Pubmed to trial new collaboration status tool to block interaction with ex-collaborators

Bethesda, MD. November 23, 2015.
Pubmed is to ease de-collaboration (when one stops working with a collaborator) woes by tweaking its ‘Collaboration Status’ function – allowing ex-collaborators to disappear from view without users removing them as a colleague.
The literature network will trial the new collaborator tool in the United States, with plans to roll out the changes worldwide after receiving feedback.
David Lippmann, product manager for Pubmed, said in a statement: “Starting today, we are testing tools to help researchers manage how they interact with their former collaborators on Pubmed after their collaboration has ended. When researchers change their collaboration status to indicate they are no longer in a collaboration, they will be prompted to try these tools.
“The work is part of our ongoing effort to develop resources for scholars who may be going through difficult moments in their lives. We hope these tools will help people end collaborations on Pubmed with greater ease, comfort and sense of control.”
The tools will allow users to limit the papers, data sets or status updates that an ex-collaborator will see. Without having to de-collaborate or block a former research partner, Pubmed will also make sure their name and ORCID ID do not appear in the site’s paper feed.
Their name will not be suggested either when users tag researchers in papers.
Users will also be able to edit who can see past papers with a former collaborator and untag from papers written with that person.

Crosspost: Using Google Scholar in Scholarly Workflows

I wrote this for the Google Scholar blog where it was posted yesterday.  I am reposting it here, in part because comments are not allowed on the GS Blog (not sure why) and some people have asked me about that.  So here it is

When Anurag Acharya asked me recently if I would be interested in writing a guest post for the Google Scholar blog in relation to the 10th anniversary of Google Scholar I immediately responded “Yes.” Literally, that was the full content of my email response email response to his request. Why did I answer so enthusiastically? Well, I can put this down to three main reasons:

So – in thinking about what to write for this post, I came up with three main topics I thought would be good to cover – how I got interested in topics of searching for and sharing scholarly papers, how I use Google Scholar, and some ideas about future possible uses of Google Scholar.

Part 1: Some Background 

One day, in ancient history, my wife came home from work (at a biotech startup up focusing on bioinformatics) raving about this new search engine “Google” that people at her company were talking about. As someone who thought of himself as on the cutting edge of web technology, I was a bit dismayed that I had not somehow discovered this myself. But I got over that and tried it out. And, after searching for my name (and being impressed with how well this new search engine worked on such an important topic) I immediately started playing around with searching for scientific papers and data. I did this, I guess, because ever since I was in college, I had been becoming more and more interested in (or some would say obsessed with) issues relating to finding and sharing scientific knowledge.

Without going into two much detail some of the factors that contributed to my obsession included:

  • Working as a shelver and then assistant in the Museum of Comparative Zoology library in college and seeing how people struggled to find papers of relevance to their work;
  • Spending many years in graduate school (in the 1990s) working on projects that had been largely unstudied since the 1960s, including one (so called adaptive mutation) where researchers claimed to have discovered something new in the 1990s but had in fact missed a rich literature on the topic from the 1950s and 1960s (e.g., see this from 1955).
  • Building and sharing databases where I was trying to include a description of every paper that had been published about specific genes. I note – thanks to the Wayback machine my Stanford website from when I was a PhD student is still available – although alas the specific linked databases are not. I have reposted some of them for people to see what they were like (though many of the links in them are busted). See for example my sites on RecASNF2MutS and more
  • Working on projects to catalog everything known about specific organisms in association with work I was doing to characterize the genomes of these organisms

In these and other projects I had seen and experienced just how much time could be spent on searching for papers and data about a particular topics. I am not sure I had a well-defined strategy in every case but I came to rely upon some preferred methods including:

  • “Citation walking” where one takes a paper of interest and then asks “how has this paper been cited?” and traverses across the literature via citations
  • Searching for keywords in abstracts and titles
  • Browsing through specific journals
  • Looking for papers by specific authors
  • For data, I mostly would look in specific centralized data repositories such as Genbank for DNA sequence information and PDB for three-dimensional structural data on proteins.

And of course many other approaches. Nothing really novel or brilliant here though I do think I got pretty good at how to carry out such searches. But one of the challenges was each approach had to be done in a different system and some of the systems were only available for a fee and some were not even online. And even with lots of time and pain, many things could be missed.

Thus when my wife introduced me to this new fangled Google thing my thoughts rapidly turned to – how can I use this new tool to help in finding and then sharing scientific papers or data about these genes and organisms I was studying? Did Google searches solve all my “issues” in this regard? Alas, no. But jump forward ~15 years to today and I am quite amazed in retrospect how much of my scholarly workflow flows through Google Scholar. But rather than try to recall and write about how my workflow changed with the advent of Google Scholar I thought I would just jump to the present time and discuss some ways that I use Google Scholar now.

Part 2: Using Google Scholar today

When working on this post I started to look around at how I use Google Scholar and I confess I was amazed at how many different ways I use it in my work. Here are some examples:

Tracking and using citations. One major general use of Google Scholar lies in tracking of citations to specific scholarly works. Here are some ways that I use such information:

  • Citations to individual works. A key aspect of scholarly work in many fields is examining how specific works are cited. Such information has many uses include discovering new works on a topic by seeing how specific papers from the past are cited, assessing impact of works, ego satisfying, and more. For many years, information on how a specific work was cited was nearly impossible to come by without paying for access to citation tracking databases. Now, with Google Scholar I (and others) can very rapidly gather such information.
  • Citation from diverse sources. One aspect of using Google Scholar to track citations to individual works is the way GS finds citations in diverse sources – not just in the peer reviewed scholarly literature. Now, in some ways this can be viewed as a limitation (some may not want to count or even know about citations from self published white papers, for example). But in others ways this is a wonderful thing as one can find citations to one’s work from very diverse sources outside of the “normal” mold.
  • Citation metrics. It is not a large conceptual leap to go from the ability to track citations to individual works to the ability to create summary statistics about citations across many works. There are many indices for such purposes – some useful and some not. But whatever you think of such indices – Google Scholar has opened up the ability for people to calculate such metrics for oneself or to offer services to calculate metrics for others. Such indices can be used in many ways but perhaps the most common is to summarize the citations for one individual researcher. Which leads into my next topic …

Google Scholar Pages. Perhaps my favorite development from Google Scholar in the last 10 years has been the introduction of Google Scholar Pages for individuals. I make use of my Google Scholar page and pages of others for dozens of things including these:

  • Citation metrics for myself. See above for a discussion of citation metrics in general. I use Google Scholar pages to examine citation metrics for myself and my papers all the time (right now GS shows two summary statistics H-index and I-10 index). And I use this information in many ways including putting it on my CV, including it in grant reports, and examining which of my scholarly works have had more “impact”.
  • As landing page for my publication list. Once one has a GS page, GS automatically adds new publications to one’s list and also updates citation counts and other information regularly. Thus I now include a link to my GS page on my blogs, my work web sites, and in my email signature.
  • To keep track of my coauthors. I have been blessed (and perhaps a bit cursed) to work in a field (genomics) where many projects involve large-scale collaborations across many institutions, involving many researchers. And I have found that a nice way to track these coauthors is via GS (although – note to GS folks – there used to be a way to show, publically, all coauthors in a list but I cannot seem to figure out how to do this anymore).
  • Author disambiguation. For people like myself with a relatively unique name, when others search for my scholarly works, they are pretty easy to find (although I note the fact that there is another Jonathan Eisen out there who publishes some works with a bit of a conspiracy theory angle has been both good and bad for me at times). But for many others, their name is not a perfect way to find their work. This may be because they have a name that is relatively common, or it may be because they have changed their name (e.g., after marriage). For such people creating a GS page can be very useful because once one trains GS with a set of works, it can find new works by that same person quite well (I first found out about this author disambiguation by GS when Anurag gave a talk at a meeting I organized last year). GS is certainly not the only tool in author disambiguation and others – like author UIDs (e.g., ORCIDare almost certainly better long term options. I note – author disambiguation may seem like a esoteric topic to many but it has major implications on important issues such as gender equity in academia, since women are much more likely to change their names during their career than men are.
  • Automated updates of new papers by specific authors. One option associated with GS author pages I use extensively is the ability to “follow” specific authors and get notified of new publications of theirs.
  • To keep track of a collection of people. Most researchers do not regularly update their individual publication pages on their websites. However, if those researchers have GS pages one can keep track of their new papers quite easily (either by the follow option mentioned above or just by browsing occasionally). For example, for my microBEnet project I curate a list of GS pages for researchers in the whole field with connections to studies of “microbiology of the built environment” and thus (hopefully) help others keep up with what is going on in the field.
  • Who is in a specific field? One feature of GS author pages that is not used a lot as far as I can tell, but which has some value is the “areas of interest” tag one can add to one’s profile. Though not everyone uses such tags, I have found they are a useful tool in finding researchers working on specific topics. For example, I list “symbiosis” as one of my areas of interest and if I click on the link for that on my page I get a list (sorted by citation counts – which is both useful and annoying) of others who have listed that same area of interest. And many of the people in this list I am not familiar with yet they do work on topics in which I am very interested.

Automated discovery of new papers by topic. Pretty much all scholars these days are drowning in information and in keeping up with scholarly works. There are many reasons for this of course, and there are also some solutions. I find, for example, that social media is a great way to keep up to date on what new papers are coming out or have come out recently. But social media does not find everything and as someone who is responsible for keeping others up to date on various fields (e.g., this is one of my jobs at microBEnet) I also rely on both manual and automated searchers of the scholarly literature to find new papers or old papers I have missed. GS has two key ways to help in this regard. The first is relatively simple in concept but takes advantage of the power of Google indexing – which is just directly searching GS for papers on particular topics. And the advanced search options allow some customization of such searches. But as someone who is quite busy, I do not actually end up searching GS for new papers all that often. Instead I rely upon automated searches through various services including PubmedPubchase, and GS. I use GS in two ways for such automated searches:

  • Create an alert. When one does a search on GS, in addition to results one is presented with an option to “Create an alert” (which I think may only come up if one is logged in with a Google account). I now have dozens of such alerts in operation. To avoid getting drowned by the results I set them up to send only once a week and I filter them into a separate mail folder that I only look at when I have time. But I frequently find interesting new papers this way.
  • GS Updates. Another option now available, if one has a GS profile, is to use the GS Updates system (which I have written about before here and here for example). This system uses one’s publication list to scan for new papers that are related in some way to one’s prior work.

Many other uses of GS. I have gone on perhaps way too long here so I am only going to briefly mention a few other uses of GS.

  • Finding online versions of papers. Unquestionably one of the most valuable uses of GS is to find online versions of scholarly works. But since others have written extensively about this I will just say the following: if you publish any scholarly work I recommend you make it freely and openly available AND that you make sure that it gets indexed by GS.
  • Full text searches of the literature. Another critically important aspect of GS is that it facilitates full text searching of the scholarly literature which is important for many reasons.
  • Finding works outside of the “normal” places to publish. Another key feature of GS is that it indexes much more than just publisher’s sites. If one posts a preprint on one’s own web server, that paper may show up in GS (which I think is a good thing). GS also indexes many diverse sources of scholarly works and thus helps in finding works that may otherwise not see the light of day.

Part 3: Where do we go from here?

As an active user of Google Scholar I of course have many comments, complaints, ideas and thoughts about what it could do better and where it might go in the future. And there are SO many things that could be added or improved upon – things like better figure and table searching, better exporting of information, better abilities to curate and create collections and to then use such collections as training sets for automated searchers, and more and more and more.  I have written about some such issues and suggestions from time to time in my blog (see for example, this and this and this).  There is certainly lots of work to be done.

But in thinking about this I realized that making a list of issues and suggestions is only of limited value. What I think GS really needs is a better public forum where GS can discuss what their plans are for the future and also where users and developers can discuss what they would find useful. And though I see some places for such discussions on the Google Scholar blog and in related sites, I don’t see a lot. So – I would like to end with a call for GS to create a better site for such discussions of the future of GS …

Update – Adding some comments and responses from Twitter

Draft post cleanup #7: Scamming Pubmed Central Deposition Rules

Yet another post in my “draft blog post cleanup” series.  Here is #7, from February this year.

I continue to be a bit annoyed by the Pubmed Central system for depositing your own papers there.  Well, actually, not annoyed with the existence of the system.  But am annoyed that you can only do it if you have an NIH grant ID associated with the paper you are depositing.  I am tempted to set up a system for sharing NIH grant IDs that would allow non NIH funded researchers to scam the system and to get their papers into Pubmed Central.  Almost certainly, people at NIH would not like this, but not sure whether this would be considered “illegal” or just “annoying”.

And I am still unclear as to why Pubmed does this.  Genbank is NIH funded but will take sequences from any researcher no matter the source of funding for the work.  Anyway – I have not set up a NIH grant ID sharing system but if you want to submit an article to Pubmed Central and do not have an NIH grant ID, you might want to just ask someone who has one for a grant covering a similar topic at a similar time period.  I do not think NIH would figure out that the grant did not actually fund your work.  And you could even use the NIH grant search engine that pops up when you use the manuscript submission system or search Pubmed directly.  Not that I would recommend anyone break their rules or anything like that.

Open Parkinson’s – need for more progress on Open Access for papers on Parkinson’s

I have a new aspect of open science I am concerned about. It is research on Parkinson’s. This comes from having a family member with Parkinson’s who is not doing so well. And I am getting frustrated with trying to read up on some Parkinson’s related research but hitting a paywall for much of it. Uggh. This is so incredibly annoying and, in many ways, immoral. If we want to speed up the work towards cures, treatments and prevention strategies, we need to share more broadly everything we know about this disease. Yes, I know – publishing costs money. And yes, I know, open access and open science does not in any way solve all the problems associated with scientific and medical discovery and research. But I do know that openness can accelerate the pace of progress.
If you look at “openness” in relation to Parkinson’s studies it is pretty disappointing. For example, of 60,400 publications that come up in Pubmed with a simple search for “Parkinson’s” 9053 have free full text available. That’s is just not enough. One thing that is interesting (and disconcerting) is what it looks like over time:

In some ways, there is good news here. The percentage of free text papers goes up over time from 2000-2009. But there is much bad news too. First – even in the best year, more than 70% of papers are not freely available. But perhaps more disconcerting, the percentage of freely available papers drops in 2010 and 2011. Why is this? I think most likely it comes from the delays in deposition to Pubmed Central that happen at many journals. So, it is good that some material gets out there, and apparently a higher fraction is getting out over time. But there is a big delay in the release of much of this material and the max percentage is still low. That is really unfortunate as the best way to catalyze scientific discovery to me is via rapid, open sharing. Imagine, for example, if Twitter posts were only available after 6 months. Useful? I don’t think so. What about weather information? Wait six months for a forecast? Sure, some aspects of scientific research do not need any input from others. But if papers are not important, then, why do we all fuss over them so much? That is because they contain knowledge, techniques, data, ideas, theories, and more. And it would be really better for all if everyone could have access to the full text of all such papers immediately.

Now mind you, I have only focused here on availability of free full text. There is another major issue in “open access” which is, well, openness. Openness of papers involves the rules on use, distribution and reuse. Many of the “free full text” papers in Pubmed Central have restrictions on how those papers can be used. The ideal to me is for the papers to be fully open such that anyone can redistribute them, repost them, take material from them, and use it in any way (with attribution). Why is this important? Well, it would allow anyone to create a Parkinson’s papers database, for example, with interesting search and discovery features. Or anyone could use a paper as part of a course, without having to worry about permissions. Or anyone could use material from a paper as part of a news story or blog post without getting into fights about fair use.
Now – there are some Parkinson’s related papers available out there outside of Pubmed, in institutional repositories and such. But these are not easy to find at this time. So in a way they don’t count for much.
I will be writing more about Open Science issues and Parkinson’s in the future. But for now I have a request. Anyone out there working on Parkinson’s please find a way to make your discoveries more freely and openly and rapidly available. I realize many/most of you are very passionate about this disease. I realize many of you work your tails off. And openness may be the last thing on your mind when working, struggling to get grants and make discoveries and deal with all your other job requirements and life issues. But even if you for some reason choose not to publish in an open access manner, at least post your papers on a website. Deposit them into repositories. Create a Mendeley account and post your papers there. Try and find a way to get them into Pubmed Central. Try to find ways to get your papers picked up by Google Scholar. Do something to increase the probability that your work will have an impact.
I will be writing more about open science and Parkinson’s in the future. Stay tuned.

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 …

Fun with Ligercat: pubmed word clouds

I have been having enormous fun over the last hour playing with LigerCat.  I was searching for ways to build tag clouds for papers in Pubmed and this came up: LigerCat: Using “MeSH Clouds” from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature.   And they have a web site to do searches: LigerCat Literature and Genomics Resource Catalogue

So, of course, like many others, the first thing I did was search for myself:

Eisen JA

I then repeated the search, but excluded articles from the SIGS journals, since I have about 100 of those articles that are in essence “Genome sequencing reports”:

So this was fun. So then I played around with a variety of other searches


Indoor Microbiology

University of California[Affiliation] Davis[Affiliation]




Some things did not work for some reason(microbiome, metagenomic) but overall this is a useful quick way to get a feel for topics covered in some area.