Proof that this blog has the Best Readers Ever
Last week I posted Rachel Walden’s readlly good idea for a useful 3rd-party PubMed/MEDLINE tool and received several exciting responses.
Martin Gerken
Martin Gerken was the first to make an attempt that you can try at:
http://www.pharmakologie-bremen.de/test/meshr.html
…but Rachel got some error messages from it.
GoPubMed
Martin and Rebecca both suggested using GoPubMed.
David (not David Rothman) confirmed that GoPubMed worked nicely but had some problems (which GoPubMed’s Dr. Liliana Barrio-Alvers later answered).
David’s (not Rothman) Tool
David (again, not David Rothman) also made an attempt at creating the tool that Rachel asked for that you can try here:
http://www.docmobi.com/mesh/.
I threw in a list of PMIDs and got useful results presented in a pleasant manner:
Nice, huh?
Rajarshi’s Tool
Rajarshi Guri was next to build a tool to do this. His, though, doesn’t have an interface- you just add your PMIDs to the URL. Here’s an example using the same PMIDs I used to test David’s tool.
Rajarshi also built a Ubiquity command (more on Ubiquity here) that functions reasonably well as an interface- though still not as well as a simple Web form- and without a simple Web form, the tool isn’t really available to a lot of potential users.
Pierre’s Tool
Pierre Lindenbaum spent 30 minutes building a tool to match Rachel’s specs. I was unable to get it to work, but you can download it here and give it a try.
You people rule.
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September 3rd, 2008 at 9:10 am
All of those folks do indeed rule.
I really appreciate everyone who tackled this.
September 23rd, 2008 at 8:39 am
Thanks Rachel for bringing this up and David for taking this further.
I responded to Rachel’s original request at Twitter by saying that I used to look for the most frequent Subject Headings by one command in the (expensive) STN-database. I had no idea that this could be done for free with a 3rd party MEDLINE/PubMed tool. And now there are several possibilities! Very useful when one wants to get a hint of which MeSH are most appropriate.
Coincidentally I found another 3rd party tool which does the job, and in my opinion, even better: PubMed PubReminer
http://bioinfo.amc.uva.nl/human-genetics/pubreminer/.
(It is produced by someone at our institute and I was asked to have a look at it).
It’s lay-out isn’t very user-friendly, but if I type the 3 PMID’s you gave, it shows several lists with the most frequently occurring words on top.
These are the lists (columns): Year, Author, Journal, (Text)Word, MeSH, Substance, Country.
What I like most is that it also includes Mesh and their subheadings. To find the combination can be very important for your search (and it is this possibility I missed most in the other tools.)
For instance, your 3 PubMed ID’s yield: Urinary Catheterization/instrumentation twice and Urinary Tract Infections/etiology once.
Especially important for words having no single MeSH, e.g.
EGFR-inhibitors –> (MeSH) Receptor, Epidermal Growth Factor/antagonists & inhibitors
It ’s also great to see the most frequent textwords and substance names as well.
I will try to give some examples at my own blog later.
September 23rd, 2008 at 10:26 pm
[...] The suggestions made by several people were summarized by David in another post (see here). The foll… [...]
March 11th, 2009 at 8:52 am
Our tool at IBMI already does this. Put in any term and get the complete list of MeSH terms, broken down into their sub -categories. Also does lots of other nice summary tricks.
See: http://www.medsum.info