Video Tip of the Week: Let Allie help you figure out those acronyms

Just ask Allie.

As I mentioned in a post nearly 5 years ago, I dislike acronyms. From my time in the army, which speaks in a language of acronyms, they’ve made me cringe. Of course, genomics databases aren’t without their acronyms from DBTSS to STRING so I’ve got used to them. As you’ve might of read, I’m taking a leave for a AAAS Science Policy fellowship (science and computing education at NSF). Working here allows me to work with many other fellows from NIH, DOD, HHS and State. Just the locations reek acronyms (except State.. they’re special :D), but to make matters worse, I haven’t been to a meeting, hearing, discussion group, panel or talk in the last month where the language wasn’t nearly all acronyms. Or so it seems.

The same can be very true of scientific research papers. It’s difficult enough keeping up with acronyms in your own field, but stray even a bit into a field you aren’t  immersed in can sound foreign. In that post 4 years ago linked to above, I mentioned two databases of science acronyms, ARGH (love that acronym) and the Stanford Biomedical Abbreviation Server,  to help the researcher make sense of the acronyms they come across in reading research. Unfortunately, both seem to be no longer active.

Allie to the rescue. Allie is an life sciences acronym database. It’s computationally derived from Medline. Here is their description:

 Allie is a search service for abbreviations and long forms utilized in Lifesciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader’s expertise. Allie searches for abbreviations and their corresponding long forms from titles and abstracts in the entire MEDLINE®

There is a lot more to Allie than just looking up acronyms. Some of the suggested uses?

  • Users can search for the long forms of abbreviations or the abbreviations of long forms.
  • Bibliographic data which includes the inquired abbreviation or long form in titles or abstracts can be obtained.
  • Users can also obtain co-occurring abbreviations in titles and abstracts.
  • REST/SOAP interfaces are available which allow the users to call upon Allie from their scripts, programs, etc.
It’s all quite useful, though I like that I can find abstracts with certain acronyms and co-occuring abbreviations. Today’s tip will introduce you to Allie. Unfortunately, today the site was down temporarily (though I’m assured it will be up tomorrow) and I wasn’t able to create a tip. THe tip above is from the developers and is quite good. You can also access the video from GOTV.
What I’m looking forward to is someone putting together an app from their REST/SOAP interface that will type out acronyms’ long forms while someone is talking to me. That’d be wonderful :).

Yamamoto, Y. (2011). Allie: a database and a search service of abbreviations and long forms. Database : the journal of biological databases and curation, 9 (5) DOI: 10.1093/database/bar013