3rd Call for Submissions for “Medical Information Matters”: Tools for Searching the Biomedical Literature

8 05 2011

It takes some doing to breathe life into Medical Information Matters” (blog carnival about medical  information).
A month ago I wrote a 2nd call for submissions post for this blog carnival. Unfortunately the next host, Martin Fenner, didn’t have time to finish a blog post and has come up with a new (interesting) variation on the theme “A Wish list for better medical information”.

Martin asks you to philosophize, blog and/or comment about “Tools for Searching the Biomedical Literature.

You can base your contribution on a recent (editable) survey of 28 different PubMed derivative tools by Zhiyong Lu (NCBI) [1].

Thus, write your thoughts on the various PubMed derivative tools mentioned here or write about your own favorite 3rd party PubMed tool (included or not).

For details, see Martin’s blog post announcing this upcoming edition. The Blog Carnival FAQs are here.

And if you don’t have time to write about this topic, you may still find the survey useful, as well as the views of others on this topic. So check out Martin’s blog Gobbledygook once in a while to see if the blog edition has been posted.

Note [1]: If you have already submitted a post to the carnival, or would like to write about another theme, we will take care that your post (if relevant)  will be included in this or the next edition. You can always submit here.

Note [2]: Would you like to host “Medical Information Matters” at your blog? Please comment here or write to: laika dot spoetnik at gmail dot com. We need hosts for June, July, August and September (submission deadline first Saturday of every month, posting on the next Tuesday)

  1. Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database. 2011 Jan;2011. doi: http://dx.doi.org/10.1093/database/baq036
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#Sciblog – a bird-eye’s view from the camera

2 09 2008

Last Saturday I learned from @AJCann and @Jobadge (Twitter) that there was a Science Blogging Conference going on in London, that you could virtually attend.

Although I planned to do something else (banking for my mom, pick up my daughter from her overnight stay; Saturday is my-shopping-&-bodyshape-sauna- & blogging-if-I-have-some-spare-time-day), I decided to follow it. In the meantime I tried to blog about something else, which didn’t work.

I largely followed Cameron Neylon’s streamed video on Mogulus. It’s main value was the audio-stream, as well as the candid-camera function peeping at the audience from behind.

I came in late (back from banking) and unfortunately missed the Keynote lecture of Ben Goldacre from Badscience.

The next session didn’t do it for me, partly because the 3 blogging ladies ( Jenny Rohn, Grrl Scientist, Anna Kushnir) were almost inaudible and what they had to say about the bridging function of blogs between scientists and the general public (also figuratively) didn’t catch my ears. In the meantime the virtual attendents including, Fang (Mike Seyfang) from Australia, AJCann, some other guys and me, chatted in Cameron Neylon’s room.

In between I followed Twitter-messages having the hashtag #sciblog (see here). I was not familiar with hashtags, but it is a predefined tag you can add to you microblogging post to easily tract what is being said about a subject (even when you don’t actually follow the persons themselves, so as a spin off you can get acquainted with some real interesting people).

Example of a twitter message on #sciblog:

#sciblog matt woods: friendfeed encourages discussion and closes feedback loop 9 minutes ago from TwitKit

However, Hashtags is an opt-in service. You must follow @hashtags -and it has to follow you- for the service to index your tweets, so it took me some time to get it done (For more information, see this twitter wiki.) Althoug the procedure in itself was very effective, the twitter messages didn’t add much value for people already attending.

Another online backchannel, the Friendfeed room appeared more lively, but I soon stopped following the threads. Furthermore I ‘m so old-fashioned that I think speakers do deserve my attention while they’re talking (but perhaps that is because I’m not yet used to chatting at the back-scene). Checking my notes afterwards with the Friendfeed comments was useful however.

Next I followed Matt Wood’s introduction to microblogging and aggregation services and Breakout 6 “Communicating Primary Research Publicly” by Heather Etchevers (Human in Science), Jean-Claude Bradley (Useful Chemistry) and Bob O’Hara (Deep Thoughts and Silliness).

I found these presentations interesting, but tracking my notes back I couldn’t see where Matt ended and the others began.

During his lively presentation with a lot of gesturing, the heavy “sequencer” Matt Wood from “Green is Good” told us he had decided not to worry to be open and just send the message out to the public. You could use blogs to communicate your scientific findings, but blogposts do not handle versioning, although you can sometimes manipulate the post’s date (WordPress blog). Another tool is microblogging services. Twitter is more of a social platform, whereas Friendfeed is more apt for more information-exchange (no 140 character-limit). A new microblogging service is identi.ca. (see for instance this readwriteweb post)

Labnote books (and wiki’s) were a recurrent subject through the 4 presentations. They are very useful to blog primary research. People should write their motives, use it as a diary (writing down all details and circumstances), recording the results (videorecording, freehand sketches, figures, prints, text), followed by periodic summing up.

Why this is useful?

  • You don’t have to remember it (people tend to forget) (although some lab-scientists don’t like to take the notebook along to the bench)
  • Archive of ideas, (to share with people in the lab, collaborators or even ‘the world’
  • (If open) some results may be available direct outside the lab, which may be very useful for cooperation and exchange of thoughts or help (why did my blot fail?-how to proceed?)
  • It may help as a bridge to the public, i.e. by showing if public money is being spent well or for direct communication of your data to the public.
  • The info is verifiable if you link to the real data
  • Science is far more efficient this way and results are revealed instantly. Why wait till everything is distilled out? The scientist’s approach is as Hans Ricke quoted Richard Feyman from his Nobel Lecture 1966 (at Bob o’Hara ‘s blog) :

“We have a habit in writing articles published in scientific journals to make the work as finished as possible, to cover up all the tracks, to not worry about the blind alleys or describe how you had the wrong idea first, and so on. So there isn’t any place to publish, in a dignified manner,what you actually did in order to get to do the work.”

As Hans said blogs may fill that hole, because they are the place to publish this!

Major Pitfall may be that journals may not accept data reported on a wiki. And another that some people may run away with your ideas. By writing it all down you make it very easy on them. Still if everybody would become open…. For Science that would be a great good.

What I liked most of these presentations is the openness and the creativity of the presenters.
As a (medical) librarian and a scientist these thoughts came to my mind:

  • I’m a bit jealous that I worked as a scientist in the web 1.0 era. This way of approaching science looks very stimulating to me, but maybe that’s only a romantic look from the outside?
  • How do we as librarians step in? Can we play a facilitating role? Should these primary findings be aggregated and made available in a searchable way?
    We should at least keep more in pace with the new scientific developments and the way researchers exchange and find their information. It’s entirely different to what we are used to. (we= most librarians I know, including myself)
  • I wonder if such an approach could also be used in medicine and/or in EBM. Are wiki’s like this useful for CATs for instance? Question, PICO + domain, best study type, search, critical appraisal, summary, power point presentation, pdf-files, video of CAT etc??? link to video of casus perhaps?

To get an impression of the great features of such a wiki/open notebook, take a look at http://usefulchem.wikispaces.com/ (Jean Claude Bradley). You can also go to the Useful Chemistry blog and click at “UsefulChem wiki”. Note for instance the links to the notebooks of the individual scientists. Really impressive.

Below you also find the (short) presentation of Heather. Hope the others will follow soon and share their presentations

Vodpod videos no longer available.

more about “Sciblog2008 Etchevers“, posted with vodpod
Other Info





Nature science blogging conference

30 08 2008

There is official forum for Science Blogging in London, today. The event is organized by Nature Networks.

You can find the program and the attendees here.

AJCann of Science of the Invisible has summarized in this post how you can virtually follow this conference.

At this moment (saturday 11.45 am) you can follow the forum live here

HATTIP: Twitter : @AJCann, @Jobadge

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Vandaag is er een conferentie voor ‘wetenschapsbloggers’ in Londen.

het wordt georganiseerd door Nature Networks

Hier kunt u het programma bekijken.

Op dit moment (zaterdag 11.45 uur) kunt u het programma hier live volgen.

AJCann van Science of the Invisible heeft hier samengevat hoe u deze conferentie kunt volgen.

HATTIP: Twitter : @AJCann, @Jobadge