About Kaura

Kaura is doing her utmost hold the reigns for David this week!
Jul 20

PubWindows – Mamma mia!

Yesterday, commenter Iskandar informed me that in Italy, they say “Mamma mia” when suffering from information overload.

Mamma mia! Mamma mia! Mamma mia!

I promised I would discuss PubWindows today, so I’ll try. Honestly, I still haven’t completely figured it all out. Partly because of time, and partly because there is soo much to it. If anyone knows/understands more about it, I invite you to leave a comment; I think others will greatly benefit from your knowledge.

So, PubWindows appears to be the brainchild of the director of Neurotransmitter.net, Shawn Thomas, who has a MLIS. Cool! From the site: “Neurotransmitter.net exists to improve online access to biomedical information in fields such as neuroscience, pharmacology, and psychology… [PubWindows] allows you to browse PubMed citations with a modified version of the National Library of Medicine’s MeSH Browser. PubWindows offers search links to the On-line Medical Dictionary and PubMed text mining tools such as Chilibot and XplorMed . In addition, links to RSS feeds and various export formats are available.”

You can select a MeSH term from PubWindows and then use it to search XplorMed, which shows the association between terms in Medline abstracts, and you can also search SwissProt, SpTrembl, OMIM and SMART. I think. Mamma mia!

Or, you can use your term to search chilibot, which allows users to “[search] PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords. The results are returned as a graph”. The example graphs provided were really very visually easy to read and I could see how they’d be quite useful.

In PubWindows itself you can view the abstracts attached to your MeSH term and create a RSS feed for new ones.

I think PubWindows is really great idea, but I found it very difficult to use. I don’t know about PubWindows users, but I usually need to search MeSH before I’m able to select the appropriate term. Also, I wasn’t able to successfully search with subheadings, which I think is a huge drawback in terms of precision.

And as Iskandar notes, you can’t navigate back to the main PubWindow page once you’ve gone into one of the other databases.

I’ve been trying to come up with something witty about this being a neuroscience engine and using MeSH not needing to be brain surgery, but its late and I’m tired.

Mamma mia!

Jul 19

A search haiku for you

I wanted to write about PubWindows today, but I simply haven’t had enough time to evaluate it properly. I’ll post about that tomorrow.

In the meantime, I want to share with you a found haiku from the ‘introduction’ section in XplorMed.


Recommended for
cases in which you do not
know exactly what
you are expecting to find.
Your interests may change
by the results obtained,
you may want to ask
new questions as analysis
develops. Also, the
results may suggest you use
additional words
that should be used to expand
your MEDLINE query
(such as, an unexpected
of a protein name, or the
synonyms of a
disease or other problem).

slightly modified to fit form; form modified to fit length!

Jul 18

GoPubMed, GO!

David reviewed GoPubMed in March, but it has already changed so much that it bears revisiting. GoPubMed uses Gene Ontology (GO) and MeSH (when David posted, it was MeshPubMed) to search PubMed.

You really should click over and check it out. The design is deceptively simple, lovely and easy to use.

There’s not enough room for everything, so here are the highlights:

Hot Topics option:
Displays visual representations of how many articles with your concept have been published, top authors and journals, and provides a graphic of countries in which the research is being done. Notably, a disclaimer is posted that states quantity is not the same as quality.

GoPubMed option:
Lists citations clearly, beautifully. Your search term (and impressively, the main topics of the article) are unobtrusively but obviously highlighted. The icons are clear and easy to use, including an option that lets you toggle between citation and abstract view for each listing. Also gives one click options for related genes, which is great, but I’m less (read: Not) pleased with the one click option for wikipedia entries.

What I like best is that on the left hand side, both GO and MeSH relevant terms are listed first in top popularity, then in hierarchy of content, and you can click on a term to refine your search. PubMed, take note!

Advanced option:
Gives the ability to search in full text, anywhere, abstract or title, title, author or affiliation (and a few others), allowing for a lot of flexibility and focus. The simplicity of this page puts Google’s Scholar advanced search to shame.

Depending on the researcher and their topic, this is one of the few free third party tools I’d recommend.

Jul 17

Twease, redux

I was going to review Twease today, but I realized that David already did a great job with it, and that one of its creators, Fabien Campagne, left additional notes in the comments section that make for a complete review of what it does and how it works.

What neither of them touched on, though, was how beautifully designed it is. Go take a look. Meant as a compliment, I’d call it the “targetization” of Medline!

Also, I think it has one of the most straight forward, easy to use and understand tutorials I’ve seen.

And while I’m on tutorials I’d recommend, check out this Ovid Medline one from Duke.

Jul 17


Earlier I was thinking about which third-party PubMed tool to review, when I noticed that something didn’t seem right. Then it hit me: I’m not being specific. I’ve been using the terms PubMed and Medline interchangeably, when that is incorrect.

MEDLINE is the largest component of PubMed…snip…In addition to MEDLINE citations, PubMed also contains:

In-process citations which provide a record for an article before it is indexed with MeSH and added to MEDLINE or converted to out-of-scope status.
Citations that precede the date that a journal was selected for MEDLINE indexing (when supplied electronically by the publisher).
Some OLDMEDLINE citations that have not yet been updated with current vocabulary and converted to MEDLINE status.
Citations to articles that are out-of-scope (e.g., covering plate tectonics or astrophysics) from certain MEDLINE journals, primarily general science and general chemistry journals, for which the life sciences articles are indexed with MeSH for MEDLINE.
Some life science journals that submit full text to PubMedCentral® and may not yet have been recommended for inclusion in MEDLINE although they have undergone a review by NLM, and some physics journals that were part of a prototype PubMed in the early to mid-1990’s.

I’ve been saying PubMed third party tools, when what I *so far* have meant is third party tools for Medline.


Jul 16

Medie, meet Hal

So, today I tried out Medie. I’d said I’d write about it as a third party Medline tool. I can’t. At least not as a hospital librarian. I was going to try to give it a pat on its back and insincerely flash it half a smile so it wouldn’t feel too badly about itself.

Instead, I’ll tell you what I really think of it. The first problem I noticed was that it doesn’t use MeSH (and therefore you can’t focus or use subheadings), so you’re losing massive precision right away. The other biggie I couldn’t get past was that it lists by PMID number, not title and author.

Sounds like I hate it, right? Not at all. Once I learned more about it and understood what it does, I was blown away.

As per David’s original post, it is a semantic search engine. The first time I learned of semantic search and natural language, I thought “interesting!” in the way that means “when’s lunch?”

This has changed my mind completely.

Let me take a step back for a moment. One of the first things I mention when I teach Medline is that you are using a computer. You can’t talk to it like you are asking me a question. You need to represent your concepts with words and terms and phrases and connect them appropriately. Then I launch into Boolean logic and MeSH.

Medie is a project of Tsujii Laboratory at the University of Tokyo that works on Natural Language Processing and Computational Linguistics. Basically, this means that it can root your word and process algorithms so that you search the database with natural language. If it doesn’t already, it will be “thinking” that when you type heart you may also like results with cardiac. That is too basic of an example, but hopefully you get the idea.

So, when you search Medie you enter search terms into basic parts of speech (subject, verb, object) and out pop your results, with the line or two of text it picked up color-coded by part of speech. It does have some additional search options that I can see as being very useful and helpful. But as I can’t recommend it for searching now, I’ll let you discover those on your own. I should note that I didn’t find any information on what text is searched or omitted, or how results are ranked.

But in the future I can see Hal saying: “I’m sorry, Dave I’m afraid I can do that.”

Jul 15

Fasten your seatbelts, I hope it will be a fun ride!

As David mentioned, he’s on vacation this week. Good for him, right? But (more importantly!) what does that mean for you?

My name is Kaura Gale, I have an ALA-accredited MLIS and am the Medical Librarian at Beth Israel Medical Center in NYC, so you’re in good hands here! Well, at least hands here? I definitely try to wash them both at least twice today. Can we start with that?

Anyhoo, when David asked if anyone wanted to fill-in, I’d been browsing through my RSS’d list of 50+ medblogs, and realized that not one belonged to me. So, here’s my turn to do something for everyone else. If only for a week.

One of the many reasons I enjoy reading David’s blog is that there are mainly tech posts, and this is both an area of interest to me, as it is an area in which I must keep up. David’s well written and chosen topics have the ability to impact my everyday searching and teaching, yet I rarely get or make the time to sort though his recommendations enough to see the shiny from the background.

I’d like to rectify that this week. I’m going to start with MEDIE, and then talk about one PubMed third party tool per day. I look forward to sharing my thoughts with you, and hopefully learning from your ideas and experiences with these tools and teaching/learning in general.
Please feel free to use the comments for further dialog.

You can talk to me directly at kauragale@gmail.com, but I’ll prolly check comments more often, so have at it!