Nov 06

UNYOC (CE slides) and NYLA Tomorrow

My apologies to the awfully nice folks who attended the CE course I taught at UNYOC a couple of weeks ago! I’ve taken far too long to get these slides posted:

Also: I’ll be on a panel at NYLA tomorrow (Friday, 11/6/2008) afternoon at 4:00 PM- please say hello if you’re going to be there! As usual at these sorts of things, I’ll know almost nobody. But hey- I might get to meet Polly Farrington!

May 26

MLA 2008: Plenary Session IV Slides

David Rothman

Amanda Etches-Johnson

Melissa Rethlefsen

Bart Ragon

Feb 04

Scinversations: Aggregating Online Conversation About an Article

I think Jon Udell started it.

Jon noted that science stories get released online and bookmarked, commented upon, and blogged about all over the Web.

It’s all happening on the web, but it’s happening in isolated ghettoes with few points of actual contact. How could we bring those worlds into closer contact?

Jon also suggests how this might best be done.

Here’s one approach that could help. When the citation engines in the blogosphere find references in blog entries to scientific articles on the web, they could resolve those to their most canonical forms: DOIs, PubMed records. And they could make equivalences among those forms. That way, conversation in the blogosophere about a scientific article, and scientific conversation about the same article, would tend to hang together and would be discoverable in the same contexts.

Alf Eaton seemed to think this was a good idea and built a tool at Scintilla to do this. Go give Scintilla Conversations a try.

There’s also a Scinversations bookmarklet you can drag and drop on to your browser’s toolbar: Scinversations

Peter Suber points out a perfect PubMed Central article with which you can take the Scinversations bookmarklet to a test drive.

Nicely done, Alf!

Feb 02

Google’s Social Graph API

The new Social Graph API from Google might prove really interesting.

I added a bunch of XFN ‘rel’ attributes to this blog’s links so I can do a little more playing (if you’re using WordPress, you can do this quickly and easily).

Someday I’ll get around to writing about microformats here- but not today.

For more on why this new API is interesting, see this item from Tim O’Reilly.

Jan 14

Favorite RSS Resources and Tools

[Updated: 8/28/2008]

(My emphasis here is on free and low-cost resources)

Explaining RSS

Resources to help you choose a feed aggregator

RSS Plugins for Outlook

(2003 or earlier- Outlook 2007 has a feed aggregator built-in)

Google Reader Tips and Plug-ins

RSS-to-Email tools

Publishing RSS content on Web Pages

Web-Based RSS-to-Web-Page tools
Hosted RSS-to-Web-Page Tools

Feed mashing and filtering tools

Creating feeds for pages that don’t offer them

Sometimes called “scraping”

Creating feeds from PubMed

Creating feeds from LibWorm (/MedWorm)

Although structured slightly differently, MedWorm and LibWorm have similar interfaces and identical search operators.
LibWorm FAQ
LibWorm-Fu for Beginners
Intermediate/Advanced LibWorm-Fu (Power Searching)

Okay, your turn: What good stuff did I miss?

Jan 08

Disliking “Web 2.0” and Hating “Web 3.0”

I was asked recently in an interview:

“You’ve written quite a bit about Web 2.0 tools and medical librarianship […snip…] Are there ways in which you see health sciences librarianship 2.0 as differing from Library 2.0?”

I answered that I’m actually not all that fond of the the “2.0” suffix, whether it is applied to “Web,” “Library,” “Medicine” or “Health.”

This answer was lame and incomplete, something I’m not proud of. Even though I’m not entirely happy with it, maybe this one will be better.

The term “Web 2.0” is a metaphor representing the idea that the Web is in it’s “second version”. It is not, in my view, a particularly good metaphor.

Some trends commonly associated with “Web 2.0” are tools for collaboration (and other “social” activities), applications that live online and in your Web browser, rounded corners (and other aesthetic choices), and the blurring of the line between content consumer and content creator. The term “Web 2.0” can be a useful shorthand with which to describe these tends and in aggregate and I’m not opposed to the idea that these trends are, taken together, significant enough to collectively merit a term referring to them. My impression is that this term is most especially useful when marketing Silicon Valley investment opportunities to potential investors.

Some other critics of the term have asserted that “Web 2.0” as a term is meaningless. I disagree. This piece by Tim O’Reilly does a great job of explaining what he means when he says “Web 2.0.”


  • The Web hasn’t been upgraded. There’s no new version of the Web. The longer a medium is around, the more interesting things people figure out how to do with it. This isn’t (or at least shouldn’t be) surprising. Tim Berners-Lee, the person generally credited as having invented the World Wide Web, saidThe entire transcript of remarks by Berners-Lee on this topic is available here.:

    “Web 1.0 was all about connecting people. It was an interactive space, and I think Web 2.0 is of course a piece of jargon, nobody even knows what it means. If Web 2.0 for you is blogs and wikis, then that is people to people. But that was what the Web was supposed to be all along…the idea of the Web as interaction between people is really what the Web is. That was what it was designed to be as a collaborative space where people can interact.”

  • Many things that are new and cool on the Web are not “Web 2.0.” Sometimes, new and cool things are the Web are just new and cool and really don’t need a numeric versioning suffix.
  • Although some might see it as semantic nit-pick, I believe that there’s no such thing as “using Web 2.0I may not like the title of Phil Bradley’s book- but I think the book itself is quite good. (Way too expensive, but quite good.) and that Web 2.0 doesn’t have “features”.At least Berci has the excuse of not being a native speaker of English, so I don’t usually give him a hard time for such things. He’s also a really nice guy with a great blog that I subscribe to. “Web 2.0” isn’t a program, a movement or a standard. It is jargon used to describe a set of trends in the sorts of things people are doing on the Web.

There’s nothing wrong with jargon in and of itself- but the term is now so widely and varyingly used that it needlessly creates more confusion among those who most need clarity. More and more, I read things about “Web 2.0” that drive me up the wall.

And now we’ve got people talking about “Web 3.0”

There are a number of things about Dean Giustini’s recent BMJ Editorial on “Web 3.0” with which I am unhappy.I should also point out here that it is a lot easier to criticize an editorial in BMJ than to write one. I admire Dean, I admire the way he promotes librarians as agents of technology and change, and I admire that he makes himself visible in this way to the greater world of healthcare professionals.

First, to continue and enhance the confusion that now comes with every use of a versioning suffix by using “3.0” is a significant disservice. Librarians should be demystifying confusing terms and clarifying definitions. I’m disappointed that neither BMJ nor Dean decided to describe some of the the ways that evolving Web technologies may impact healthcare. Instead, the article appears impressive to people who aren’t familiar with the buzzwords (most of BMJ’s readership are not, I am guessing, professional technologists) and says almost nothing to those for whom these buzzwords are all too familiar.

Second, the entire editorial about “Web 3.0” or “The Semantic Web” lacks a definition either term. Is the assumption that perhaps these terms are familiar to the average BMJ reader?

Now, with apologies, some fisking:

Dean writes:

“Each new version of the web should be a better iteration of its predecessor, and web 3.0 should be no exception.”

Except that there has been, as Berners-Lee points out, no new version of the Web. Part of the problem with the hype surrounding “2.0” is that people who should know better forget that it is a metaphor.

Dean writes:

“In medicine, we should focus on the ability to locate trusted clinical information, while creating the means to produce new knowledge.”

What, because we don’t focus on these things now…?

Dean writes:

“Information retrieval in web 3.0 should be based less on keywords than on intelligent ontological frameworks, such as the National Library of Medicine’s Unified Medical Language System, Medline’s trusted MeSH vocabulary, or some other tool.”

I do not believe that we will live to see a time where the World Wide Web is thoroughly indexed and made searchable with a controlled vocabulary like MeSH. It is a poor analogy for what technologists mean when they speak of “the Semantic Web” and it is a disservice to lead librarians to think that searching the Web will eventually be like searching MEDLINE. It won’t.

Dean writes:

“The question of whether and—two popular social tagging sites—will be useful in web 3.0 remains doubtful.”

This statement confused the hell out of me. Allan Cho (with whom Dean collaborated in writing this article on the Semantic Web) has said one of my favorite things on this topic:

“…use of folksonomies could help overcome some of the inherent difficulties in ontology construction, thus potentially bridging Web 2.0 and the Semantic Web. By using folksonomies’ collective categorization scheme as an initial knowledge base for constructing ontologies, the ontology author could then use the tagging distribution’s most common tags as concepts, relations, or instances. Folksonomies do not a Semantic Web make — but it’s a good start.”Confession: I literally clapped my hands while sitting at my desk the first time I read this quote by Allan and wished I’d written it.

Nicely said, Allan.

Dean writes:

“In medicine, finding the best evidence has become increasingly difficult, even for librarians.”

I don’t think I can agree with this premise. I think that Web tools have made the best stuff increasingly easier to find for those with the skills to use the tools.

Dean continues:

“Despite its constant accessibility, Google’s search results are emblematic of an approaching crisis with information overload, and this is duplicated by Yahoo and other search engines.”

Huh? How are Google search results emblematic of information overload?

Dean continues:

“Consequently, medical librarians are leading doctors back to trusted sources, such as PubMed, Clinical Evidence, and the Cochrane Library, and even taking them to their library bookshelves instead.”

Okay, maybe- but how is this a “Web 2.0” trend? Haven’t librarians always struggled to get their patrons to use the best tools?

Dean continues:

“Unless better channels of information are created in web 3.0, we can expect the information glut to continue.”

Dean has previously blamed “Web 2.0” for “information overload”, now he seems to say that Google is responsible for an “information glut”. Both of these assertions are just silly.

The Web makes a whole lot of information easily available to a whole lot of people (which I see as a good, desirable thing) and many people lack the information skills to get just the stuff they want- but to assert that “Web 2.0” or Google cause information overload (with absolutely no support) is just beyond my ability to comprehend.


Because in the hands of a skilled user, Google is a powerful tool for filtering out the chaff. Because I routinely use “Web 2.0” tools (like RSS feeds from or blogs) to benefit from the readings and tags and opinions of friends and colleagues- this helps me stay focused just on the good stuff. How else would I keep on top of all the stuff this blog covers?

Okay. Enough fisking.

What about “Medicine 2.0” and “Health 2.0”?

“Medicine 2.0” bugs me perhaps even more than “Web 2.0”. It is a way of marketing tools that apply newish Web trends to the needs of health professionals. How does the term serve anyone but investors and those who have something to sell investors? Why the heck should healthcare professionals embrace and adopt this marketing schtick when they could instead demand terms that are clear and descriptive?

“Health 2.0” is term for hyping the application of newish Web trends to the needs of healthcare consumers. Again, it appears to be useful in selling investment opportunities. Do the rest of of need the term? No. We can instead refer with more clarity and simplicity to Web sites and Web services for healthcare consumers.

So what about “Library 2.0”?
I think that I have come to agree with T. ScottThough I still think T. Scott was, in this instance, unfair to Casey and Savastinuk. The work is important and good, but the term is not. I urge librarians, particularly bibliobloggers, to use the term carefully (if at all). We don’t need it to describe the application of Web trends and technolgies to library work, we REALLY don’t need it in order to describe making libraries more patron-centric, and when we use it (usually failing to explain/define it) we add to the confusion and needlessly alienate potential ALLIES for improving computer literacy in libraryfolk and in patrons.

I like Wikis and blogs and RSS and APIs and mashups and portable data and rich user experiences and social networking tools and online productivity tools and social bookmarking. I’m fascinated by the new and interesting things people keep doing with the Web. I believe that librarians need to be technologists and need to know what “Web 2.0” means- but that doesn’t mean they need to add to the existing confusion. It means they need to help smooth it away.

Jargon is fine in small groups of specialists- but information professionals, I think, have a special responsibility to help others overcome and dismiss jargon when it gets in the way of sharing information. Not only to bring the benefits of these new technologies to all our colleagues, but to all our patrons.

For that reason and to keep me sane, please: No more talk of “Web 3.0.”

In case it isn’t obvious by now: I’d like to hear your thoughts, whether you agree or disagree with mine. Leave a comment, wouldja’?

Dec 09

Web Geekery in the Recent Literature – 12/9/2007

  • This article points us to, a consumer-oriented site for information about radiology.

    J Am Coll Radiol. 2007 Nov;4(11):809-15.
    RadiologyInfo: reaching out to touch patients.
    Ellenbogen PH, Tashjian JH.

    RadiologyInfo is a public information Web site created and maintained as an unprecedented joint collaborative effort of the Radiological Society of North America and the American College of Radiology. Conceived in 1997 and operating since 2000, the site has grown to become a leading medical information site, currently with more than 100 radiologic examinations and treatments described. Each month, well over half a million visitors connect to RadiologyInfo (660,000 visits in March 2007). The information is now also available in Spanish and French. New procedures, current topics, and additional images are added on an ongoing basis.

  • Haven’t gotten my hands on a copy of this one yet. Emphases in abstract below are mine:

    Postgrad Med J. 2007 Dec;83(986):759-62.
    Web 2.0 technologies for undergraduate and postgraduate medical education: an online survey.
    Sandars J, Schroter S.

    OBJECTIVES: To identify the current familiarity and use of Web 2.0 technologies by medical students and qualified medical practitioners, and to identify the barriers to its use for medical education. METHODS: A semi-structured online questionnaire survey of 3000 medical students and 3000 qualified medical practitioners (consultants, general practitioners and doctors in training) on the British Medical Association’s membership database. RESULTS: All groups had high familiarity, but low use, of podcasts. Ownership of digital media players was higher among medical students. There was high familiarity, but low use, of other Web 2.0 technologies except for high use of instant messaging and social networking by medical students. All groups stated that they were interested in using Web 2.0 technologies for education but there was lack of knowledge and skills in how to use these new technologies. CONCLUSIONS: There is an overall high awareness of a range of new Web 2.0 technologies by both medical students and qualified medical practitioners and high interest in its use for medical education. However, the potential of Web 2.0 technologies for undergraduate and postgraduate medical education will only be achieved if there is increased training in how to use this new approach.

    Hmm…who could be providing the expertise, the knowledge and the skills to help medical students and practitioners use these tools?

  • This one mentions several tools I’ve posted about, like Healthmap, BioWizard and WhoIsSick.

    Nurs Educ Perspect. 2007 Sep-Oct;28(5):286-8.Links
    Nursing education 2.0: are Mashups useful for nursing education?
    Skiba DJ.
    Free full text: [PDF] [HTML]
Jun 18

Librarian (Server Side PDF Organizer)

Where Papers, iPapers, Sente and BibDesk are personal PDF managers, Librarian is a server-side application to allow groups of people to collectively build an annotate a shared PDF library that is managed from inside their Web browsers.

Librarian was designed to enable a small trusted group of researchers to create an annotated virtual library of articles in portable document format (PDF). All users may participate in the creation of the virtual library, and all users may then browse and search articles by words or phrases, much like at journal sites. The difference is that you have instant access to full text of the article, which you identified in seconds.

Metadata about each article is imported from PubMed and users can annotate articles. To get a better idea of how it works, check out the demo.

If this might be useful to you, check out the requirements, note the fact that it is free, open-source software (GPL) and give it a try.

If you try it, please be sure to let me know what you think– I may install this myself, if only because it looks neat and I’d love to start a little article-sharing database with a few friends.

May 25

ExpertMapper (Third-Party PubMed Tool)


ExpertMapper is similar in purpose to Authoratory. It uses bibliometric analysis of MEDLINE data.

ExpertMapper examines all medical publications that are indexed in the National Library of Medicine’s MEDLINE database. We rank the expertise of each author according to the number and type of articles that each expert has authored on the specific condition, disease, or treatment of interest to you.

However, ExpertMapper can only do this for 105 pre-defined topics from which the user can select. (The site indicates that they’re open to adding new topics based on user feedback.)

But my favorite thing about ExpertMapper is that it allows the user to narrow his/her search geographically and find the nearest “most expert” institutions or persons. I might look for what institutions are most expert in IBD and find that the Mayo Clinic in Rochester, MN is highly ranked. From there, I can see which individual persons are most expert and what the top articles are on the topic from persons at Mayo.

The interface is wonderfully straightforward and easy-to-use, but ExpertMapper has a nice walk-through and a short FAQ page.

May 10 (Third-Party PubMed Tool)

The more I play with, the more I like it.

Say you want to post a link to the PubMed abstract for PMID: 12472752. The appropriate gigantic URL would be:


But lets us shorten that to:
(Get it? The URL is[Your PMID].)

If we want to fetch two abstracts, we can do that by adding a “+” and the second PMID:
([First PMID]+[Second PMID])

We can even retrieve three abstracts this way:
([First PMID]+[Second PMID]+[ThirdPMID])

Or we can fetch articles related to PMID 17146093:
([your PMID])

You can even run a (simple) search with
([First search term]+[Second search term])

You can also look for (/link to) full-text articles (though I still prefer PubMed Gold for this purpose):
([Your PMID])

But these aren’t even the coolest thing about The coolest thing about is the batch search, which runs multiple searches simultaneously so the user can compare counts of hits. The default demonstration search is a great illustration, but I thought I’d try one of my own.

In the Search for: field, I enter:

colitis OR “ulcerative colitis” OR crohns OR crohn’s OR “crohns disease” OR “crohn’s disease” OR “inflammatory bowel disease” OR IBD

In the AND with: field, I enter:

probiotics OR prebiotics
probiotics AND prebiotics runs these four searches, gives me a link to each set of results, and will count the number of hits in each.

There’s no indication on the site of who created and and why (although the domain appears to be registered by Terry Bird of Palatine, IL). I just want to know to whom my thank-you card should be sent.

Other posts about third-party PubMed tools:

May 08

More on JournalReview (Digg for Medical Literature, Part 6.5)

I’m grateful to Jeff Ellis for providing some clarification and additional information in response to my previous post on

I criticized JournalReview for not having feeds. It turns out that it DOES have feeds- the problem it that they’re hard to find. Jeff writes: was our assumption (perhaps incorrectly)… that users who where techi enough to want an RSS feed are using a browser that automatically detects them. If you visit any of our specialty pages with a browser capable of detecting an RSS feed… you will see ours throughout the site.

When I first checked out JournalReview, I was at work using IE6 and could not have known there were feeds available unless I viewed the source. I strongly urge Jeff to clearly advertise the presence of RSS feeds as a feature.

Jeff also let me know about other cool community communication features:

If you sign up at, and discuss an article where the author has provided a corresponding e-mail, you will have the option to CC your comment to the author. See attached photo.

In addition, if other members have started to discuss this article – they too will be notified of additional comments left on an article. In this way… we too notify users of updates who are actively discussing an article.

We are setting up a section of user preferences where any user can “monitor” any article, set of articles, or search term for updates… and this too should be live in the coming months.

Whats more… is that not only do we contact the author of an article, but we contact up to 15 experts on that specific topic. Our goal is to call the world experts together to discuss the literature, answer questions, and make progress through the world of scientific publication.

This is all pretty cool and pleasantly different from other sites of this kind, but completely invisible to a new user. Now my largest complaint about is that it does a poor job of tooting its own horn. 😉

Thanks so much for the follow-up, Jeff!

Related Posts

JournalReview: Digg for Medical Literature, Part VI (Digg for Medical Literature, Part V)

MediNews: Digg for Medical Literature, Part IV

Dissect Medicine: Spanish and German Editions

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

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

Dissect Medicine: ‘Digg for Medical Literature’, Part II

BioWizard: The start of ‘Digg for Medical Literature’?

May 03

Medical Librarian 2.0

Now available for order from Haworth Press:

Medical Librarian 2.0: Use of Web 2.0 Technologies in Reference Services
Edited by M. Sandra Wood, MLS, MBA, AHIP, FMLA

Interesting, I think, that the experts sought out to write about Web technologies are disproportionately bloggers and/or people you’ve read about online.

Alexia Estabrook and I co-authored the chapter on RSS. The chapter on mashups is written by Michelle Kraft. The chapter on Wikis is by Mary Chimato (formerly of, now making waves at Circ and Serve). The chapter on social networking is written by Five Weeks to a Social Library instructor Melissa Rethlefsen.


  • Introduction (M. Sandra Wood)
  • Library 2.0: An Overview (Elizabeth Connor)
  • Virtual Reference Services for the Academic Health Sciences Librarian 2.0 (Ana D. Cleveland and Jodi L. Philbrick)
  • Applications of RSS in Health Sciences Libraries (Alexia D. Estabrook and David L. Rothman)
  • P.O.D. Principles: Producing, Organizing, and Distributing Podcasts in Health Sciences Libraries and Education (Nadine Ellero, Ryan Looney, and Bart Ragon)
  • Streams of Consciousness: Streaming Video in Health Sciences Libraries (Nancy T. Lombardo, Sharon E. Dennis, and Derek Cowan)
  • Social Networking (Melissa L. Rethlefsen)
  • Content Management and Web 2.0 with Drupal (Chad M. Fennell)
  • It’s a Wiki Wiki World (Mary Carmen Chimato)
  • Mashing Up the Internet (Michelle A. Kraft)
  • Index
  • Reference Notes Included
May 03

Demonstration of Zentation

Zentation is pretty neat and could be very useful in making instructional materials.

Slideshare lets us upload a set of slides for sharing online, and Google Video lets us upload video for sharing online, but Zentation lets us display slides and a video together, and has tools to set the intervals of slide transitions to synch with the video.

It is easier to demonstrate than to explain, so check out the demonstration embedded below. It took about 30 minutes to slap together and takes just a couple of minutes to watch.

Above: Embedded Zentation demonstration. If you’re reading this post in an aggregator, you may need to visit the blog to see the demonstration.

May 01

Article on eTBLAST (Third-party PubMed Tool)

eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.
Nucleic Acids Res. 2007 Apr 22
Errami M, Wren JD, Hicks JM, Garner HR.
PMID: 17452348

PubMed Citation

Free full text:

| HTML | PDF |


Other posts about third-party PubMed tools:

Apr 26

CILIP HLG Newsletter on Third-Party PubMed Tools

I often stumble across good and useful things by accident.


Case in point: While using Google to look for a document I had misplaced, a typo caused me to stumble across an article from the March 2007 issue of the CILIP Health Libraries Group Newsletter titled “Internet Sites of Interest,” featuring short descriptions of a number if third-party PubMed tools. I recognized the name of the author, Keith Nockels, because I have subscribed to his blog’s feed since I first discovered it through the Masterlist of MedLib Blogs.

I recently wrote a similar item for publication, but selected a completely different set of tools to focus on- so it was loads of fun to see which ones Keith decided to feature. (Mark Rabnett recently wrote a similar piece. Again, there is very little overlap between his selections and mine.)

Snag Keith’s article here: PDF

Now that I know this newsletter exists, I’ll be keeping an eye out for future issues. Thanks, Keith!

Quick question I’m hoping a U.K. Health Librarian will answer: I understand that CILIP is to the U.K. what the ALA is the U.S.. Is the HLG the closest U.K. analogue to the U.S.’s MLA? If you’re not sick to death of acronyms and initialisms yet, please leave me a comment and let me know? Many thanks!

Other posts about third-party PubMed tools:

Apr 23

JournalReview: Digg for Medical Literature, Part VI

Okay, so far we have BioWizard, Dissect Medicine, MediNews and Onexamination– time for one more:


In conversations with friends, I have previously referred to sites like BioWizard and Dissect Medicine as a sort of “digital journal club,” so it is sort of neat to learn that’s how sees it, too:

In the academic world, “Journal Clubs” are a common way to discuss and critically question medical literature. The knowledge gained by this activity can be immeasurable, and often leads to ideas both relating to patient care and to future research. However, many clinicians are unable to participate in these academic activities. In addition, information shared within an individual journal club is seldom disseminated.

JournalReview is an international interdisciplinary Internet based unbiased forum for review of medical literature. Very much like an on-line journal club, we aim to provide a venue which will improve communication amongst physicians and lead to better understanding and interpretation of medical literature.

You can browse previously submitted articles by one of 28 specialties…

…or search PubMed from inside the JournalReview interface:

When you find the article in the PubMed search results that you wish to submit, can leave comments about it by clicking “Discuss Article,” send an article’s link to a friend by clicking “Email Article,” or rate the article on three different scales of one to five by clicking “Rate Article:”

JournalReview is more like Biowizard than the others in that it only allows articles to be submitted from PubMed. Like BioWizard, this means it should encourage a user base of medical professionals where tools like Dissect Medicine which allow articles to be submitted from absolutely any URL.

However, where BioWizard has RSS and email alerts to keep users up to date on the articles most highly rated by users, JournalReview has no analogous feature. It is for this reason more than any other that BioWizard is still my favorite by far of the “Digg for Medical Literature” tools.

Related Posts (Digg for Medical Literature, Part V)

MediNews: Digg for Medical Literature, Part IV

Dissect Medicine: Spanish and German Editions

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

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

Dissect Medicine: ‘Digg for Medical Literature’, Part II

BioWizard: The start of ‘Digg for Medical Literature’?

Apr 16

Web 2.0: Tools for Clinical Practice

Resources from Judy Burnham, used to teach her class for the 2007 Medical Association of Alabama Meeting:

These are definitely worth flipping through if you have even a casual interest in the application of Web technologies to medicine. I like to consider myself well-informed on the topic, but a handful of the resources Judy notes are new to me.

Many thanks, Judy!


Apr 09

Who is sick (Amateur Epidemiology 2.0?)

Who is Sick logo

Where EpiSPIDER and HEALTHmap get the data for their mapping mashup endeavors from sources like WHO and ProMED, Who is Sick gets its data from YOU.


Users enter their location and their symptoms, then see how commonly those symptoms are by reported by other users by location and other simple demographics.

The site’s creator explains Who is Sick:

The CDC (Center for Disease Control) provides flu data but only to the State level and only on a time scale of 1 week. For example, they will report that in the state of California, last week, there were 539 cases of the flu reported. While this information may be useful for some health practitioners or academics, for the average individual, this does not come in handy when they are trying to figure out what kinds of sicknesses are going around their area. It is not local enough, timely enough, or broad enough because they don’t cover different types of sicknesses.

In contract, whoissick provides local (down to the zip code level), timely (within a day), and broad (many different symptoms, not just the flu) sickness information.

Who is sick screen capture

The idea for the site came from a (typical) four hours spent in an emergency room:

The genesis of the idea for Who Is Sick was actually from an acute need that our founder had when his wife started experiencing severe stomach pain while they were on vacation. With no way of knowing whether the pain was from appendicitis, food poisoning, or some other stomach illness, our vacationing couple went to the emergency room and waited for 4 hours (BTW – this was from 11pm until 3am) to be seen by a doctor…only to be told that there was a stomach flu going around and that if the pain didn’t go away in 24 hours, to come back. Wow. 4 hours wait for that…in the middle of the night… (of course the doctor did check to see if it was appendicitis so they weren’t all bad…).

Our founder thought, “if only there were a website that had current AND local sickness information, maybe we could have avoided the long wait.” Needless to say, this started the wheels spinning and a couple of months later, Who Is Sick was born.

But since the data will come from self-selected participants (disproportionately hypochondriacs?), won’t that skew the data? It’ll be interesting to see if it is of any use.


Apr 03

WikiProfessional and WikiProteins (A BioMedical datamining Wiki mashup?)

Have you seen news about WikiProfessional?

Its first project is WikiProteins.


Lots of details in this Nature article:
Key biology databases go wiki
Jim Giles
SUMMARY: Collaborative approach aims to keep pace with discoveries.
News@Nature 445, 691 – 691 (15 Feb 2007) News

Barend Mons, “a bioinformatician at the Erasmus Medical Centre in Rotterdam,” seeks to “meld some of the most important biomedical databases into a single information resource.”

But that’s not all.

Mons…also wants to apply the Wikipedia philosophy. He’s inviting the whole research community to help update a vast store of interlinked data. If he and his colleagues can pull it off — and even the project’s advocates are not sure they can — they could transform the databases that are central to the work of many life scientists.

View the demo.

ars technica writes:

As with Wikipedia, users can sign up for alerts when content changes, but a key difference comes in how these alerts are managed. Instead of tying them to changes in a specific page, WikiProteins will send out an alert to anyone interested in a topic, no matter where within the system those changes took place. In the example above, anyone interested in migration will receive an alert of the changes to the YFG page, even if they’d never heard of the gene previously. Not only is this potentially more useful to users, but it should improve the quality of content, as the community of researchers interested in migration can police content they might never be aware of in a standard wiki system.

I signed up for the mailing list- sounds like a really interesting project.

Further reading: