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Archive for Mashups

Ali Baba (3rd Party PubMed tool)

Ali Baba is pretty neat.

Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts.

Perhaps the best way to explain what it does is with an example:

A patient with cough is treated with codeine. He becomes unresponsive after a while — what is going on?

screen_codeine
Click for larger image

The query entered in Ali Baba was “codeine intoxication”.
Ali Baba shows the relationship between codeine (marked in the graph with blue frame), cough, morphine, and poisioning. Poisioning is also connected to morphine and CYP2D6. The solution thus is that codeine is bioactivated by CYP2D6 into morphine, certain patients show an ultrarapid form of this metabolism, which leads to a life-threatening intoxication (see Gasche et al. (2004)). The connection codeine->CYP2D6->morphine is directly visible in Ali Baba.
To make this example a bit more concise and focused on the central problem, we used the minimum degree filter (in the menu, see Preferences|Filter preferences). This allows to remove all nodes without any neighbors (unconnected nodes) using the ‘Degree’ slider on the bottom panel.

I’m not sure Ali Baba will be of any use to me, but it really is neat. Please note: Ali Baba requires Java 1.5 or higher.

[via]

Other posts about third-party PubMed tools:

FABLE (3rd Party PubMed Tool)

Fable Logo

FABLE = “Fast Automated Biomedical Literature Extraction”

Why FABLE?
FABLE currently tags only genes and proteins and only normalizes human genes. This allows us to design a customized tool that is tailored specifically for this task, rather than a generalized tool such as PubMed that provides broad search capabilities with less specificity.

FABLE mines the biomedical literature for information about human genes and proteins. FABLE v2 allows a user to find articles mentioning a gene of interest (Article Finder), or to generate a list of genes associated with one or more keywords (Gene Lister). Try one of these tools at right or learn more.

Fable Screen

Other posts about third-party PubMed tools:

Notes on ReleMed

A lot of bibliobloggers have been posting about ReleMed, but wanted to avoid doing so until I felt I understood it. ReleMed came up on MEDLIB-L recently and a good question was asked:

I tried it just now and I like that it shows a little bar graph of each articles' relevance, but I fail to see how it is different from HubMed (http://www.hubmed.org/), which allows you to sort by date or relevance. Am I missing something?

I think I now understand ReleMed a bit, so I attempted to answer the question. You can judge for yourself how well I did.

The Krafty Librarian points to this recent article from Medical Design Online that is worth checking out for a brief introduction.

What I’d really like to see is this kind of relevance sorting added to the PubMed interface. I’d love to be able to search PubMed as I normally might, then sort results by ReleMed score. Something like this:

Barring that, it would be great if ReleMed allowed the user to choose between a variety of search interfaces, including one that works like PubMed’s. I think that might do a lot to encourage use by medical libraryfolk. The option of simple keyword- searching is nice to have, but it would be great to be able to apply ReleMed’s sorting power to a more expert search.

MusicTonic: Cool Music Search Mashup

MusicTonic

MusicTonic lets you browse through music artists by genre or directly search, returning related images, videos, blog posts, and a list of “Related Artists”- all in one interface.

Screencap of MusicTonic

Just to put it to the test, I thought I’d try searches on musicians not quite as well known as the Beatles, and was fairly impressed with the results.

Richard Thompson
The Wood Brothers
Jurassic 5
Youngblood Brass Band
Paul Pena

Data is mashed up from YouTube, Last.fm,Yahoo Search, Amazon, Technorati, and OpenStrands- but I’d love to see it use news from Topix or Google News, too.

[via]

For a different sort of musician searching, check out LivePlasma (does movies and actors too).

MeshPubMed.org

meshpubmed1.png

MeshPubMed is a (new?) third-party search tool for PubMed.

MeshPubMed

  • retrieves PubMed abstracts for your keywords,
  • detects Medical Subject Headings (MeSH) in the abstracts,
  • displays a subset of MeSH relevant to your search, and
  • allows you to browse the ontology and display only papers containing specific MeSH terms.

After performing a search, the resulting abstracts are annotated with your query keywords and MeSH terms. The abstracts are grouped using the MeSH terms, which appear in the text. You can use the MeSH hierarchy to systematically explore your search results.

Note that only a subset of all terms may be relevant to your query. This subset – the hierarchy of relevant terms – is presented on the left hand side. Sorting documents to a highly organised network facilitates the finding of relevant documents significantly.


Click thumbnail for larger image

MeshPubMed instructions

More info here

[via Oliver]

An introduction to mashups for health librarians

A librarian-in-training at UBC’s School of Library, Archival and Information Studies, Allan Cho has published an article in the Journal of the Canadian Health Libraries Association called An introduction to mashups for health librarians. A very quick skim indicates that is definitely worth reading, especially for those who need an introduction to the concepts. I’ll be giving it a slower read this evening.

Allan Cho

Snag yourself the free full text here.

(Thanks for the heads-up, Dean!)

Click here for other posts about Mashups.

PubMed Gold

On Feb 12th, Doris Samojluk posted to MEDLIB-L an updated checklist for finding free full-text articles online. I tucked it away for later reference, but there was one resource I didn’t see mentioned that I thought should have been: PubMed Gold

pubmedgold.png.

Created by MLIS student Shawn Thomas, PubMed Gold is an alternative search interface for PubMed that simultaneously uses Google to search for the full text. I wouldn’t use this to replace the checklist, but I’d certainly add it.

Other posts about third-party PubMed tools:

Books I Must Have

I’m not the first to blog about these and I certainly won’t be the last, but I wanted to say a few brief “me too’s”:

I’m going to order Social Software in Libraries

…and not just because Meredith mentions LibWorm in Chapter Three, either! I’m going to order it because Meredith’s writings on technology (at both her own blog and at TechEssence) are smart, clear and practical- and they don’t leave out the human element. I expect her book will have similar qualities.

I won’t go so far as to recommend that others purchase a book that I haven’t myself yet read, but I will say that I am definitely ordering my copy the instant I can.[1]. [Other biblioblog chatter about this book]

I will also need to buy a copy of Phil Bradley’s new book, How to Use Web 2.0 in Your Library[2]:
phils-book.png

Like Meredith’s book, Phil’s has a companion Web site, and also mentions LibWorm (curiously, also in Chapter Three). I subscribe to Phil’s blog and routinely learn new things from him, so I can’t be without this book. I just hope it gets published in the States, too- the exchange rates from Pound to Dollar and shipping from the U.K. are probably going to be painful.

Lastly, I’m going to order a copy of this book [3]:
lib2oh.jpg

While I don’t yet have any indication that it mentions LibWorm ( ;) ) and I’m still not yet wholly comfortable with the term “Library 2.0″, everything I’ve read that Casey and/or Savastinuk have written on the topic has been thought-provoking, required reading. I wouldn’t miss getting my own copy for any reason. [Other biblioblog chatter about this book]

If I read German, I’d also want a copy of this book by Oliver Obst.


__________________________
[1] – It goes without saying that if Meredith wants to send me a copy, I will of course devour it and write a detailed review.

[2] – Naturally, the same offer is extended to Phil.

[3] – Ditto for Michael and Laura.

I’d also be willing to write a review for a publication if it means I get to keep a copy of any of these.

(I’m subtle, huh? My subtlety is inversely proportionate to my budget for discretionary spending.)

Web 2.0 and Publishing (edited)

Interesting article from Information World Review.

Some excerpts:

Tom Coates, a technologist from Yahoo Technology Development, kicks off by summing up the disruption in attitude that is affecting information providers. “It’s in your interests as an author, researcher or scientist to get your work read, so you slap it on the internet, but that is not in the interests of your publisher,” he points out.

[My emphasis]

[...snip...]

Coates divides Web 2.0 usage into two areas: “Collective intelligence and social software is one clump; the reuse and openness with data is a second theme of Web 2.0.”

Put another way, the first clump he’s talking about contains things like del.icio.us and Wikis. The “second theme” is exemplified by RSS and mashups.

Paul Miller, technology evangelist at library automation supplier Talis , adds: “The debate is how do publishers and scholars share data, yet formulate a business model?” For Talis, Web 2.0 is anything but disruptive. “The library market is not growing,” Miller says. “We were looking at taking our information management knowledge out to new markets.”

[My emphasis]

Miller also says “[b]logs and wikis are buzz – they will go away.”

While I agree that they are subjects of a lot of buzz, they’re not going away. The buzz will die down as they (and/or their descendent technologies) become commonplace, but I don’t believe they will go away.

(EDIT: Please see Paul’s clarification of this point.)

I was also tickled to see these buttons at the bottom of such an article:

buttons.jpg
There’s the “first clump” at work.

Go read it.

(Thank you, InfoBunny!)

HEALTHmap (& EpiSPIDER)

healthmap.png

HEALTHMap Press Release

[via]

HEALTHmap is really neat, though it reminds me a lot of a similar mashup, EpiSPIDER.

epispider.png

I don’t know nearly enough about epidemiology/infectious diseases to make a useful comparison, but I did notice that the data sources are similar.

EpiSPIDER gets its data from:
epispider-data.png

HEALTHmap gets its data from:
healthmap-data.png

PubMed Reader: Flexibility for PubMed RSS Feeds

Ever notice that once you’ve decided on your query in PubMed and made an RSS feed from it, you can’t make any changes to the query? If you want to adjust it, just make one small tweak, you have to start from scratch, make a new search, and output a new feed. This could be especially unwelcome if you’re doing something more than reading the feed in an aggregator. What if you’ve created it FOR a clinician and the clinician is already subscribed to it? What if you’re using the feed in another application or Web page?

PubMed Reader allows some flexibility that can be handy in these circumstances.
pubmedreaderlogo.png

You can run your search from PubMed Reader and export your RSS feed from PubMed Reader. Should you want to change the query that generates the feed, you can do so without changing the URL of the RSS feed.

PubMed Reader also has nifty export functions:

The output of this export is a bit of javascript that can easily be pasted into a Web page:

However, if I click on a link from a PubMed Reader feed, I’m taken to the PubMed Reader login prompt and made to log in order to read the item. I’d much rather that the links went directly to PubMed.

Other posts about third-party PubMed tools:

Using Pipes: Feed Translation and Topping Technorati

If you are comfortable with web-based feed mashing/filtering applications like BlogSieve, FEEDblendr, FEEDcombine, FeedRinse, Feedshake, or FeedSifter, you can jump right into Pipes and start using it. You won’t be building mega mashups right away, but you can benefit from using it as the best RSS filter/combiner yet seen.

pipes.png

Feed Translation

A couple months ago, Oliver asked if any tools existed for machine translating RSS Feeds.

It occurred to me while playing around with Pipes that it would take about two minutes to produce versions of this blog’s feed that are machine translated by Babelfish.

Here are the machine translated feeds:

Dutch
French
German

(I routinely use Babelfish to translate blogs written in French, German, or Dutch to English. It is far from perfect, but is usually good enough to let me get a solid idea what the blogger is writing about. If you’re a native reader of German, Dutch, or French, I’d be curious to hear if you think Babelfish works well enough FROM English.)

It’s really easy to do. Plug the source feed URL into a Fetch Module, pipe it to a Babelfish module, and pipe that to output.

Also, I can use one of the RSS-to-Web page tools to display the feed in an alternate language on a web page:

One-upping Technorati


You’ve seen these on blog sidebars, right? You click on it to see what other blogs have been indexed by Technorati has having linked to the blog. I decided to use Pipes to make something that would catch more references to this blog than Technorati can. I also used RSS Feed Converter to output it to a page of the blog itself using the blog’s CSS for formatting (so it looks like it fits in with the blog). I think it came out pretty well, but have a look and let me know what you think. You can see how it was built here (requires a Yahoo account, but that only takes a minute to sign up for).

Web-based tools for manipulation of feeds just took a big leap forward. Pipes was only just released in beta, and neither of these is an especially complex application.

Additional Info

Libraryfolk talking about Pipes.

A quick basic tutorial to get you started with Pipes.

More notes on BioWizard (Digg for Medical Literature, Part 3.5)

I’ve been looking at BioWizard more. I still think it is a great idea executed well, but I’m seeing a couple of problems with its “tags”.

They’re not really tags

The first problem is that the word “tags” implies that the terms assigned to each article are a part of a user-created folksonomy, but this isn’t actually the case. If you look at the citation for PubMed ID 17146093, you’ll see it was indexed with these MeSH terms:

If you look at the article’s tags after it has been imported into BioWizard, you’ll see that these MeSH terms have become BioWizard tags:

So, calling these “tags” is a disservice both to people who know what MeSH terms are, and to users accustomed to participating in the creation of folksonomies with user-generated tags.

Missing MeSH terms

Rachel Walden noticed instances where articles that have been indexed in PubMed with MeSH terms, but those terms do not appear in BioWizard as tags. The best guess we came up with was that these articles were submitted to BioWizard by users when their citations were in-process.

Suggestions for the good folks at BioWizard

  • Replace the word “tags” in each article with “MeSH” or “MeSH terms”. Researchers in the biological sciences (BioWizard’s target user base) know what MeSH terms are.
  • If the “tags” are to useful in describing aggregate features of the articles tracked in BioWizard, all articles should have them. BioWizard could considering disallowing the submission of articles where citation is in-process, but perhaps it’d be better to set all articles to update themselves with metadata from PubMed.
  • Although I like that clicking on a “tag” brings up a list of articles also in BioWizard that were indexed with the same MeSH term, it’d be great to have a link to all the articles in PubMed indexed with the same MeSH term

Previous related posts:

Journal of EAHIL – New issue available

jeahil.png

There’s lots of interesting content in this latest issue of the Journal of the European Association for Health Information and Libraries, but I’m especially intrigued by Guus van den Brekel’s article on The Changing of the User Environment (tenth PDF page, numbered page eight).

I only gave it the one quick read, but that was enough to make certain I’d read it again more slowly later. Since I couldn’t fly to Norway to see Guus present the paper, I’m glad he has shared it in print.

Thanks for the heads-up, Benoit!

More Alternate PubMed interfaces via Journalology

Matt Hodgkinson, an editor with BioMed Central, points out a couple of alternative PubMed interfaces I didn’t know about on his new blog, Journalology.

Among the tools Matt points out, PubReMiner looks especially interesting- but I hadn’t yet seen e-Biosci, Kfinder, or PubNet either.

Journalology looks like it is going to be a blog worth reading, so I’ve just subscribed to its feed.

Some previous posts on PubMed alternative interfaces and mashups

[Thanks to Peter Suber at Open Access News for pointing out Journalology]

BioWizard Enhancements: ‘Digg for Medical Literature’ Part III (Edited)

biowizard_logo.png
I thought BioWizard was pretty cool the last time I wrote about it, but hadn’t been to see it in a couple months when I got an email from BioWizard’s Dr. Raju Raval:

“We have been fully redeveloping the site, and yes the new site has a completely different functionality, with usefulness and simplicity as our main aims. We incorporated many suggestions, and are truly excited about how quickly the site is taking off…”

Hardly surprising that it’s taking off- the redesign is really, really good.

For those new to BioWizard, here’s a brief overview of how it works:

BioWizard users submit relevant, timely research articles they have found to be useful and interesting to the BioWizard site. Just perform your usual PubMed search on BioWizard and submit your favorite research. The articles you submit are then read by the rest of the community who promote articles they feel are deserving of recognition. The best articles in a research field are brought to the top page for all to read and discuss. Think of it as a supercharged way to find and share the best research in your field.

The first thing I noticed about the redesign is that it looks a lot like Digg.

Here’s Digg:
digg.png

Here’s the new BioWizard:
biowizard.png

I should clarify here that I am not criticizing this emulation of Digg (I’m actually applauding it), and BioWizard doesn’t seem shy about admitting it. Dr. Raval told me “[w]e were definitely inspired by Digg and Netscape in creating our site…” The design works. It is efficient and easy for the eye to browse and skim. I really like BioWizard’s innovation of the colored horizontal line over each item that indicates the item’s category. (Edit: Thanks to Vikas Sah for letting me know that the colored lines indicating category are not original to BioWizard, but to Pligg. Pligg is a freeware CMS that’ll let anyone run a digg-like site, and is the architecture behind LISZEN: Trends.)

Last August, I wrote about BioWizard that I would “…like to see RSS integration.” While they haven’t done exactly what I wanted to see, they have added useful features. Feeds for “New Articles”, “On the Rise,” and “All” help keep the user appraised of new developments and trends, enhancing BioWizard’s utility as a current awareness tool.
biowizard_rss.png
I’d still like to see the sort of feeds I described previously and it seems to me that feeds based on categories wouldn’t be hard to provide and would be warmly welcomed by users, but this is a really great start.

Also last August, I wrote this about Biowizard:

“Also, it would be great if members of your community could “tag” articles. For instance, they might tag an article as “Policy:FPIN” to make an article they think should be considered when reviewing or rivising policy. This would require, though, that BioWizard make tags or comments searchable.”

As near as I can tell, BioWizard has done just this sort of thing. Users can now tag items, and BioWizard has a tag cloud, and clicking a tag in the cloud searches for all items marked in BioWizard with that tag.

On the whole, BioWizard’s redesign has resulted in a dramatic improvement of what was already a very decent application of a great idea.

I’d still like for groups of users to be able to form their own groups and take advantage of ratings within that group (an addition to ratings from the entire user base as a whole), but I have few other critiques to offer.

Dr. Raval’s email described BioWizard’s goals in an extremely appealing manner:

“…we hope BioWizard will become an integral tool in keeping up to date on the most important published literature in the scientific and medical fields. We also want great papers that might be otherwise overlooked to come to light, as many important papers come out in middle tier journals yet are deserving of recognition. In addition, we wanted to create a useful source of medical/scientific news, and to consolidate the table of contents from many of the major journals into one location. This allows scientists and physicians to save time, and to communicate with one another directly.”

This is one of those instances where I see the application of a “social software” model as potentially being a tremendous benefit to clinical users, and I am excited to see how it develops- both as a tool and as a community.

Previous related posts:

Authoratory

http://www.authoratory.com/

The content of Authoratory is produced by analyzing large amounts of data from PubMed. PubMed is a service of the U.S. National Library of Medicine that includes over 16 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources.

You can browse, search by author, or search by keyword. Say I want to find out who has written a lot on Ulcerative Colitis. I can search on the term:

…and that’ll confirm the hits:

…Click on that to get a list of authors:

authoratory3.png
(Click thumbnail to see larger image)

…Then chose one of the top authors produced by the search to see a display of co-authors:

authoratory4.png
(Click thumbnail to see larger image)

This is just scratching the surface. Try playing with it a bit, and check out the “tutorial” page. The look and interface leave much to be desired, but Authoratory seems to me like a good and potentially useful idea.

Thanks for the heads-up, Melissa!

Previous posts about other PubMed tools, mash-ups, and “alternative interfaces”:

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