EBM and Clinical Support Librarians@UCHC

Entries categorized as ‘Medicine 2.0’

Visualization, PBL: Visit with Wordle Occasionally

October 14, 2009 · Leave a Comment

One aspect of participating in problem-based learning is that by the end of the semester, every student in the group has taken their turn at the group tasks involved, which are:

  • The Reader narrates the case as it is made available online. The written case with any supporting visual materials such as radiology or histology about the patient are posted on Blackboard and are no longer distributed in paper handouts.
  • The Scribe is the person with the marker who listens to the groups’ discussion and synthesis of the pertinent data about the patient such as chief complaint, presentation, past medical history, current labs values, medications, tests to be ordered, treatments to begin, etc.  They are writing down the data, hypotheses, learning issues as they become available.
  • Before every student in the room brought a computer to class — which sounds like the olden days but it was less than 6 years ago — the Scribe may or may not have been the one creating hand-drawn concept maps of that week’s PBL work.  Nowadays, concept maps are created not by drawing on the whiteboard but by using CMap, a free software program from IHMC (Institute for Human and Machine Cognition).  This brings on a new role in the group: Concept Mapper.
  • The Facilitators mostly listen, occasionally asking clinically-oriented questions or providing a bit of background or narrative about a patient, a procedure or a disease without being “teacherly”.
  • Each week, one person bakes and brings in goodies for 9 people.  That is an important function, too.

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On a basic science or biomolecular level, concept maps can get pretty complicated.

Recently I wrote down some of the medical terms, processes or conclusions which were heard during PBL, and made a Wordle map out of them.   Here is what it looks like:

WordleNPC1

Image credit: http://www.wordle.net – All rights reserved – Copyright 2009

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This week I learned more about the function of Purkinje fibers (oh my duh – I’d never make it through medical school!).

Here are two other Wordles.

This one is based on words found on the EBM and Clinical Support Librarians@UCHC blog:

WordleEBMBlog

Image credit: http://www.wordle.net – All rights reserved – Copyright 2009

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The last one is formed from words taken from my Delicious account called Onc2009, a set of bookmarks about cancer, that was created for Mechanisms of Disease-Oncology:

WordleOnc2009

Image credit: http://www.wordle.net – All rights reserved – Copyright 2009

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Wordle, an elegant piece of software, was created by Jonathan Feinberg.

Categories: Academic Medicine · EBM/Clinical Decisionmaking · Educational Sites · Instruction · Medical Students · Medicine 2.0 · Other Stuff · Teaching-and-Learning in Medicine · Virtual Environments · Web 2.0 and Geek Stuff
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Search Engines, Genomics, Medical Literature: Tag Clouds come to PubMed via LigerCat

September 29, 2009 · 8 Comments

LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed, summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “.

Except from:  http://ligercat.ubio.org/about#contact_us

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LigerCat is an abbreviation for Literature and Genomics Resource Catalog, which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory.

LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature.

LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed, 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list, 3) search using keywords, 4) search on Genes found in the NCBI databases.

Following is a screenshot of the LigerCat start page:

LigerCATfullscreen

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A screenshot of the “in process” retrieval process using LigerCat for the MeSH term “pancreatic neoplasms” and keyword term, “pain“,  is shown below.

Notice that LigerCat provides the searcher two choices for getting the results, which could take a few minutes: the option of simply waiting a few moments for the search to execute, or save the shortened URL of the search-strategy to revisit the results at a later time.  That’s nice!

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ligerCatPancreaticNeoplasmsandPain

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.Here is a screenshot of the retrieval from LigerCat - which took about 20 seconds to execute:

ResultsLigerCat

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.Next:  I used LigerCat do a Gene Search for specific protein sequences.  This is how the site authors described the process of searching genes:

LigerCat is performing a live BLAST to find similar sequences to your query. Once the sequences are identified, LigerCat will use its indices to map the genes into a set of PubMed articles that reference those genes, and extract all the MeSH terms for those articles. “

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I went to NCBI to  find the Entrez Protein page and then searched FASTA for P53 and Homo Sapiens.  The search statement I found looked like this:

>gi|14993572|gb|AAK76358.1| P53 [Homo sapiens]
VGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDS

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This string was copied-and-pasted into the LigerCat Gene search box for the following result:

LigerCatBLASTP53HomoSapiensresult

All images above – Courtesy  of LigerCat – All rights reserved – Copyright 2009

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As a medical librarian, I think LigerCat is a great step forward — but because the value of information lies in the eye of the beholder — I’ll wait to hear the opinions of geneticists and research scientists as they weigh in on this new search engine.

For a different example of using this resource, see this link from the blog Biology of Aging, dated Aug 21 2009.

Categories: EBM/Clinical Decisionmaking · Educational Sites · Library 2.0 · Medicine 2.0 · News & Medical News
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Online Search Tools: Stump the Librarian? Maybe Not

August 4, 2009 · 3 Comments

Scientists: do you lay awake at night, thinking up how to Stump a Librarian with your latest inscrutable search queries?

Recently I had a reference question about a patient with NASH, and I thought:  “Uh…  Nash…. a stubby car produced by American Motors Corporation in the 1960’s? Nash, as in gnashing your teeth?  Nash, as in John Nash who suffered from schizophrenia but was able to continue working as a mathematician and econ0mist?  NaSH, as in the chemical symbol for Sodium Hydrosulfide?”

It was none of those NASHes.  NASH is not a medical subject heading in PubMed, either.

Thanks to the folks from Text to Knowledge (Text2K), who made my day when I discovered a link to their Acronym Finder.

Here is an example: a search on the term NASH

AcronymFinder

resulted in this retrieval:

AcronymFinderNASHImage credit:  Courtesy of  Text2Knowledge - All rights reserved – Copyright 2009.

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NASH stands for non-alcoholic steatohepatitis which, as shown above, can be spelled in a number of different ways.  Nice retrieval!  There is also useful Gene Synonym Finder on the Text2Knowledge site.

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A search on an entirely different website, AcronymFinder.com, turned up seven definitions of NASH, one of which was non-alcohol steatohepatitis; another definition was from NASA, which defined NASH as “No Acronyms Spoken Here”.

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A search for NASH on the Wordsmyth.net resulted in many suggestions for synonyms, but non-alcoholic steatohepatitis wasn’t on their list.  The search engine is fairly sophisticated, allowing a user to search within one or all of these fields:

Definition

Synonym

Similar Word

Example

Antonym

Related Word

Image credit:  Courtesy of http://new.wordsmyth.net/ - All rights reserved – Copyright 2009

Wordsymth.net also provides a page called Crossword Puzzle Solver… although crossword-purists would disdain using such a crutch.

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The Free Dictionary defines itself as “ the world’s m0st comprehensive dictionary, in English, Spanish, German, French, Italian, Chinese, Portuguese, Dutch, Norwegian, Greek, Russian, Medical, Legal, and Financial Dictionaries, Thesaurus, Acronyms and Abbreviations, Idioms, Encyclopedia, a Literature Reference Library, and a Search Engine all in one! “  But there were no hits for Nash or non-alcoholic steatohepatitis at the site.  It did refer me to poet Ogden Nash, however.

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Finally, a less scientific glossary is the Australian Slang Dictionary which provides no explanation for Nash, but defines many unique Australian phrases, such as the word Wobbly : excitable behaviour, as in:  “I complained about the food and the waiter threw a wobbly“.

Categories: Educational Sites · Humor · Libraries or Librarians · Library 2.0 · Medicine 2.0 · News & Medical News · Other Stuff
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News, Scientific Literature, Bioinformatics, Search Technologies: MedlineRanker

July 28, 2009 · Leave a Comment

Anyone who works with geneticists and biomedical researchers already knows that learning the language of their science is daunting for a non-scientist to understand. This international community has developed dozens of highly specific databases, data-mining software and cooperative, collective digital libraries for their own use.  In an approximate sense, one could even imagine the mapping of the human genome as one vast wiki.  Clinical care follows the translational research of these investigators.

This month in Nucleic Acids Research, Volume 37-July 1 2009, the Supplement 2: Web Server issue was published, described by Oxford University Press as:

“…the seventh in a series of annual special issues dedicated to web-based software resources for analysis and visualization of molecular biology data. The present issue reports on 112 web servers with a special emphasis on metagenomics, molecular network and pathway analysis, and biological text mining”..


Full-text of the NAR-Supplement 2 is available open-access for anyone in the world to read, on PubMedCentral.

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An article in that special issue attracted my interest, entitled MedlineRanker: flexible ranking of online literature” and written by a group of computational scientists affiliated with the Computational Biology & Data Mining Group of the Max Delbruck Center for Molecular Medicine (MDC) in Berlin.

The six authors describe their project in this way:

We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time.

Source: Link from Nucleic Acids Research – Vol. 37, Suppl. 2: W141-W146

Please view the four Supplementary Data (note: these open as either Word or Excel documents) that describe search terms used to search  PubMed using the MedlineRanker server.

The illustrations in the article look like a cross between a tag cloud and a Wordle picture.

MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker.

A list of current research projects from MDC can be viewed at this link.

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In January 2009, Supplement 1 – Datatabase Server Issue was published in  Nucleic Acids Research, Vol. 37 and that is also available online on the PubMedCentral archive.

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The 122 sites listed in the July 2009 NAR supplement will be added to the 1,200 already listed in the Bioinformatics Links Directory which:  “... now expands to almost 1400 unique web servers, databases and resources for computational research in the life sciences. All links are freely accessible to the public, and may be browsed by biological category and research task subcategory. “

For more information on text-mining programs written by scientists from around the world, go to the Bioinformatics Links Directory-Literature: Text Mining page.

Categories: Educational Sites · Medicine 2.0 · News & Medical News · Scholarly Publications · Scholarly Publishing & Open Access · Web 2.0 and Geek Stuff
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News, Scientific Literature, Visualization: Cell Press and Elsevier introduce Article of the Future

July 20, 2009 · Leave a Comment

STM publishers Cell Press and Elsevier ratcheted up the technological ante this month with their announcement on Monday, Jul 20 2009, of a shared project called Article of the Future, which they are funding to provide:

“… an on-going collaboration with the scientific community to redefine how the scientific article is presented online. The project’s goal is to take full advantage of online capabilities, allowing readers individualized entry points and routes through the content, while using the latest advances in visualization techniques“.

Text source: http://beta.cell.com – All rights reserved – Copyright 2009

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Currently available are two “prototypical” articles which the companies have put up in order to solicit feedback about the page and suggestions from the worldwide scientific community about useability and function.

Here’s one nice feature of the demo: “Integrated audio and video [will] let authors present the context of their article via an interview or video presentation and allow animations to be displayed more effectively”.

Below is a screenshot showing visualizations of tables from article Prototype #2, entitled “Identification of Positionally Distinct Astrocyte Subtypes whose Identities Are Specified by a Homeodomain Code” by Christian Hochstim, Benjamin Deneen, Agnes Lukaszewicz, Qiao Zhou and David J. Anderson.

This article was published originally published in the journal Cell (Vol. 133, issue 2 – May 2 2008, p 510-522).

CellPressElesevierJuly 2009collaborationExample

Image Source: http://beta.cell.com/hochstim/inc/hochstim_article.pdf – All rights reserved – Copyright 2009
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Visitors to the Article of the Future page are encouraged to provide direct (anonymous) input about the site using a 10-item online survey.

Thanks to AD for telling me about this.

P.S. This news release was first read on Twitter – Cell Press News around 1oopm today – http://twitter.com/CellPressNews – but the funny thing is, neither of the companies have posted a press release on their official websites yet (as of 3:15pm EST – Jul 20 2009).

Note: Chronicle of Higher Education also wrote about this venture – see entry dated July 20, 2009 at this link.

Categories: Academic Medicine · Educational Sites · Library 2.0 · Medicine 2.0 · News & Medical News · Scholarly Publications · Videos & Podcasts · Virtual Environments · Web 2.0 and Geek Stuff
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News, Medicine 2.0, Current Awareness: The debut of Clinical Reader

July 9, 2009 · 1 Comment

ClinicalReaderMultimedia

.Photo credit: http://www.clinicalreader.com – All rights reserved – Copyright 2009

Clinical Reader, introduced Jun 29 2009 in beta, is getting a lot of buzz* on Twitter, blogs and librarian discussion lists.  Thanks to librarians posting about it on Medlib-L listserv and to Berci for blogging about it.

Following is an excerpt from their About page:

Clinical Reader was brought to life in 2009 by a junior doctor and a small group of forward thinking young tech programmers spread across London and Toronto. The conceptualized idea was to manage clinical information overload and deliver relevant news from an authoritative source on a daily basis.… it is truly quality collection of accessible clinical, scientific and health literature aiming to filter the river of information presented to the online medical community.”

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I noticed that the creators of the site have constructed it using sets of criteria which include journal performance indicators; two of the criteria for inclusion in the site are shown in this screenshot of their FAQ page:

ClinicalReaderFAQ#3and#4

Photo credit: http://www.clinicalreader.com – All rights reserved – Copyright 2009

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There are currently about 3,000 readers who subscribe to the Clinical Reader newsletter.  Anyone can use the site, at no cost.

This is a rich and multi-layered site targeted at medical and dental clinicians.  It can be used to read daily health news, journal scans, searching links for training or educational videos, clinically-oriented podcasts and medical specialties. Site content is divided in three sections: News (links to UK-oriented news), Sections and Multimedia.

Below is a screenshot from Virtual Reality Training for Surgeons (8 minute video), featured this week:

ClinicalReaderVirtualRealityTrainingforSurgeonsScreenshotVideo credit:  http://tinyurl.com/n7c4lu

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There is a page for medical students, medical education and dentisty/oral surgery (among many others).

And links to Del.icio.us, Connotea, Digg and (of course) Twitter.  Finally: a hand-picked list of fourteen Medical Blogs is included, which features a Canadian librarian-blogger, Dean Giustini and Scienceroll blogger, Bertalan Mesko ~ woot for that!

ClinicalReaderCircle

Photo credit: http://www.clinicalreader.com – All rights reserved – Copyright 2009

Best wishes to the creators of Clinical Reader.com, who have rolled out a working website designed to meet the information needs of physicians, by physicians. I look forward to watching this site develop over time.

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* Edit: On July 15, after reading posts from other medical librarians (see EagleDawg blog and Steve Lawson (both dated Jul 13 2009), and other discussions who collectively remind administrators at Clinical Reader to proceed with caution in regard to commercial and copyright laws, to intellectual and graphical property, I think I’m going to retract what I wrote on Jul 9 2009 (above).

And ask Clinical Reader folks to take a look at the Creative Commons site at http://creativecommons.org/ and the doctrine of fair use.


Categories: Libraries or Librarians · Library 2.0 · Medicine 2.0 · News & Medical News · Scholarly Publications · Videos & Podcasts · Web 2.0 and Geek Stuff
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News, Searching the Medical Literature: Two Expert Opinions on Searching, or PubMed and Beyond

July 1, 2009 · 1 Comment

Today is a great day to highlight the recent posts of two fellow medical bloggers:  the first is from Laika’s MedLibLog, written by a Dutch research-scientist/medical-librarian; the second post is from Life in the Fast Lane, a blog written collectively by a group of Australian physicians.

Each author has written definitive posts about the mechanics – and utility – of searching the medical literature, and evaluating what has been found.

These posts should be seen as instant classics – and required reading for new graduate students in medicine, dental medicine or biomedical research or just about anyone with an interest in finding more-pertinent clinical information (in less time).

Their descriptive clarity in explaining what to search, and how to search is pitch-perfect.

Thank youLaika and SandNSurf – for writing them!

Please read:

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Next: Following are several quite different compilations of medical information resources written by librarians.

Elena Giglia, a medical librarian from Central Library of Medicine, University of Turin, Italy,  wrote in 2007 an excellent overview of the medical literature entitled “Beyond PubMed: Other Free Biomedical Databases.  This 11-page article was published in the European Journal of Physical and Rehabilitation Medicine (Europa Medicophysica) – Vol. 43(4):563-9 (Dec 2007). It is available online for anyone to read.

Ms. Giglia is the author of a very recent article, “Medline/PubMed revisited: new, semantic tools to explore the biomedical literature“, published June 2009 in Eur J Phys Rehabil Med – Vol. 45(2):293-7 (subscription required).

Law librarian Gloria Miccioli wrote a summary of medical sources targeted for legal professionals, entitled  “Researching Medical Literature on the Web” (published Sept 22 2008), found on LLRX.com.

The LLRX website also offers a list of links for librarians (or others) doing legal research.

My own Home Week: Evidence Based Medicine Resources page on Libguides.com was created – and is updated annually – as a source-sheet for third-year medical students at UCHC as they rotate throug h their clinical clerkship year.

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Finally:  Librarians working in academic health science libraries offer a variety of digital training tutorials or subject lists for orienting their students, residents and faculty to the technical aspects of searching the literature of medicine.

A quick search on Google for “tutorials searching medical literature” brings up an eclectic group of 968,000 retrievals.

The same search using Bing f0und 1,530,000 well-filtered retrievals.

Categories: Academic Medicine · Blogs or Wikis about Medicine · EBM/Clinical Decisionmaking · Educational Sites · Instruction · Libraries or Librarians · Library 2.0 · Medical Students · Medicine 2.0 · News & Medical News · Teaching-and-Learning in Medicine
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News, Blogging, Health Information Online: Healthcare Bloggers Code of Ethics

June 30, 2009 · Leave a Comment

HBCE: Healthcare Blogger Code of EthicsImage credit: http://medbloggercode.com/ – All rights reserved – Copyright 2009

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My thanks to the good folks at Healthcare Blogger Code of Ethics who recently added the EBM and Clinical Support Librarians@UCHC blog to their lengthy list of medical bloggers.

Here is the written Code of Ethics promoted by this non-profit, volunteer group.

Link here to view the newest additions of medicine bloggers, or patient bloggers, endorsed by HBCE (updated June 26 2009).

Categories: Blogs or Wikis about Medicine · Consumer/Patient Health · Educational Sites · Healthcare-Administration · Medicine 2.0 · News & Medical News · Teaching-and-Learning in Medicine

News, Public Health, Emerging Technologies: Delivering the News… Online We Are

May 1, 2009 · 1 Comment

It’s been a big news week.  Global health developments have occurred with such rapidity that reporting the news of this week  gives additional meaning to the use of the term “viral” as in… tracking the global spread of a novel virus:  A/H1N1 – swine influenza.

After writing this post, I then noticed that only one of items on the list below refers to materials which are in print (that of the journal Public Health Reports).  It is online that we are.

  • DynaMed, an evidence based medicine resource which UCHC Library subscribes to, announced this week that an online section for current clinical information on Swine Influenza A/H1N1 will be available to anyone in the world at no cost – at this link.  The database, produced by Ebsco, is updated daily.
  • Finally, the cartoonist-blogger XKCD drew a great comic this week, arguing against getting one’s news of the day from Twitter and re-tweets.  Many other bloggers worldwide have featured this cartoon this week, but in case you missed it…
xkcdtwitterfluPhoto/Source credit:http://xkcd.com/574/

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IMHO: The option of becoming a vegetarian is growing more and more attractive.

Categories: EBM/Clinical Decisionmaking · Epidemiology/Public Health · Journalism · Library 2.0 · Medicine 2.0 · News & Medical News · Web 2.0 and Geek Stuff
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News, Public Health, Global Health: A Potential Pandemic of Influenza

April 27, 2009 · 6 Comments

Public health concerns dominate the news headlines this week, as evidence continues to unfold of a global outbreak of a novel strain of swine influenza A/H1N1.

Thanks to an active international group of Medical Bloggers and Librarians connected through social networking sites such as FriendFeed or Twitter, as I arrive at work on Monday morning, this connectedness becomes a great advantage for those of us in the United States, as our European colleagues have already scanned and posted many news or website links on items of vital concern, as emerging news continues to pour in from many places around the world.

Following are a brief set of links to global health information, disease-tracking and interactive-maps for the spread of Swine Influenza A/H1N1 (reported as of Monday, Apr 27 2009):

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tweetdeck4272009

Image credit:  http://www.tweetdeck.com – All rights reserved – Copyright 2009

International

  • The International Society for Infectious Diseases (ISID) produces ProMed-Mail, described as the global electronic reporting system for outbreaks of  emerging infectious diseases & toxins, open to all sources“. Subscription to ProMed-Mail is available to anyone, free of charge; updates can be set up for daily or weekly email alerts.
  • UCHC Library subscribes to GIDEON (Global Infectious Diseases and Epidemiology Online Network), which is a specialized database for epidemiologists used for “… diagnosis and reference in the fields of tropical and infectious diseases, epidemiology, microbiology and antimicrobial chemotherapy.  GIDEON currently tracks 337 diseases, 224 countries, 1,147 microbial taxa and 306 antibacterial (-fungal, -parasitic, -viral) agents and vaccines, including over 10,000 notes outlining the status of specific infections within each country and over 20,000 images, graphs, interactive maps and references“.  GIDEON is updated daily.

United States

Tracking the Outbreaks

  • Google provides a free service called News Alert, which you can create yourself using any key-words to search on.

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I’d like to acknowledge the cooperative work of many European scientists and medical librarians – and in particular, bloggers Laikas, Berci and DigiCMB – who are always 6-8 hours ahead of me, both literally speaking in the real world and in many Web 2.0 innovations, who have posted scientific links and news about swine flu and steered  me to several links for this post today.   Thank you to these talented, and generous, colleagues.


Categories: Epidemiology/Public Health · Medicine 2.0 · News & Medical News · Virtual Environments
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