Tag Archives: Pubmed

Happy 2023 (aka “Reset!”)

6 Jan

Happy New Year, everyone! As we crawl our way into another year, I find myself believing 2023 is going to be a reset year. For one thing, I’m facing a significant birthday. “Get busy living or get busy dying,” as Andy Dufresne said in The Shawshank Redemption. Also, surviving 2020, 2021, and then 2022 kind of feels like Andy, “who crawled through 500 yards of shit and came out clean the other end.” I don’t think I’ll ever be ready for the “post-COVID new normal”, but I’m definitely ready to wash off some of the stink.

So I say hello again to this space. I’ve gotten so far from my regular (usually Friday) writing. I’m out of practice, both in thinking and in writing thoughts about work and life, that I’m going to challenge myself with an easy goal at first: 3 Things and a Question. To give myself some structure, I’m going to share 3 interesting and/or fun things I came across each week, along with one question I’ve been mulling over. Feel free to use the comments section to share your wisdom to the latter.

Here goes for the first week of the year:

Self-Evaluation Tool for Culture of Open Scholarship Service

This is a terrific tool for libraries, scholarly communications departments, data management services, and other working in the open science arena. Developed primarily to address the efforts in Europe towards policies and frameworks in Open Science and Research Coordination, it provides guidance and definitions to help groups and/or institutions measure where they are meeting the goals around open access, open education resources, and data management and sharing. I’ve asked my staff to read it and I plan to lead us through a self-assessment over the coming months. It will be a worthy and worthwhile effort.


Tip of the hat to my friends and colleagues at the University of Maryland Health Sciences and Human Services Library for this one. I was working on a reference question that led me to seeking out how to easily get the XML for a record in PubMed. I googled something like, “how to get XML from PubMed entry” and top o’ the results was a link to the HSHSL’s “Ask Us” page, How do I save a reference from the new PubMed in xml text file format? BINGO! It led me to PubMed2XL, a super easy web application where all you have to do is enter a PMID(s), click “Download XML File”, and VOILA! I’ve bookmarked this site, for sure.

The World’s Largest Beaver Dam

I subscribe to the weekly email from TED-ED and this week I learned all about why beavers build dams. I also learned that the biggest beaver dam in the world is in Alberta, Canada. Road Trip!


How long is something “new”?

P.S. That’s my new pup, Bayer. He came home the week before Christmas – the best present and a great new start!

Larry, Darryl, and Darryl

17 Jun

[A Monday afternoon editorial.]


Sometime within the past couple of months, the National Institutes of Health decided to start enforcing the requirements of its public access mandate that went into effect in April of 2008. On the one hand, it was nice of NIH to give its funded researchers a year or two or five to come around to following the rules. Yet on the other, the recent applied pressure has sent a flurry of befuddled and irritated biomedical researchers, clinical researchers, research coordinators, administrative assistants, and any number of other folks my way, usually in a deadline-induced panic, trying to figure out what the heck they’re supposed to do to get in compliance with the law.

For awhile, I was slightly irritated myself – at the researchers, that is. When it comes to “the Mandate,” I’ve been announcing and instructing and updating and troubleshooting ad nauseum for these past years. I’ve sent out countless invitations to talk to departments, to labs, to admins, to the staff in research funding (and to their credit, many – though hardly a majority – took me up on it). I have made it my business to know every in and out and upside down aspect of this Policy since before it became law, lo those many years ago now. And so, over the past couple of months, I’ve stifled more than one, “What rock have you been living under?!” retort to more than one, “NIH has instituted another new thing!” whine landing in my email inbox or coming across my phone line.

All of this said, as I have worked to smooth and soothe and clean up messes these past weeks, I can’t help but come to the conclusion that NIH, and more, the National Library of Medicine, could have done us all a HUGE favor if they had taken just a moment to think through the naming conventions that they chose for the various resources and tools associated with this Policy. Why, for the love of Pete, did you name PubMed Central, PubMed Central? Why is there something so crucial as “My Bibliography” buried within “My NCBI”? Why are there “journal publishers that submit articles on behalf of authors,” as well as “journal publishers that submit manuscripts on behalf of authors”?

If you think that I typed the same thing twice there, read again. Closely. Which is EXACTLY what you have to say to researchers over and over and over again.

And that’s kind of my point. In one of the most basic textbooks of library science, Richard Rubin’s, Foundations of Library and Information Science, every aspiring librarian learns a handful of principles related to information management and organization. As Rubin warns, “Unless there are ways to organize it,it (information) quickly becomes chaos.” (p. 171)

Perhaps one can make a strong argument that the conundrum that is the naming conventions of NIH/NLM resources and tools isn’t really a naming convention problem at all. There certainly are distinctions between them. “My Bibliography” is not the same as “My NCBI.” PubMed is a completely different database than PubMed Central. How hard is this to grasp?!  I argue, harder than the average librarian and/or programmer and/or chief resource namer of highest level (aka CRNHL – pronounced “colonel” – on Twitter) ever realizes.

I bring this topic up on my informationist blog because I find it pretty funny (in a black humor, ironic sort of way) that one of the primary reasons I was placed on a research team was because of my expertise in information organization. Librarians are the experts in applying the standards, language, and processes that help people communicate, find, and access information more easily and efficiently. This being the case, I can’t help but wonder why we shot ourselves in the foot here, choosing labels that are so easily confused and swapped one for the other. Like homology, homography, or holograms and homograms… who can’t help but get these mixed up? And when there is a compliance officer, grant funding, and a deadline all in play, well, we in the information arena could do better to make things a little easier on everyone.