Ok, it has something to do with having been in the Army reserves and active duty, but I really have an aversion to acronyms.. BDU, MRE, AWOL, and the list goes on and on. The Army speaks in an acronym language nearly impervious to outsiders.
So do scientists. MAP, HIV, TE, LTR, DNA, BLAST, YAC, BAC and on and on. Even though some of these acronyms have made it into general parlance (DNA, HIV), some can be not only be life-science specific, but also field-specific. You’ll see something like “Transposable elements (TEs) are known in every… ” but sometimes you won’t see them so nicely spelled out and it’ll be more like “TEs are known in every…” Sigh.
How do you decode?
I guess you could go list them in one big alphabetical list. But the problem with that is keeping up with the amazingly fast changing field of biology and genomics.
Lately I’ve been searching through literature, text mining and ontology resources online to find useful ones for a curriculum. In that search I’ve found several acronym search tools. These are not just lists, these are search engines that automatically crawl through pubmed abstracts to find acronyms and their meanings. Type in that acronym that has baffled you and viola, there it is with definitions and pubmed context. For the most part.
Some that I’ve found are, unfortunately, dead or broken (as far as I’ve been able to ascertain). But that is the nature of online genomics and biology resources isn’t it? Lots come, many go, some stay and become indispensible.
Two I’ve found work pretty well: the appropriately named (both as a definition and acronym of an acronym search) ARGH and extensively named of “Standford Biomedical Abbreviation Server.” I did a sample search of a term that is dear to my heart: “LTR” as in “Long-terminal Repeat Transposable Elements” (that’d be LTR TEs). I studied the evolution of non-LTR TEs in drosophila.
The results for SBAS (see, I’ve made my own acronym!) gave me 212 hits or definitions. Many, of course, overlap (Long Terminal Repeat Sequences, HIV long terminal repeat) and others are very unique (Louisiana Tumor Registry with 3 references). The top find was long terminal repeat with 1873 abstracts (with links to all the abstracts for you to browse). Unfortunately, it appears the last scan of pubmed was 2002. Though if you are adventurous, you can download the code.
The results for the ARGH had 105 definitions. The top one, as with SBAS, is long terminal repeats with a frequency of 2002 abstracts (relatively frequency of 82.3%). One nice thing here, for “huh, didn’t know that” kind of thoughts, is that the results include the first occurrence of the acronym (LTR is 1980!). Unlike SBAS though, you can’t (as far as I can tell) browse through all the abstracts with the acronym in them, only one example abstract. Also unlike SBAS (in a good way), ARGH seems to be regularly updated, as late as 12/13/2007 when I just checked.
Test out “DNA.” The first occurrence is 1959, and I won’t tell you why that year is significant to me other the the first abstract in PubMed to use the acronym DNA for dioxyribonucleic acid :).
Well, thankfully (for several reasons, least of which is acronym language), I’m not in the reserves any longer, but I’m still in Science. These tools might be useful in translating science acronym language. Know any others?