Exporting multiple Google Scholar citations to reference managers like Endnote

Google Scholar (GS) is a very useful addition to the searchers arsenal; following a “cited by” trail nicely complements results retrieved by keyword/subject heading searches in databases such as Embase and Medline.

One area where GS is less useful is exporting records to reference management software. Using the settings,  you can set up an export to BibTex, Endnote, RefMan and RefWorks. However, there are two limitation:

  1. You can only export a single record at a time
  2. You don’t get the abstract included

GS, after a little fiddling about, does allow you to save citations to a list (My library) but citations in this list can still only be exported one at a time so this produces no benefit at all. Then I read an interesting pager by Bramer and de Jonge – Improving efficiency and confidence in systematic literature searching* – which mentioned that Harzing’s Publish or Perish can be used to download 1000 references from GS into reference managers such as Endnote.

Could this speed up my click by click populating of Endnote libraries with GS citations (and maybe throw abstracts in as well for good measure)?

Publish or Perish, ” designed to help individual academics to present their case for research impact to its best advantage”, is a small bibliometrics program (approx 1 MB) that can be installed without admin privileges.  You can indeed export multiple GS (and Microsoft Academic Search) results but – alas, alack, alay – it is not the solution to problems 1 and 2 above. Abstracts – not totally surprising as GS doesn’t provide them – aren’t included.  And while you can search the Publish or Perish program in various ways (author, journal, all words etc), it just doesn’t match the way you search GS which is generally a mixture of keyword and cited by searching so you cannot easily replicate a set of results.

The subject line of this post implied a solution to the multiple GS export problem. Actually it is more a request to see if anyone else has found a fix – sorry about leading you on like that. But this issue is one of those not-so-large-but-there-must-be-a-better-way ones so I’m hoping someone can suggest a workaround.

The easiest solution would be for Google to make the My library list bulk exportable. While holding my breath and waiting for that, I wonder if anyone out there has found a clever way around this problem? Perhaps a search from Endnote GS citations to an external database such as PubMed to grab the abstracts in some fiendishly clever way?


* The systematic searching paper mentioned about can be found in PDF format and Word format, with the latter incorporating a couple of corrections as detailed at the end of this post. The paper itself is interesting for giving all sort of search tips as well as providing a framework (including online macros) for translating search queries from one database platform to another (Embase into Ovid Medline etc). It also has some nifty GS search tips and a table giving a useful search syntax summary across various platforms; the PDF version is good for printing this out. Indeed it is a paper that you need to print out and read at your leisure as not really one you can just scan through online so well.

***Note from Krafty*** 10/28/15
This post seems to generate a lot of spam mail in the comments despite anti spam measures.  As a result I have disabled comments from this post. If you want to comment you must email krafty(atsign)kraftylibrarian(dot)com and if the comment is related to the post I will post it manually in the comments.  Sorry for the inconvenience. Thank you.

Brief Intro: Emily Hurst

Emily HurstHello all! Another guest librarian blogger, happy to be joining in to post while Michelle is engaged with MLA Presidential duties. Update: Apparently my scheduled post of this did not go out as expected over an month ago.

My name is Emily Hurst and just as Irene, I too work at the Virginia Commonwealth University Tompkins-McCaw Library for the Health Sciences. I currently serve as the Head of Research and Education. While I only joined VCU Libraries in December I have been a medical librarian for several years. I previously worked with the National Network of Libraries of Medicine, South Central Region.

I am currently active in both the Mid-Atlantic Chapter and South Central Chapters of MLA. This summer turned out to be a busy one. I’ve completed two web migration projects for MLA, worked on recruiting for a new librarian, and learned a whole heck of a lot along the way!

My interests are varied, while I am focused on management and leadership topics I have an extensive history with teaching, training, and technology.

For more about me visit me online or follow me on Twitter.

Preparing for National Medical Librarians Month

Several years ago, the Medical Library Association declared October National Medical Librarians Month. The theme for this year is “Are you a Risk Taker? When you need to be right, ask your medical librarian.” Check out the free available materials at http://www.mlanet.org/p/cm/ld/fid=320.
Will you use those materials or design your own using your library logo and colors? Will the library logo show up on your giveaway pencils, pens, totes, flashlights, caps, magnet, or drinking bottles? Will there be a contest to guess the number of gummy worms in a jar or a contest to guess the number of your institution’s authors displayed on a table trifold? Have you put together quick facts about the Library? Have you designed a special banner for your website?Have you scheduled product demos, a book signing, guest speaker or an art show reception? Will you introduce a new service, a new product or your staff members?

Take advantage of this opportunity to promote and celebrate your Library.

Happy National Medical Librarians Month!

Join this conversation and share your plans with your colleagues.

Helen-Ann Brown Epstein

The Incidental Informationist is officially an informationist!

I recently found out that the NLM Administrative Supplement for Informationist Services that I am included on received funding! This opportunity is very exciting to me because I will be working on an interesting project with a great group of people.

I will be providing data curation services for an R01 project by Dr. Katerina Kechris that generated a Next Generation Sequencing (NGS) dataset from an inbred mouse panel. The mice are closely related, but have known genetic differences. They also exhibit an array of behavioral traits that relate to alcohol use disorders, such as ethanol sensitivity, tolerance and consumption. The NGS dataset is limited to a small RNA molecules known as micro RNAs (miRNAs). These molecules typically regulate gene expression rather than getting read by ribosomes to make protein, as the central dogma dictates. The goal of this project is to discern whether expression any of these miRNAs correlates with the alcohol use phenotypes mentioned above. Additionally, these miRNAs are closely related to those in humans, which could give clues to the mechanisms of alcohol use disorders in humans.

The mouse panel that the NGS samples came from can be used for much more than this alcohol use disorder study, and Dr. Kechris had already written in her R01 proposal that she wanted to share this resource with the research community in the PhenoGen database. Thus, we proposed the following Aims to increase the usability of this dataset by other research groups:

Aim 1 Make the NGS data, appropriate metadata, and code publicly available.

I will deposit the raw data in the NCBI databases along with appropriate metadata, or data that describes their data, to give it context and reusability. I will also deposit the code that they have used to clean and analyze their data to GitHub, so other people can repeat their analyses. This aim also supports a web programmer who will add functionality to the PhenoGen database to support this new dataset. We are also creating an entry for our institutional repository to link all this information together and to our campus.

Aim 2 Create tutorials to show other researchers how to use these data.

All the information is on the web, so it should be usable, right? Well we’re going to make it even easier to use these data by making tutorials in a variety of formats: video, text/static images, and Guide on the Side. These resources will also be referenced on the repository entry.

Aim 3 Evaluate the efficacy of Aims 1 and 2.

Finally, we will evaluate whether the first 2 aims are effective. I will do this by tracking data download and citation statistics, and by including assessments within the tutorials to evaluate their efficacy.

I’m so excited about this project! I can’t wait to get started. Now I just need to figure out how grant funding works here.

Questions and feedback are, of course, welcome.

– Tobin

Demo-ing Apps in the Classroom

Does anyone have any handy tips they use for demo-ing mobile resources in their workshops and presentations to students, residents, nurses etc? I just happened upon a very neat new (at least to me) feature in Chrome that I had not noticed in the “inspect element” development tool, which I occasionally use to look at source code for troubleshooting purposes. If you’re not confident about, responsible for, or interested in coding intricacies, you may not have ever explored this set of tools, and while there are a number of interesting and useful features for the non-techie person, this trick really jumped out at me as being something that I could immediately incorporate into my everyday work.

Apologies in advance for the many readers who are in institutions that don’t support Chrome. I weep for you daily. For the rest, here are the instructions:

When you right-click on a page in chrome, or CTRL-shift-I, you’ll see an option at the bottom of the list to “inspect element”. There’s an icon in the lower panel of the display, which shows the code, that represents a mobile/tablet device, and which, if clicked, resets the page to display as if it were on such a device. At the top of the page, there is also a drop-down menu with options for specific devices, so you can display a page which emulates the display of different iPhone models, iPads, Android devices- even BlackBerry (in case you are going back in time to do an instruction session.)

While, obviously, the display on-screen in the classroom will be small, if one is discussing mobile resources, there’s something to be said about showing them in their native habitat. Does anyone have a favorite tip or tool that they like to use? I’ve struggled with this in the past and basically given up, because the various emulators that were on-line for this kind of use were not especially reliable and certainly weren’t integrated into the instructional process in the same way. Comment away.

I need a vacation after my co-worker’s vacation…

As I stated in my introductory post, I work in a One Librarian Library. I have a .24 FTE library tech. Time manages us more than we manage it.

I dread the middle of August. That is when my co-worker goes on vacation every year. So, last week I was alone. The time alone caused me to gain a greater appreciation of actual One PERSON Libraries. I don’t know how they manage to get everything done. Everything is important to everybody.

So I sat down each morning and had to decide who I would make happy and who I wouldn’t. Do I do searches or do I process Interlibrary Loans? I think the only thing I new for sure that week was that journal renewals would not be on my radar. Especially after I discovered that EBSCO had migrated us over to their Full Text Finder product.

I finally decided that I should try to make each group at least a little happy. I divided up my day into three parts. I spent the first 3rd of my day doing searches. Spent the next 3rd processing article requests. Spent the last 3rd getting myself up to speed on the new product. Did it work? As best as it could I suppose.

I would love to read in the comments how other OPL’s or OLL’s do it. What are your tips and tricks that keep you sane?

Searching in a Comparative Effectiveness Research Way

I know you have been thinking and searching in an evidence based way, but have you switched to thinking in a broader comparative effectiveness way? The mantra for EBP is “based on the evidence available to me today, I will practice.” The mantra for CER starts there and pays attention to real life settings and can have different sizes to the populations. So, for CER, the mantra chatted is, “what works best for what populations in real world settings.” EPB and CER involve experiences of the health care provider, what the literature shows and the preferences of the patient.

There are 4 main ways to search for CER information, PubMed Health, PubMed Topic Specific Queries-Comparative Effectiveness Research, ANDing effectiveness[sb] to your strategy, or just ANDing the phrase “comparative effectiveness“ to your search strategy.

PubMed Health http://www.ncbi.nlm.nih.gov/pubmedhealth/ searches in an clinical effectiveness way. It is geared for the lay public. It has topic reviews, systematic reviews, guidelines and a drug database. When you search PubMed Health, you are searching PubMed at the same time. Be more general in your search topic. It is not a huge database.

Get to PubMed Topic Specific Queries-Comparative Effectiveness Research from the PubMed front page or http://www.nlm.nih.gov/nichsr/cer/cerqueries.html. Put your topic in the search box and click on All for CER results. Notice also you can select a type of study, health disparities, costs and cost analysis or CER as topic.

ANDing effectiveness[sb] to your search strategy is the same as clicking on the Topic Specific Queries-CER page.

Remember you want to search PubMed with words, phrases and MeSH to retrieve all the citations, including inprocess, supplied by publisher or PubMed Central papers. So the phrase “comparative effectiveness” will bring citations for all of PubMed, including the MeSH term, comparative effectiveness research.

Try out any of these methods and send in your comments and questions.

Helen-Ann Brown Epstein

The Incidental Informationist: NCBI Office Hours

I attended a web meeting last week hosted by NCBI staff member Peter Cooper. These meetings are open to anyone who has participated in the course A Librarian’s Guide to NCBI. This course is composed of an asynchronous web class (Fundamentals of Bioinformatics and Searching) and a week long training at NCBI. The course itself is free, but you have to provide your own lodging and travel expenses.

I attended this course last spring, and it was great. Because of my background, I already knew a lot of the molecular biology background information, but attending the course allowed me to observe and example of how to teach this material to novices.  As far as the content about the databases, the amount of information we received was mind-blowing! I can say with certainty that most of the researchers where you work are not proficient at using these tools (even if they think they are) and that you will be able to use them more effectively than they can if you take this course.

Once completing the course, you will have access to a web forum and monthly web meetings to discuss topics covered in the course and implementing NCBI database services at your library. it’s a great, responsive community that has been invaluable to my work.

Follow the link above if you’re interested in applying. I can’t say enough about how great this course was for me.

In addition to a plug for the Librarian’s Guide, we talked about PubMed Labs: a forum for NCBI to test out new functionality of their databases earlier in the development process. New features are being announced via a new category on the NCBI insights blog. Currently, they have two new features: PubMed Also Viewed and SmartBLAST. Let them know about what you think of the new features by commenting on their respective blog posts.

– Tobin

Plain Language Summaries for Translation in Science


At MLA last May, I was walking around the vendor hall, like most of us who attended, I assume. I was on a mission, though. I stopped by every vendor table that had anything to do with publishing or translational science, and talked with them at length about the idea of having plain language abstracts. I’ve been a fan of plain language initiatives for a long time, as evidenced by our library’s Plain Language Medical Dictionary app from some years ago. I wish I could say that I was doing this as a direct result of the PNAS article on the topic published in March, but no such luck. That would have helped make my arguments more compelling, I’m sure. I found the article today, thanks to the National Science Communication Institute retweeting Len Fisher.

A circuitous route, but effective enough to reach me. The article in question was this.

Lauren M. Kuehne and Julian D. Olden. Opinion: Lay summaries needed to enhance science communication. PNAS 112(12):3585–3586. doi: 10.1073/pnas.1500882112 http://www.pnas.org/content/112/12/3585

The article was short and sweet. It talked briefly (very briefly) about alternative modes of science communication, such as social media and blogs, and how they impact on audience, understanding, and adoption of new ideas. The authors then pointed out that these are limited to the few who choose to follow that channel, and it misses the benefits and affordances of mass media channels, a concept which they illustrated with a diagram of how they perceived the connections between the information channels and the audiences. Here’s the gist of it.

Scientists communicate with the public through these channels:
1) Social media and press releases
2) Journalist contacts
3) Lay abstracts
4) Traditional abstracts

The potential audiences are:
1) Public
2) Managers and decisionmakers
3) Scientists in other fields
4) Scientists in your own field

So far so good? There are obviously many more potential audiences as you subdivide these. In my conversations I was rather fond of mentioning insurance companies and agents as critical links in the chain of adopting healthcare innovations who are perhaps more likely to benefit from a plain language abstract. I also talked about the importance of highly motivated patients who take new articles to their clinicians as a recent and influential loop in the information chain that changes practice. For benefits to come through these channels requires not simply that there be a version of the abstract that is in plain language (a lay summary) but also, and equally important, that those lay summaries not be behind a paywall. One of the publishers was absolutely sure their abstracts were not being a paywall, and then when they went to show me, well (ahem), they found they were. As in, the abstracts were locked behind a paywall. Oops.

The most important part of the article’s diagram was the very subtle sideways dashes. Where do the journalists get the hook, the info that leads them to ask more questions and write those mass media articles that reach such large audiences? What triggers the journalist to reach out for those important conversations with the scientists? Well, the press releases, of course. That’s why our organizations work so hard on them. Seeing something posted and reposted on social media is another good way to reach them. But the traditional abstract? Not so much. The traditional abstract is crafted explicitly for other scientists in your field, and only partly for scientists beyond that. Now, a lay summary, a plain language abstract, that has HUGE potential as a way to reach journalists. It’s another marketing tool, beyond being the right thing to do to help patients, or to help get science into the hands of those who actually use it, or to help influence clinical practice and foster more rapid adoption of new discoveries and treatments.

Value of Libraries: Presentations at IFLA

I went to the session for the Measuring Impact and of course like all conferences there is another session, What is Value, I want to attend is at the same time and on the opposite side of the convention center. I have my walking shoes on today.

Here is the summary of the two sessions I mentioned.

Measuring Impact: This focused on measuring the impact on IFLA’s Lyon Declaration. Interesting to an American because I think we take our access to information so granted.

What is Value: I came late to this program so I only got some of the session. British National Library talked about the value to the cities they serve. They were able to determine that for every pound the government spend on libraries they had a ROI of 4 pounds in business, development and jobs. They had a really good slide on the different values which is on my Facebook page.

Awesome presentation from Elliott Shore, executive director at ARL, Measures of Our Time: The Value of Libraries. Perhaps it is because I’m a big proponent of killing of sacred cows but Elliott’s talk really hit home. The best way for me to describe his talk is to point you to the pictures of his slides on my Facebook page. But here are some memorable quotes.

-The world has changed, have we?

-We need a radical change in how we collect statistics.

-We need predictive analysis rather than descriptive analysis.

He also gave a nice shout out to Becker Medical Library as example of a library that is doing a good job of rethinking and showing their value. Good job Becker!