Cytometry and Antibody Technology

Core Facility Acknowledgment Accounting 101 – How to make sure your work is being recognized.

by | Dec 19, 2014 | Archives | 0 comments

This archived post was originally written by Ryan Duggan when he was the Technical Director. Ryan has since moved to a position outside of the university. 

A recent article in Biotechniques has spurred some interesting discussions in the Academic Core Facility (or as we cytometry cores like to call them, Shared Resource Laboratories – SRLs) world. The gist of the article states that all too often core facilities are not properly acknowledged in publications that clearly are using the services provided by their institutional cores. The flip-side of this argument is that investigators are already paying for the services rendered so that fee is essentially all the “acknowledgment” that is required. However, since many times core facilities are partially funded by government agencies, the services (and more accurately the service recharge rates) are being subsidized. Therefore, the payment isn’t payment enough.

Whether you agree or disagree with this basic tenet is really beyond the scope of this post. What I’d like to share here is my way of fostering the proper relationship with my users such that they feel compelled to acknowledge the excellent work of the core instead of feeling obligated to do so.

What follows is basically a three-part approach to accomplishing the goal of being acknowledged as a core facility in publications that utilize your services. The reason you may wish to do this could vary, but likely involve justification of your core facility’s existence to your institution’s administrators or various “Centers” you may receive funding from. For example, as part of the University of Chicago’s designation as a Comprehensive Cancer Center from the NCI, we must keep track of cancer-related publications that utilize our core facility. So, obviously it would be easiest for us to search PubMed for the inclusion of our core facility’s name or even the cancer center support grant number in the reference. However, many times our facility is omitted from the acknowledgement section of the publication. To help modify this behavior, we need to first find the publications, then organize them, and lastly reach out to our authors/users to help them understand why acknowledgements are important. Here are these steps.

Part 1 – Finding publications that should designate attributed to your core facility’s work.

Fig. 1 – Keywords to find references based on your core’s services.

You can use the “Saved Searches” functionality within PubMed to find relevant articles and have them emailed to you directly as soon as something meets the search criteria. There’s already a good tutorial on PubMed that will walk you through the steps, so I won’t go into that in great detail, but let me summarize my steps.

Figure 2. Part #1 of search yields over 168,000 results.

I jump right into the Advanced Search Builder in PubMed using various keywords for different parts of the search structure. For example, I limit the search results to an affiliation of University of Chicago. There are a few external users that I’d like to track as well, but I put them in a separate search. The first part is to put in keywords based on any part of the text that your users may use to describe what they did in your facility. Remember, many users refer to any part of flow cytometry as “FACS” so you’ll want to make that part of your search criteria. Figure 1 shows you some of the ones I use (note the use of ‘Or’ boolean to search on any of these keywords).

Figure 3. Search restricted to affiliation of University of Chicago

Next I use the “Add to history” link near the search to hold onto those search results temporarily (Figure 2).

I click the “Add” link next to search #1 to add these 168,000+ results back into the builder, and then refine the search by using the “And” boolean and restricting the “Affiliation” field with ‘University of Chicago (Figure 3.)

Figure 4. Search based on keywords, affiliation, date range

You can further refine the search based on Date ranges or excluding reviews or a bunch of other search criteria using the same strategy (Add to history, then add those results back to the Builder and refine again). I find this method of going back and forth between the history table and the builder easier than trying to put everything into one complex boolean structure. Click search to view your results (Figure 4).

Once you’ve created your search criteria and confirmed that it is giving you what you’ve intended, you’ll want to save the search, using the “Save search” link below the search box. Figure 5 shows you some of the options available for setting up the saved search. Note that you’ll need a PubMed profile to set this up, so the first time you try and save a search, it’ll ask you to create an account. Here, I’ve chosen to send me an email

Figure 5. Saving the search and setting up email digest.

weekly on Mondays (when I’m likely to have free time) so I can review the new references. I’ve also placed some text (or even a custom #) so that I can filter my email properly and it doesn’t get lost amongst the email clutter. I save the search and wait for the emails. By the way, you can now set up all sorts of notification. For example, I’ve recently been doing a lot of microparticle stuff, so I have a separate digest setup to send me email notifications of new publications using flow/image cytometry to analyze microparticles (or microvesicles or micro particles, etc…)

Part 2 – Organize references and tag them to easily create reports later.

In part 2, my goal is to receive these email notifications, skim through the publication and then find a way to organize the references neatly and efficiently.

Figure 6. Email notification from My NCBI

The emails arrive in my inbox on Monday mornings as references become available. If there are no new references, you will not get an email. Figure 6 shows an example of what this email looks like.

Next, I follow the link, and read through the manuscript to ensure the work being reported was in fact from my core. If I’m unsure, I can always ask the author, but I tend to recognize work done on my instruments.

Figure 7. One-click add to Zotero button in URL bar

One thing that becomes evident is you need to have a way to manage all these references. There are a ton of ways to do this from the most rudimentary word doc or spreadsheet to sophisticated software management tools. The tool I like for this part is Zotero. It’s similar in function to things like Endnote or Mendeley, but it’s basically an organization tool for references. The part I like most about Zotero is that there’s a Chrome extension that allows one-click adding of references to my database (Figure 7). Plus it will go out and find the PDF of the full-text reference and store that locally as well (when available). It lives in the cloud and can be accessed anywhere.

Figure 8. Zotero Organizing tool for references (running on Mac)

Once in Zotero (Figure 8), I can add tags to the references to help organize them further. I like to tag things by services used (Cell Sorting vs. Analyzer Usage vs. Other things), Instrument referenced (e.g. FACSAria), Whether this could be used for my Cancer Center grant renewal (UCCCC), and other informative tags. Then, down the road when I need to pull up some justification for a new sorter, I can include a list of publications that utilized the cell sorting service or maybe even a specific sorter.

This makes organizing and searching through references a breeze.

Figure 9. Thanks for the acknowledgement

Part 3 – Compel investigators to acknowledge your core facility.

Now comes the hard part. How to suggest to your facility users that they should be acknowledging your core without sounding like a jerk.

As I’m skimming references, I’ll quickly jump to the acknowledgement section and check for recognition of the core, or perhaps individual members of the core (either is fine with me). If the user does acknowledge the core, I make sure to send them an email thanking them for doing so. This positive reinforcement goes a long way toward ensuring this type of action recurs in the future. I also explain why it’s important to us that the core be acknowledged. An example email is shown in Figure 9. Of course congratulating them on a job well done can only help to sweeten the deal.

Figure 10. Maybe next time…?

If I see there is no mention of the core in the acknowledgements or methods section, I’ll send a similarly positive email, but ask them to consider acknowledging us in the future. I make sure to include some example text of what I would like them to say, as well as send them a link to the example text on our web site (Figure 10).

Of course, you can save these emails as templates and simply change the name and journal to personalize them.

The responses I’ve received from these emails has been tremendous. I think they are both appreciative of the recognition of their work as well as understanding of the needs of the core to be recognized.

We all understand the need for metrics such as publications and their importance in validating the success of core facilities. However, instead of taking a passive approach and hoping people read your web site asking to be acknowledged, the method proposed here takes a proactive approach that has already increased the desired result.

PubMed is pretty comprehensive, but there could be other sources for finding work being discussed that should point back to your core facility. Magazine articles, intra-institutional articles or highlights, blog posts, etc… all should be explored and stored. You can use a series of other rss feeds or Google search alerts to help you find this information too. Asking a PI to mention the core facility in an intra-institutional newsletter is certainly within your purview.

Happy Hunting!


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