-omics in 2013

What You're Doing Is Rather Desperate

Just how many (bad) -omics are there anyway? Let’s find out.

Update: code and data now at Github

1. Get the raw data

It would be nice if we could search PubMed for titles containing all -omics:

However, we cannot since leading wildcards don’t work in PubMed search. So let’s just grab all articles from 2013:

and save them in a format which includes titles. I went with “Send to…File”, “Format…CSV”, which returns 575 068 records in pubmed_result.csv, around 227 MB in size.

2. Extract the -omics
Titles are in column 1 and we only want the -omics, so:

Note: grep changed so the following now works. Note: this approach will miss a very few cases where omics is preceded by a hyphen. That included the classic stain-omics.
It also ignores the standalone term “-omics”, which is used quite often
.

Of course, this results in some…

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Un pensamiento en “-omics in 2013

  1. Pingback: How Three Decades of Reaganomics Destroyed the American Economy | kjmhoffman

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