving “free” papers under the control of the publishers is a bad idea.

UPDATE 6/27/2013

Saw this Tweet

//platform.twitter.com/widgets.js Seemed potentially really interesting. Read the story and got pointed to a new Nature paper on the ancient horse genome. I guess not so surprisingly, despite the fact that they report a new genome sequence, it is not openly available. We really cannot trust Nature on this can we? They could say “Well, this is a draft genome, and we did not mean to apply our policy to draft genomes.” Well, that would be weird since, well, they have applied this to draft genomes before. And then I decided to search for other examples … and in about ten minutes I found a few. See

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Quick post – Nature Publishing Group buys into #OpenAccess publisher Frontiers

In case you have not hear – Nature Publishing Group continues to play around with open publishing and other open science initiatives (when they switch some of their big journals to fully OpenAccess I will stop referring to it as playing around …).  The latest is that Nature has bought into the Frontiers publishing group which publishes a series of Open Access journals.  For more on this see:

Hat tip to many people who have sent this info to me.  Not 100% sure what to make of it, but it is interesting …

Ten simple ways to share PDFs of your papers #PDFtribute

There is a spreading surge of PDF sharing going on in relation to a tribute to Aaron Swartz who died a few days ago.  For more on Aaron and tributes to him see the collection I am making here: The Tree of Life: RIP: Aaron Swartz.  For more on the PDF sharing see this CNET story for example: Researchers honor Swartz’s memory with PDF protest and http://pdftribute.net.

I should say, sharing your PDFs is not necessarily clearly not enough (the license on the PDF may affect what people can do with them if they feel constrained to follow the law).  It is also critical to think about the level of openness of a paper, but I will save most of the comments on that for another time. What I wanted to do here is point out various ways to share PDFs for people who don’t know how …

UPDATE 1/14: See follow up post 10 things you can do to REALLY support #OpenAccess #PDFTribute

Ten simple ways to share PDFs of your papers.

1. Publish your paper in a fully #openaccess journal (so called GOLD OpenAccess).

Such journals immediately post your paper online for all to see and frequently also post your paper in various formats to repositories like Pubmed Central.  For a list of such journals see the “Directory of Open Access Journals“.  In my opinion, this is the best, and, well, really only viable long term option.  This is what I do for papers from my lab.

2. Publish your paper in a non #openaccess journal that has the option of selecting / paying for #openaccess on a case by case basis. 

Many journals that are not fully #openaccess have the option of paying extra to have your paper be published in an #openaccess manner and then the journal handles not only posting the paper on their site but also frequently depositing in a repository of their or your choosing.  UPDATE: Note – in many cases the licenses used by journals for such one-off “open” publishing are not fully open, despite what some of the journals claim so proceed with caution (see PLOS Biology: Why Full Open Access Matters for example).

3. Publish in a non #openaccess journal that releases papers to a repository after a delay.

Many journals put papers behind a paywall initially but then “free”them up in some way after a set period of delay.  For example a large number in biomedicine will deposit papers to Pubmed Central and also make them freely available on their website after 6 months.  Frequently as with #2 above, the licenses associated with such release of papers are not fully open, but this is a way to have your papers be at least accessible to others after a period of time.

4. Deposit your paper in a preprint server before you submit it for publication.  

For more on preprint servers see

Examples of commonly used preprint servers include

5. Self-archive your PDF in a repository (so called GREEEN OpenAccess).

Various repositories out there exist for posting ones papers.  They work in essence like a preprint server though some people use them more for posting papers after they have been published so I am listing them separately here.  More detail on self-archiving can be found here.  A good source of information about repositories is the Registry of Open Access repositories.  Also the Directory of Open Access repositories.  Another good source is SPARC. Also see here.

One repository commonly used in biomedicine in Pubmed Central.  Alas one is only allowed to post papers there by oneself if the work in the paper was funded by an NIH grant.

Another approach is to use arXiv as a repository where you can post things even after they are published.

Another growing venue for self-archiving is an institutional repository.  As many universities expand their commitment to open access or access university repositories are becoming a source of more and more publications.  Check to see if your institution has a repository and use it.

UPDATE: Note, just depositing your paper in a repository or preprint server does not necessarily mean your paper is open access.  Look in detail at the license and copyright policies of the archives you are considering before using them.

6. Self post your PDFs to a website you control.

If you do not have a personal website and/or do not know how to post a paper to your website, well, you should learn more about this.  A few simple ways to quickly post a PDF for others to get access to include

Create a new blog / website with a system that allows posting PDFs.  There are many many options for this.  One is Posterous.  Another is WordPress.Com.  There are certainly a million other ways.  Upload a PDF to Google Docs and then share the Google Doc link.  Post to Dropbox and share the link there.  Etc. etc. etc.  I ended up using WordPress.Com to create my lab page and to post all my PDFs.

7. Post your PDFs to an online reference collection.

Many systems now exist for collecting and collating and sharing reference collections online.  They include CiteULike, Zotero, and Mendeley.  I particularly like Mendeley right now in part because it makes it very easy to share PDFs privately or publicly.  I for example have posted all my own papers on Mendeley as well as papers of my father’s (for more on this see The Tree of Life: Freeing My Father’s Publications and Free Science, One Paper at a Time | Wired Science | Wired.com).

8. Create an academic profile page and post PDFs there.

Many systems now exist for creating a personal Academic profile of sorts.  One example is Academia.Edu. I have created a page here  Jonathan Eisen | University of California, Davis – Academia.edu although I confess I have not been updating it much.

9. Post to Slideshare.

Though many people end up only posting slideshows to Slideshare, and I use it for that purpose, I have posted many of my papers there as well. See for example:

10. Post to “Data” archives.

There is a large growing collection of places to post “Data” to share it with others.  Some of these sites also allow posting of papers.  For example, I have posted multiple papers to Figshare, a great data sharing site that can be used to post and share just about anything. I have also used Figshare for this (for example – here is my PhD thesis there).

11. Ask a Librarian. (Yes it goes to 11)

Probably the best way to figure out how to better share your PDFs if the options above don’t work for you (or even if they do) is to talk to a librarian.  They are the most knowledgable people in regard to methods and systems and other issues for sharing academic work.


Some related posts from The Tree of Life



Other ideas? Please post in comments …


RIP: Aaron Swartz (collection of news stories, articles, etc)

Aaron Swartz from the AWL

Compiling links to stories, posts, information about Aaron Swartz and his untimely death. RIP Aaron.

About Aaron

News and Posts about his death
More from 1/14
More from 1/17-22

Storifies about Aaron Swartz

PDF upload tribute

And the winner of ‘most nimble new science journal web site’ is mBio

Kudos to mBio the recently announced new open access journal from ASM. I posted a little bit about it a few days ago. There was some back and forth in the comments w/ people involved in the journal and, impressively, they have already modified some sections of the web site to clarify some of the things I and others felt were unclear. A pretty rare thing in the world of journals as far as I know, to make changes quickly. Normally there would be some sort of deliberative, painfully slow, and annoyingly conservative process in response to comments/feedback. Good job Barbara Goldman and ASM. And happy to have ASM moving a bit more towards an Open Access future.

Science journals: asking for concision-good, restricting # of refs-bad

Once again, I am being driven crazy by some aspect of scientific publishing. And today it is arbitrary (or silly) restrictions some journals place in the number of references allowed. I have been dealing with this because I have a paper in Press in one such journal (alas not an open access journal, and not my first choice of journals, but the paper will be published under a CC license …more on this in another post )

Anyway, on top of my own issues, I was reminded of the perils of length/reference restrictions by an email from Jean-Michel Claverie from CNRS. In the email he told me of a situation involving a recent paper in a high profile journal with a name that begins with the letter N. This paper did not cite some highly relevant earlier work of Claverie’s in PLoS One and when he wrote to the author to politely point this out, he was told that the reference was basically removed for space reasons. I have seen this happen many times with a variety of journals and the explanation for some lack of reference to relevant work is always something like “oh yes, of course we knew about that, but had to leave it out for space reasons” or “well, you know, they only allow 30 citations, so we had to leave some things out”.

Sure, in the past, when printing articles and keeping track of references was difficult, this may have made sense. But a HUGE part of science is giving and getting credit for work. And thus it baffles me why some journals enforce strict restrictions on the number of references allowed. Basically what this says is – it does not matter what type of work you did – it could only possibly have been built up the work of (insert # here) previous studies. This is just wrong in so many ways. One option to solve this would be for these journals to allow expanded reference lists in online material – and for these lists to somehow get picked up by citation indexing systems. But this is something they need to solve. And until then, people should be aware that by publishing in such journals you may indirectly be doing a disservice to the people whose work contributed to your own.