This nifty tool from the University of Michigan Comprehensive Cancer Center makes it extra easy to search PubMed for articles by authors affiliated with the institution.

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Today I’m looking at the University of Wisconsin-Madison Ebling Library for Health Sciences RSS E-Journal Feeds by Subject and at the Harvey-Semester JournalBot.

I learned that UW-M libraries were up to good RSS-ish things from Ratcatcher’s post the other day that contained an abstract of an upcoming paper:

Developing and Marketing an RSS Journal Service for your Library
Authors: Erika L. Sevetson, MS, Christopher Hooper-Lane, MA, AHIP, Allan R. Barclay, MLIS, AHIP, Ebling Library, University of Wisconsin – Madison; Deborah Copperud, MA, School of Library and Information Science, University of Wisconsin – Madison
Abstract: More and more journals are making their tables of contents available via RSS feed; however, barriers still exist between the user and the content. A working group at a large, Midwestern academic health sciences library set out in Fall 2006 to “explore possibilities for developing an RSS current awareness service that would categorize health sciences RSS feeds and integrate them with SFX, document delivery, and RefWorks.” We developed a 4-phase plan, including overhauling our existing RSS journal feeds pages, developing bundled OPML packages for quick subscription to several journals, developing a shopping cart-like application for users to easily create customized collections, and developing instructional and promotional plans for staff and patrons. This panel will provide an overview of the project, focusing on work process, technology, marketing, and instruction and education. The panel discussion will include 15 minutes for audience discussion.

(Since I won’t be able to make it to this event, could someone please send me lots of detailed notes? Transcripts? Video recordings? Holograms?)

A little digging turned up this page at Ebling which lets the user select a subject, then see available RSS feeds for journals covering that subject (without reloading the page- a nice AJAXy touch). For example: Say we’ve got a hypothetical cardiologist: she could click “Cardiology” and get a nice list of TOC feeds for journals (through EZproxy) of interest to cardiologists.

Since the feed is retrieved through EZproxy, I’m guessing that these feeds will allow the user to click on an item in an aggregator and log in through EZproxy to get the full text. I also like that it offers an OPML file for ALL the feeds in the subject. Awesome. (Next, maybe they could add filtering functions to let our example hypothetical cardiologist user filter the journal feeds she selects for keywords she cares most about.)

The Harvey Semester JournalBot takes a sort of a “wizard” approach, guiding our hypothetical cardiologist through a process of creating a personalized feed (via PubMed API?) tailored for her specific needs and preferences.

First, the JournalBot asks the user to select a subject from a drop-down menu:

(The JournalBot can also let the user enter a MeSH term, but if the user had mastery of MeSH, she wouldn’t need the “wizard.”)

Next the JournalBot prompts the user to select a specific cardiovascular disorder:

Now JournalBot prompts the user to select from which journals she wants articles on this specific cardiovascular disorder…

…and asks the user to choose how many articles from each journal she wants and how old the articles can be:

Lastly, JournalBot offers the user a vanilla feed and a link to add the feed to Google Reader or iGoogle:

I love to see that academic medical libraries are developing services like these, and can’t wait to see what else is coming.

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More about McKean here and here.

Also be sure to check out McKean’s blog, Dictionary Evangelist.

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I finished writing this post last night, but hadn’t posted it yet. Since Berci has beat me to it, I’ll go ahead and post it now.

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Curehunter.com has a “visual medical dictionary” that I’m having lots of fun playing with, even though I’m not sure that it is best described as a “dictionary.”

Really, it’s a nifty third-party PubMed/MEDLNE tool to visually browse MeSH (as an alternative to the NLM’s MeSH browser). As shown in the screen capture below, it gives the MeSH scope note for “colitis, ulcereative” as the definition for “ulcerative colitis.”

Then it grabs related terms from the MeSH Tree Structures and counts the number of citation hits for each:

Lastly, it gives you a visual, color-coded representation of related strongly related terms from the literature…

…and it does this all in three side-by-side frames:

Neat!

Other posts about Third-Party PubMed/MEDLINE Tools

• PubViz (3rd-party PubMed/MEDLINE Tool Prototype)
• Almost Everything About HubMed (Third-party PubMed Tool)
• Verbs in MEDLINE Searches & MEDIE (Third-Party PubMed Tool)
• MLA News: Third-Party PubMed Tools
• Pmid.us (Third-Party PubMed Tool)
• ExpertMapper (Third-Party PubMed Tool)
• Twease (Third-party PubMed Tool)
• Article on eTBLAST (Third-party PubMed Tool)
• CILIP HLG Newsletter on Third-Party PubMed Tools
• Ali Baba (3rd Party PubMed tool)
• FABLE (3rd Party PubMed Tool)
• Managing Medical Literature on a Mac: iPapers, Papers, Sente, BibDesk
• Notes on ReleMed
• MeshPubMed.org
• PubMed Gold
• PubMed Reader
• For MedLibs who use Macs: iPapers
• PubMed2Connotea / PubMed2CiteULike
• More notes on BioWizard (Digg for Medical Literature, Part 3.5)
• More Alternate PubMed interfaces via Journalology
• BioWizard Enhancements: ‘Digg for Medical Literature’ Part III (Edited)
• Authoratory
• Some Alternative Interfaces and Mashups for MedLibs
• LitMiner
• PubFocus
• BioWizard: The start of ‘Digg for Medical Literature’?
• Article on HubMed

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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.

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.

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.

Sorry!

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.”

Provided by the Dartmouth Biomedical Libraries, Dartmouth College and the Cushing/Whitney Medical Library, Yale School of Medicine, the EBM Page Generator looks like a wonderful tool to help a medical library create an EBM page on its intranet, even without extensive Web development skills.

Welcome to the EBM Page Generator!

Let us help you create your own EBM web page with your resources for your website. Once you’ve gone through the process, you’ll end up with the code to export to your own web site.

In five simple steps, your library can select the resources it has available and wishes to include, plug in the appropriate URLs, then copy and paste the code it generates into the appropriate intranet page.

Click here for an example of the kind of page you can make with this tool.

This is a great idea, implemented very nicely.

Hat tip: Ratcatcher’s del.icio.us favorites

Created at the Institute for Computational Biomedicine (Weill Medical College of Cornell University) by Matthew J. Wood, Kevin C. Dorff and Fabien Campagne, Twease is a…

..web-based tool to search Medline at the abstract level (available from http://twease.org). Twease indexes each word of Medline and provides features that can transparently expand your search to help find the information you are looking for.

Twease searches are also partially case sensitive. Short terms are case sensitive, while longer terms are not. For instance, TnT is different from TNT (TnT often stands for Troponin T while TNT often stands for trinitrotoluene). For more details on Twease’s case sensitivity, see the Case Sensitive Searches tutorial page.

Finally, Twease can automatically discover common abbreviations for search phrases (e.g., “protein kinase C” will discover PKC, PK-C, aPKC, etc.) and rewrite queries to use these abbreviations. This feature is available through the Slider (on the top right) and the Advanced pane.

I like the way you can save an individual references to a list that can be exported to BibTeX or EndNote.

Still, I’m not entirely clear on when Twease would actually be preferable to PubMed’s native interface. Would I pretty much save it for when I need to write a query that uses abbreviations or case-sensitive terms?

The Twease project home page includes sources, binary and other information.