Feb 01

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]

Jan 29

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

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:

Here’s the new BioWizard:

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.
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:

Jan 18

MedlinePlus to be Enhanced by Vivísimo

vivisimo logo nlm.png

ResourceShelf beat me to it (good lord, they’re amazing), but it is worth repeating.

The whole press release is available here.

Vivísimo today announced its selection by the National Library of Medicine (NLM) to enhance searching on www.nlm.nih.gov. The NLM, the world’s largest biomedical library, will leverage Vivísimo’s enhanced search functionality to provide quick and easy access to information on linked Web pages. Vivísimo will also enable search functionality for the NLM’s consumer health web sites, MedlinePlus (http://medlineplus.gov) and MedlinePlus en español (http://medlineplus.gov/spanish/), aggregators of medical and health information from government agencies and other authoritative organizations.

clustermed logo biometacluster

When I first saw Vivísimo’s ClusterMed and BioMetaCluster, I thought they demonstrated a lot of potential. I wonder if these were developed for the specific purpose of pitching the NLM…

I can’t wait to see what Vivísimo is going to do for MedlinePlus! I already find it powerful and easy to use, so enhancements are just icing. Sweet, delicious, gooey icing. 🙂

Jan 16



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:

(Click thumbnail to see larger image)

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

(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”:

Nov 29

Update: Consumer Health & Patient Education Custom Search Engine (CSE)

Update, 12/2/2006: Further information on the CSE and the Second Life Library Search HUD at InfoIsland.


Guus van den Brekel (a.k.a. Namro Orman) made my day today.

He’s going to try to make the CSE that I made available from the Second Life Librares in the Library Search HUD (HeadsUp Display).


Guus, don’t worry about the delayed guest post. Doing the work is more important than writing about it, but you gotta’ write about it eventually. 🙂

Nov 16

Clinical Information Technology Gaps Among Physicians

BHIC points out a new report from the Robert Wood Johnson Foundation on the difference in access to information technology between larger medical practices and smaller ones.

Full text (PDF)

We have a full range of practices affiliated with our hospital. Of course, access to technology is directly related to ability to use that technology, and I think I see that correlation in our library.

Now that our library’s digital resources can be accessed by any physician from any internet-connected computer with Internet Explorer, our new goals need to be promoting awareness of those resources and providing lots of pleasant options physicians take take advantage of in order to learn to use them.

One of the things I did when I made our library’s portal was throw a bunch of training materials in the path of the user. One can’t get to OVID from our portal without tripping over three different kinds of training materials on using OVID. That helps even the access to resources a bit.

Nov 14

Hurray for OCPL!

I know it is a little off-topic, but I wanted to take a few minutes to thank my local public library for a couple of services I just noticed today.

First, Onondaga County Public Library has a new visual discovery tool which is neat:

In addition to the visual discovery on the left and titles with summaries in the middle, the right side of the page lets the user filter search results by format, author, subject, language, series, year, or data sources. But that’s not even the cool part.

The cool part is that OCPL has RSS feeds from their catalogue. 🙂

Patrons can now subscribe to a feed of all new additions to the catalog, or to feeds containing new items that match their query.

I’d still like to see a feed for their events calendar, and I’d love to see them do some blogging- but this is a great start.

Nov 02

The CDC has an office in Second Life

It seems the U.S. Centers for Disease Control and Prevention has set up shop in Second Life.

Here’s the whole story from Nedra Weinreich at Social-Marketing.com.

[via MicroPersuasion]

Previous posts about Second Life:

Oct 27

Happy 35th Birthday, MEDLINE®!

I usually try to avoid posting on topics that other bloggers on medical librarianship have covered, but it seems wrong not to mention this.

Today is MEDLINE’s 35th anniversary, and this item from the NLM Technical Bulletin compares “MEDLINE and what was happening in 1971 with events today.”

When people kvetch about federal income taxes, I (after griping along with them) sometimes mention MEDLINE, PubMed, and the NLM as wonderful uses for my tax dollars.

When the new version of Dr. Who came out a couple years ago (perhaps only Michael Sauers will appreciate the comparison), I joined a discussion board about the new series that was populated mostly with citizens of Great Britain. Halfway through the season and loving it, I decided to take a moment to thank the people of Great Britain for maintaining the BBC with their tax dollars to the benefit of anglophones worldwide. Many received this thank-you with surprised (and gracious) responses- most hadn’t ever considered that the taxes they paid benefited the entire English-speaking world.

Along the same lines, the existence of MEDLINE, its maintenance, and its free availability of through PubMed are paid for by citizens of the United States, and benefit the entire world. In these politically difficult times, it is great to have the NLM making me so very proud of something my government does with my tax dollars.

Oct 27

Uses of Google Custom Search Engine (including Librarianship Feed Finder)

Update: THIS rocks. Garrett Hungerford used Google’s CSE to make LISZEN, a Library & Information Science Search Engine.

(My “Librarianship Feed Finder” CSE is at the bottom of this post if you want to skip down to it.)

So when Google announced its new custom search engine tool, I pretty much ignored it. After all, Rollyo has been offering a similar service for a good long while now. Eurekster’s Swicki does something similar, and Google’s direct competitor, Yahoo, has had the Yahoo! Search Builder since August.

However, recent readings suggest this may have been a hasty judgement, as creative uses of googles new tool pop up all around.

Last week, I posted about Give Me Back My Google, a tool that executes your google search and excludes link-spam sites. Well, the Google Customized Search Engine tool can also exclude domains and accept wildcard characters, so someone has used it to create Putch Search, which has some advantages over Give Me Back My Google. The most important advantage is that anyone can join the collobrative and add spammy sites to be excluded.

Putch Search

Another interesting use is being explored by librarian Bill Drew (of blogs Baby Boomer Librarian and Wireless Libraries). Bill has put together a custom search engine for information WLANs and Libraries.

Of course, the application most interesting to me so far is the Google Medicine portal tha Dean Giustini made. Dean has offered a list of most of the sites searched by his engine (20 of 27), and shows us the results of the same search (“common cold” AND “vitamin C”) in Google, Google Scholar, and his new Google Medicine.

For other interesting applications of Google CSE, check out eWeek’s slide show of Google Custom Search Engines.

But I think consideration of the bigger picture is called for here. Google has more to gain from this than just more places for adsense advertisements. Note that the service is branded as “Google Co-op”. What makes it different from the previous version of Google Co-op? It seems to me that with Google Marker for the co-op CSEs, Google has provided an incentive for users to annotate the web for them.

I don’t think I have a problem with this, but it is something that users should keep in mind.

Anyway. This morning I decided to try making my own. I’ve been collecting feeds for information libraryfolk care about for a few months (I’ll explain why in a future post), so I uploaded about 1000 of them and created a CSE to be a “Librarianship Feed Finder.”

Give it a try:

Here’s a test search to see which LIS feeds have recently mentioned Meredith Farkas.

Here’s a test search to find feeds that mention Library 2.0.

Its neat and sort of interesting, but really not extremely useful.

Oct 26

InformationWeek review of web-based aggregators

InformationWeek logo
This article at InformationWeek by David DeJean reviews and compares BlogLines, Google Reader, and Newsgator Online as web-based aggregators. It’s not a bad review of features, but I’m interested in DeJean’s view that “…there are three things that a good RSS reader must do well…”

First, it must make it easy to find RSS feeds and subscribe to, manage, and display feed entries in ways that make sense to you. Each of these three readers handles read and unread items differently, for example. There isn’t any right way or wrong way, but one of them may work better for you, and it’s easy to try them all out.

Second, an RSS reader must provide knowledge management tools to help you prioritize and categorize entries so that information can be put away and found again. This can be as simple as marking an entry “Keep New” so it doesn’t disappear from the feed, as Bloglines does it, or the much more complex and useful tagging features of Google Reader.

And finally, an RSS reader should support collaboration by giving you a variety of ways to communicate both the information in the entries and the metadata: the blogroll (the list of subscribed feeds), the original URLs of the source entries, any categories and tags you apply, and comments.

I have utterly no complaints about his second crtierion, but the first and third deserve comment.

His “first,” needs to be split into two separate criteria. “must make it easy to find RSS feeds” is one, and “display feed entries in ways that make sense to you” is …well…one-point-five. These two criteria are very, very separate in all three aggregators reviewed, and it makes no sense at all to roll them together.

Regarding the first (“must make it easy to find RSS feeds”), I don’t necessarily want an aggregator to aid me in discovery of new feeds. I have nothing against these features, but I would never rely on them, any more than I rely on a single search engine. Besides, I think that in the not-so-distant future, pretty much all web-based content (and lots of content that doesn’t have a display-in-your-browser component) having feeds. Because of this, I think the time of specialized portals designed for feed discovery may be limited. It might be handy to have such a service rolled into an aggregator, but it is far from essential for me.

Regarding DeJean’s third criterion (“an RSS reader should support collaboration by giving you a variety of ways to communicate both the information in the entries and the metadata”): I think this is true, but that it doesn’t go nearly far enough. I want an aggregator that provides limitless flexibility in reparsing any data from feeds or metadata that I apply to any output format I want.

Also, I’m still waiting for a web-based aggregator that can be used by an enterprise and centrally administrated so that users can receive assistance troubleshooting aggregator problems and receive immediate updates of new feeds available through the enterprise (See paragraphs under “What I’d like” in this post).

I’d also like to see aggregators that can combine and/or filter feeds for the user instead of forcing the user to use 3rd party solutions.

Oct 24


SearchMedica Logo
UK-based SearchMedica, an advertising-supported search portal run by CMPMedica (part of United Business Media) bills itself as “The GP’s search engine.”

SearchMedica’s editorial policy explains from whence search results are drawn:

Our list of ‘medical sites chosen by GPs’ is exactly that. It contains around 1,200 websites – all of which have been selected by GPs for their usefulness. The list currently contains the sites of all the pre-eminent medical organisations in the UK, US, Australasia and Europe, some 600 checked and vetted patient information websites – most of them based in the UK, all of the medical journals of relevance to UK GPs and a wealth of other authoritative medical websites our users have suggested to be of value in their work. GPs are constantly suggesting new sites to us via our ‘Suggest a site’ link. Every new site is tested against the following criteria by our editorial team before inclusion in SearchMedica:

  • Relevance: We bring all of Pulse’s editorial experience to bear on this question. To be ‘relevant’ in this context sites must be useful to GPs in one or other aspects of their day-to-day work.
  • Authority: Sites must be professional in their aims and execution. Accreditation or endorsement by a recognised medical body is a good indicator of authority in this context. Independence is also an important factor
  • Reliability: Sites must be stable and consistent.

Extra care is taken with sites run by commercial organisations. These can hold useful content for GPs but they must meet the criteria above in order to be included.

Interesting that they confirm the view that commercial sites must be held up to extra scrtuiny … even though SearchMedica is itself advertising-supported.

A few interesting features:

  • Filters allow users to restrict search to UK content only or NHS sites only. This reminds me of the need Dean Giustini has expressed for medical search services that are particular to the needs of Canadian clinicians.
    SearchMedica Filters
  • Development of the site has a social aspect to it, as it invites users to join their Super User Group, and encourages users to submit new sites to be included in SearchMedica’s indexing and search resullts.
  • SearchMedica’s interface does include some faceted (or ‘clustered’) searching. When I searched for “Ulcerative Colitis”, SearchMedica returned along the left side of the screen categorized links for Evidence, Patient Information, Patient Support, and Guidelines.
  • There is an interesting function called “Broader Searches.” When I clicked this after searching for “Ulcerative Colitis, it recommended a search for “inflammatory bowel condition.”
  • SearchMedica also provides a set of “Related Concepts” search links. Here’s a screen capture of the Related Concepts displayed following my search for “Ulcerative Colitis”
    Related Concepts
  • I couldn’t help but notice at the bottom of the About page a disclaimer: “This site is intended for healthcare professionals only“.

More aboutSearchMedica on their Help page.

Oct 23

Pageflakes for MedLib Blogs

I saw on Michael Stephen’s Tame the Web the Pageflakes page Phil Bradley made out of a number of biblioblogs. Intrigued, I decided to try the same thing with the feeds in the Masterlist of MedLib Blogs (see previous post).

Here’s the result:
MedLib Blogs in Pageflakes


Meh. Sort of interesting, but nowhere near as useful and having the list in BlogLines or Google Reader. Also, the AJAX interface is a nice idea, and works well in my Google Personalized Home Page, but was wonky in Pageflakes. The item I was dragging somehow often ended up half a screen away from my cursor.
Cursor vs item dragged

Oct 22

Comparison of Librarything, GuruLib and Shelfari

librarytwopointzero has a decent comparison of Librarything, GuruLib, and Shelfari. Can’t disagree with the conclusion.

The marks added together are as follows and (out of 40):

Librarything = 32
Shelfari = 24
Gurulib = 23

I think you can see that Librarything is my favourite. I think, in comparison to the other two, Librarything really gives you that extra. Its main area I like is being able to transfer your data both into it and out of the site.

Related posts:

Oct 19

Some Alternative Interfaces and Mashups for MedLibs

Answering a comment from Michelle yesterday, I listed some other “alternative interfaces” to PubMed/MEDLINE, some of which could be called Mashups:

SLIM (http://pmi.nlm.nih.gov/slim/)
MedKit (http://metnetdb.gdcb.iastate.edu/medkit/)
PubMed Assistant (http://metnet.vrac.iastate.edu/browser/)
XplorMed (http://www.ogic.ca/projects/xplormed/)
GoPubMed (http://www.gopubmed.org/)
ClusterMed (http://clustermed.info/)
PubFinder (http://www.glycosciences.de/tools/PubFinder) – I haven’t been able to reach it today. I did reach its google cache, though: http://tinyurl.com/u3zev

I was pleased today to find this page at neurotransmitter.net, which lists these and a number of others that I can’t wait to explore.

Oct 19



LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process:

  • Genes: Names of genes and gene products. Gene name recognition is based on Ensembl . Synonyms and aliases are resolved.
  • Chemical Compounds: Names of chemical compounds and their respective aliases.
  • Diseases and Phenotypes: Names of diseases and phenotypes
  • Tissues and Organs: Names of tissues and organs

Article from Biomedical Digital Libraries
Provisional PDF

This paper examines how the adoption of a subject-specific library service has changed the way in which its users interact with a digital library. The LitMiner text-analysis application was developed to enable biologists to explore gene relationships in the published literature. The application features a suite of interfaces that enable users to search PubMed as well as local databases, to view document abstracts, to filter terms, to select gene name aliases, and to visualize the co-occurrences of genes in the literature. At each of these stages, LitMiner offers the functionality of a digital library. Documents that are accessible online are identified by an icon. Users can also order documents from their institutions library collection from within the application. In so doing, LitMiner aims to integrate digital library services into the research process of its users.

Oct 18


PubFocus Logo

This page gives a good, quick idea what PubFocus does.

From BMC:

Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts.

PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies.

Full text (Provisional PDF)

Via MedLIB-L (Thank you, Benoit Thirion!)

Oct 16

Integrating Reference Tools with the EMR

Ran into a press release the other day from EBSCO, touting the ease of integrating it’s point-of-care tools into EMR/EHRs, “[w]ith the EBSCOhost® Integration Toolkit (EIT)” which “…provides a comprehensive set of flexible web services based on XML/SOAP standards for establishing direct links from their EHR/EMRs to applicable clinical reference resources from EBSCO.”

This makes me sigh and fret.

I know that the integration of information tools into our hospital’s EMR system is absolutely essential, but haven’t gotten far with this yet. The CIO did agree to link to the library’s portal from the EMR (Eclipsys Sunrise Clinical Manager), and that’s great because it makes the library’s resources accessible to any clinican with an internet connection and an Active Directory account for a our network- but it isn’t enough. There are too many steps between the identification of a need for clinical information based on a patient’s chart and the retrieval of that information. Clinicians won’t use tools they find inconvenient.

I’m not immediately finding a lot of literature to use as a guide, either. Before I submit a call for advice to MEDLIB-L, I thought I’d post it here first. Any thoughts? Any favorite articles on the topic? Anyone who has integrated tools with Eclipsys Sunrise Clinical Manager?

Oct 15

OPML auto-discovery

…wouldn’t it be cool if OPML files could be auto-discovered, similar to what Firefox has been doing for RSS feeds?

I love people who start sentences with “wouldn’t it be cool if…”

Marjolein Hoekstra at CleverClogs has made “an OPML Auto-discovery Bookmarklet that displays a list of hyperlinks to the OPML files that have been made available by the author of any web page.”

Marjolein is constantly pointing out neat stuff about RSS, and I’ve really enjoyed chatting with her.

Check out this bookmarklet. If you’ve got an extra 5 seconds, go Digg it.