Posts

Introducing Collection View!

A few days back, I had the distinct pleasure of debuting my newest project, Collection View, at my talk “Looking Beyond the List: Enhancing Search with Interactive Visualizations” at Code4Lib 2021. You can find the slides for that talk at osf and the recording on YouTube.

(more...)

Call for Collaborators: Testing Covid-19 Hedges

There are a number of publicly available search strategies for finding Covid-19 related literature in PubMed, but there’s not a lot of information about how well they work. Let’s fix that by testing them!

(more...)

Updating News in Proportion

I’ve made a couple of updates to my project News in Proportion. As before, this application renders a search of the items in Chronicling America into a choropleth map showing the relative proportion of results for each state. However, due to an increase of content in Chronicling America, it now covers a couple of states that it did not before: Maine, New Jersey and Wyoming. After closer examination, I also decided to remove Massachusetts from the counts – at the moment, only one (partially) Massachusetts newspaper is included in Chronicling America (the Cronaca sovversiva), and the bulk of its text is in Italian.

(more...)

Trends in COVID-19 Publications

The recent emergence of COVID-19 has led to a flood of publications about it (as well as SARS-CoV-2) in the biomedical literature. Indeed, items found with the PubMed term “COVID-19” (which is still probably the best single term to use have gone from nothing a year ago to a bit over 4.5% of all PubMed citations for 2020.

(more...)

Testing the PubMed Search Tester

As I mentioned earlier, I’ve refined the user interface for the PubMed Search Tester, an application designed to facilitate the process of refining a complex strategy by allowing you to automatically compare different search variants against a validation set of “known-good” items.

(more...)

(Re)introducing the PubMed Search Tester

I have made some significant changes to an application that I first introduced at MLA 2019. This app, the PubMed Search Tester, is designed to facilitate the process of refining a complex strategy by allowing you to compare search variants against a vaidation set.

(more...)

Covid vs Covid

Medical Librarians and other folks who search PubMed on a regular basis are likely familiar with the process of Automated Term Mapping, where PubMed takes your search terms and “translates” them into different synonyms, variants and Medical Subject Headings. This process is often extremely helpful, but it does mean that small differences in the wording of your search can have big impacts on what it retrieves.

(more...)

Plotting Ideology vs Engagement

Introducing a new visualization in Members by Interest – scatter plots that show the relationship between a member’s engagement with a given topic (as measured by adjusted score) and their ideology (as measured by Dimension 1 DW-NOMINATE scores).

(more...)

Changing the formula for Members by Interest

I’ve made a small but important change to Members by Interest. It currently uses an “adjusted score” when ranking a member’s interest in a given topic as reflected by those measures about that topic (as cataloged by the folks at LC) that they sponsor and cosponsor. Sponsoring a bill or resolution counts for three points, being an “original” cosponsor counts for two points and joining as a cosponsor after a measure has been introduced counts for just one. This is intended to account for the fact that it is more difficult to sponsor a bill than to cosponsor another’s, as well as the fact that an initial cosponsor may have had some input on a measure.

(more...)

As seen in the July issue of JMLA...

Do use the PubMed Clinical Queries? If so, you should be aware that the “Broad” scope may not be as broad as one would like. Instead, there are many occasions when items that appear in a “Narrow” scoped search just don’t show up in their Broad counterpart. This is particularly true for Prognosis, where a searcher could easily miss one (presumably relevant) Prognosis/Narrow citation for every ten Prognosis/Broad citations retrieved.

(more...)

Introducing PubTrees

Introducing PubTrees, an interface for searching PubMed that visually reveals the textual relationships within the results of that search.

(more...)

I went to Madison

A few weeks ago I was given the opportunity to present at the Spring 2019 meeting of the Georgia Health Sciences Library Association in lovely Madison, Georgia. It was a great chance to chat with my medical librarian colleagues, and I’m always eager to talk about Search Workbench. If you wander over to the UGA IR, you’ll find my slides for “Beyond the List: Refining your PubMed searches with interactive visualizations”.

(more...)

(Re)Introducing Members by Interest

…Or how I learned to stop worrying and love having a database.

(more...)

Things may be slower than usual...

As noted in an earlier post , NCBI wants one to restrict calls to E-Utilities to no more than three per second.

(more...)

Are Narrow NOT Broad citations any good?

One critique I received on my presentation about what gets missed when only using the “Broad” version of the PubMed clinical queries was that maybe the citations missed were not “true positives”. That is, they might have characteristics in common that make them both invisible to the Broad query and also somehow less fit for purpose than their Narrow AND Broad fellows.

(more...)

I was honorably mentioned!

I am pleased to announce that Members by Interest took “Honorable Mention” in the Congressional Data Challenge! Many thanks to the judges and the folks at the Library of Congress. Many congratulations to the winners as well!

(more...)

Mind the Gap!

Another talk I presented at the 2018 Meeting of the Medical Library Association was on something I discovered while testing the hedges feature in Search Workbench. To wit, some searches using the “Narrow” version of a Clinical Query return results that are not seen when using the “Broad” version. This is particularly apparent when you examine the “Prognosis” queries:

(more...)

(Formally) Presenting Search Workbench

While attending the 2018 Meeting of the Medical Library Association, I had the opportunity to present Search Workbench in a lightning talk. If you have access to the online meeting materials, you can check out the video here.

(more...)

Introducing Members by Interest

Members by Interest is another entry for the Congressional Data Competition.

(more...)

Introducing Committee Flow

I’ve put together a couple of new applications in response to the Library of Congress-sponsored Congressional Data Competition. The remit for this was to “…leverage that data to create new meaning or tools to help members of Congress and the public explore it in new ways.”

(more...)

Tweaks to News in Proportion

I’ve done some Fall Fixin’ on News in Proportion to reflect recent changes to the Chronicling America API and make the app layout more well-behaved.

(more...)

Same but different

Poking around in PubMed with a visual search tool such as Search Workbench can reveal an interesting pattern: different concepts sometimes perform similarly over time even though they refer to fairly distinct sets of citations.

(more...)

Printing tweaks

If you use PubVenn, you will note a small improvement in the way the printable output is handled. Now, when you click the “Printable version” link at the bottom of the Venn diagram, you will find that the image that shows up is savable as a PNG file in all browsers. This seems more directly useful than a SVG file for most use cases.

(more...)

Introducing Search Workbench

Today marks the formal release of Search Workbench. A natural extension of the work in Visualizing PubMed, Search Workbench allows you to examine, edit and visualize your PubMed searches from a single interface.

(more...)

Poking at Parentheses

Software Projects are sometimes 99% done, but they’re rarely completely finished. This is particularly true when the process of developing something new causes you to go back and reevaluate earlier design decisions.

(more...)

MeSH Notes

Just (virtually) attended Advanced PubMed: MeSH from NNLM. Very cool! I was playing around in PubVenn with some of the examples we covered, and I found some (potentially) interesting things.

(more...)

Minor Enhancement Alert!

This is a quick announcement that I have added a new feature to PubVenn. You can now share a favorite search via URL (just as you can with PubMed by Year).

(more...)

Five minutes goes by fast!

Just posted the recording of my lightning talk at the 2017 meeting of the Medical Library Association where I talked about Visualizing PubMed. You get five minutes and three slides (though one could stretch that by using animations). Still can’t believe how fast it went by…

(more...)

We've Got Updates...

PubVenn has been (finally) updated to the newest verion of Ben Frederickson’s excellent venn.js.

(more...)

The Littlest Webservice

As (hopefully) demonstrated by Visualizing PubMed, there is almost no end to the cool things you can do using the E-Utilities API to PubMed (and other NCBI databases). However, there are some limitations that one needs to keep in mind when developing interactive tools. Chief among these is the admonition that one should make no more than three requests per second to the API.

(more...)

Slides from Code4Lib Southeast 2017

I just put the slides from my presentation at Code4LibSE 2017 up on Athenaeum (the UGA IR): http://hdl.handle.net/10724/36962.

(more...)

Going to Atlanta

Assuming that the rest of Atlanta’s transportation infrastructure doesn’t catch fire between here and then, I’ll be headed West to Code4LibSE 2017 to talk about Visualizing PubMed

(more...)

subscribe via RSS