Links for 2009-02-06 [del.icio.us]
relemed® search engine
davidrothman.net » novo|seek (3rd-Party PubMed/MEDLINE Tool)
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DigiCMB - February 11, 2009 Author: Guus van den Brekel
When the user actually *is* broken (Anna Kushnir and PubMed)
I have distinct childhood memories of asking my mother what one word or another meant. She would point out that there was a dictionary close at hand designed exactly for that purpose and invite me to make use of it.
I remember asking my father to teach me to program in BASIC. He cheerfully agreed and handed me the big brown manual.
So maybe I’m weird and so are my folks, but these memories inform my take on the chatter in the blogosphere and on MEDLIB-L about this post by Harvard PhD student Anna Kushnir in which she expresses her frustration with PubMed. Kushnir writes (in part):
“I hate PubMed. I hate it w...
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davidrothman.net - March 31, 2008 Author: David Rothman Tags: Technology Search Perception of Libraries/Librarians For Medical Libraryfolk Medical Librarianship Blogs 3rd Party PubMed/MEDLINE Tools
Poster: PubMed Alternative Interfaces
From the Wiki des Bibliothèques Universitaires de Médecine et Santé Publique - Lausanne, check out this great poster on Alternative interfaces for PubMed searches by Isabelle de Kaenel.
Thanks for pointing this out, Gaétan!
Other posts about Third-Party PubMed/MEDLINE Tools
(Perhaps it is time I made this a WordPress category…?)
Pubconn (Firefox Plugin for Connotea in PubMed)
PubMed Citations (Greasemonkey Script)
PubMed2Wikipedia
Healia searches PubMed/Medline
CureHunter Visual Medical “Dictionary” (MeSH Browser)
PubViz (3rd-party PubMed/MEDLINE Tool Prototype)
Almost Everything About HubMed (Third-party P...
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davidrothman.net - November 29, 2007 Author: David Rothman Tags: Technology Search For Medical Libraryfolk
Healia searches PubMed/Medline
Healia PubMed/Medline Search is a search engine specifically designed to help consumers find information in the PubMed/Medline dataset in a user-friendly way. Healia PubMed/Medline Search retrieves abstracts (published summaries) of journal articles.
Healia’s PubMed search (currently in beta) might be one of the best interfaces available for clinicians who don’t have the search skills to effectively search PubMed through its native interface.
Some notable features:
Automatic “AND”
By default, Healia inserts a boolean “AND” between all search terms (as Google does). While the expert sea...
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davidrothman.net - October 1, 2007 Author: David Rothman Tags: Technology Search For Medical Libraryfolk
CureHunter Visual Medical “Dictionary” (MeSH Browser)
Dangit!
I finished writing this post last night, but hadn’t posted it yet. Since Berci has beat me to it, I’ll go ahead and post it now.
————–
Curehunter.com has a “visual medical dictionary” that I’m having lots of fun playing with, even though I’m not sure that it is best described as a “dictionary.”
Really, it’s a nifty third-party PubMed/MEDLNE tool to visually browse MeSH (as an alternative to the NLM’s MeSH browser). As shown in the screen capture below, it gives the MeSH scope note for “colitis, ulcereative” as th...
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davidrothman.net - August 31, 2007 Author: David Rothman Tags: Technology Interfaces For Medical Libraryfolk
PubViz (3rd-party PubMed/MEDLINE Tool Prototype)
From the Microarray Lab, Department of Psychiatry / Molecular and Behavioral Neuroscience Institute at the University of Michigan comes PubViz, a powerfull, flexible prototype interface (built in Flash!) for MEDLINE information retrieval.
In short, PubViz is developed to provide the capability of utilizing external knowledge as well as interactive visual query functions for more efficient exploration of the Medline database. The current version has the ability to utilize protein-protein interaction data during Medline search and enable researchers to identify functionally related Medline records not retrievable in existin...
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davidrothman.net - July 30, 2007 Author: David Rothman Tags: Technology Search For Medical Libraryfolk
Almost Everything About HubMed (Third-party PubMed Tool)
With tons of screen captures and good, simple descriptions of features, this seems like a really nice introduction to HubMed.
Previous posts about third-party PubMed tools
Verbs in MEDLINE Searches & MEDIE (Third-Party PubMed Tool)
MLA News: Third-Party PubMed Tools
Pmid.us (Third-Party PubMed Tool)
ExpertMapper (Third-Party PubMed Tool)
Twease (Third-party PubMed Tool)
Article on eTBLAST (Third-party PubMed Tool)
CILIP HLG Newsletter on Third-Party PubMed Tools
Ali Baba (3rd Party PubMed tool)
FABLE (3rd Party PubMed Tool)
Managing Medical Literature on a Mac: iPapers, Papers, Sente, BibDesk
Notes on relemed
MeshPub...
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davidrothman.net - July 26, 2007 Author: David Rothman Tags: Technology Search For Medical Libraryfolk
PubMed Relevance Tool
relemed is an alternative search interface for PubMed. Users can search for PubMed citations but relemed will sort the results by the relevance to the topic. It also links to other resources such as Google, Scirus, and full-text vendors. relemed was created by researchers at the University of Virginia School of Medicine.
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Medicine/Health Sciences - July 15, 2007 Tags: website
Verbs in MEDLINE Searches & MEDIE (Third-Party PubMed Tool)
Created by the University of Tokyo’s Tsujii Laboratory, I was reminded of MEDIE by seeing the title of a recent article:
Bertaud, Valerie; Said, W.; Garcelon, Nicolas; Marin, Franck;
Duvauferrier, Regis. “The value of using verbs in Medline searches”
Medical Informatics & The Internet in Medicine 32.2 (2007). 05 Jun. 2007
MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE. You can find abstracts/sentences in MEDLINE by specifying semantics of correlations
http://www.informaworld.com/10.1080/14639230601140711
MEDIE formulates queries by offering the user three fiel...
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davidrothman.net - July 3, 2007 Author: David Rothman Tags: Technology Search For Medical Libraryfolk
Greasemonkey for PubMed/PubMedGold (Courtesy of my brother)
I might’ve mentioned before that I have geek pedigree. My father was a geek before it cool and programmed for IBM for 30 years. He printed my birth announcements on IBM computer punchcards (Yes, really). He’s in Wikipedia.
One of my brothers, Andrew, has been a greater recipient of that geek DNA. Just recently, he decided to start playing with Firefox Greasemonkey scripts and told me that he’d code one for me if the idea struck him as “sufficiently easy and sufficiently interesting.”
Here’s the first thing that came to mind:
Sometimes, PubMed doesn’t have the link to free, full...
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davidrothman.net - June 25, 2007 Author: David Rothman Tags: Technology Search Browsers For Medical Libraryfolk
Disagreeing with a PubMed Instructor about MeSH
Rachel at Women’s Health News posted yesterday about her week-long course in biomedical informatics in a post wonderfully titiled “Dispatches from Nerd Camp.” She writes:
…our PubMed instructor declared, “I’m over the whole MeSH thing,” in the context of explaining that she thinks it’s completely unnecessary to know about and too hard to use.
[snip]
The instructor suggested that keyword searching is always just fine because it will map to MeSH anyway. This is often true. However, I did a keyword search on “HRT” (a popular topic that most adult humans would understand) and discovered th...
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davidrothman.net - May 31, 2007 Author: David Rothman Tags: Technology Search Bioinformatics Professional Development For Medical Libraryfolk Medical Librarianship Blogs
Pmid.us (Third-Party PubMed Tool)
The more I play with pmid.us, 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:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12472752&dopt=AbstractPlus
Yuck!
But Pmid.us lets us shorten that to:
http://pmid.us/12472752
(Get it? The URL is http://pmid.us/[Your PMID].)
If we want to fetch two abstracts, we can do that by adding a “+” and the second PMID:
http://pmid.us/12472752+17146093
(http://pmid.us/[First PMID]+[Second PMID])
We can even retrieve three abstracts this way:
http://p...
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davidrothman.net - May 10, 2007 Author: David Rothman Tags: Technology Search Interfaces Mashups For Medical Libraryfolk
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 |
Try eTBLAST
Other posts about third-party PubMed tools:
CILIP HLG Newsletter on Third-Party PubMed Tools
Ali Baba (3rd Party PubMed tool)
FABLE (3rd Party PubMed Tool)
Managing Medical Literature on a Mac: iPapers, Papers, Sente, BibDesk
Notes on relemed
MeshPubMed.org
PubMed Gold
PubMed Reader
For MedLibs who use Macs: iPapers
PubMed2Connotea / PubMed2CiteULike
More notes on BioWizard (Digg ...
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davidrothman.net - May 1, 2007 Author: David Rothman Tags: Technology Search Interfaces Mashups For Medical Libraryfolk
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 differen...
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davidrothman.net - April 26, 2007 Author: David Rothman Tags: Technology Search Interfaces Mashups For Medical Libraryfolk Medical Librarianship Blogs
Search: Relemed Sentence-Level Search Engine with Relevance Score for the MEDLINE Database of Biomedical Articles, January 2007
"relemed increases specificity and precision of retrieval by searching for query words within sentences rather than the whole article. It uses sentence-level concurrence as a statistical surrogat...
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Info To Go: Navigating the Internet - April 16, 2007
Search: New Search Engine for Finding Articles in PubMed
"relemed search engine from the University of Virginia School of Medicine searches PubMed for medical literature by assigning relevance to results in addition to looking for keywords. Covering th...
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Info To Go: Navigating the Internet - April 2, 2007
Ali Baba (3rd Party PubMed tool)
Ali Baba is pretty neat.
Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts.
Perhaps the best way to explain what it does is with an example:
A patient with cough is treated with codeine. He becomes unresponsive after a while — what is going on?
Click for larger image
The query entered in Ali Baba was “codeine intoxication”.
Ali Baba shows the relationship between codeine (marked in the graph with blue frame), co...
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davidrothman.net - March 30, 2007 Author: David Rothman Tags: Technology Interfaces Mashups For Medical Libraryfolk
FABLE (3rd Party PubMed Tool)
FABLE = “Fast Automated Biomedical Literature Extraction”
Why FABLE?
FABLE currently tags only genes and proteins and only normalizes human genes. This allows us to design a customized tool that is tailored specifically for this task, rather than a generalized tool such as PubMed that provides broad search capabilities with less specificity.
FABLE mines the biomedical literature for information about human genes and proteins. FABLE v2 allows a user to find articles mentioning a gene of interest (Article Finder), or to generate a list of genes associated with one or more keywords (Gene Lister). Try one of these...
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davidrothman.net - March 29, 2007 Author: David Rothman Tags: Technology Search Mashups For Medical Libraryfolk
SIMPLE, QUICK, BUT EFFECTIVE NEW PUBMED SEARCH ENGINE
relemed is so simple that it couldn’t be any good, right? Wrong. It provides the same results as a PubMed search, but faster and easier, plus it arranges them by relevance. Other neat features are planned, including links to the full-text. Try it.
URL: http://www.relemed.com
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OPL Plus (not just for OPLs anymore) - March 24, 2007 Author: Ms. OPL
Relemed: un nuovo PubMed
Avevo da qualche giorno in bozza l’articolo su relemed, di cui si è dibattuto nelle liste di discussione dei bibliotecari. Mi ha preceduto il collega del blog The Krafty Librarian e io mi limito a segnalarvi il suo bel post che vi guiderà alla scoperta di questo nuovo strumento
Post correlati: Hubmed: l’alternativa amichevole a [...]
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Blog @lla tua biblioteca - March 23, 2007 Author: Blog Bioingegneria Tags: PubMed strumenti Ricerche bibliografiche Banche dati
Notes on Relemed
A lot of bibliobloggers have been written about relemed, but wanted to avoid doing so until I felt I understood it. relemed came up on MEDLIB-L recently and a good question was asked:
I tried it just now and I like that it shows a little bar graph of each articles' relevance, but I fail to see how it is different from HubMed (http://www.hubmed.org/), which allows you to sort by date or relevance. Am I missing something?
I think I now understand relemed a bit, so I attempted to answer the question. You can judge for yourself how well I did.
The Krafty Librarian points to this recent article from Medical Design Onli...
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davidrothman.net - March 20, 2007 Author: David Rothman Tags: Technology Search Mashups For Medical Libraryfolk
Relemed
What is relemed? relemed, short of Relevant Medicine is a "Google-like search engine for medical literature," created by researchers at the University of Virginia School of Medicine. relemed is intended to provide medical professionals, researchers and the public with "more efficient and targeted way to search PubMed." relemed was designed to increase specificity and return more relevant results by finding the query words within sentences and statistical relationship between the them.Some folks on MEDLIB-L have already begun to look at and discuss relemed. David Rothman who has been "playing with relemed for a few weeks...
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The Krafty Librarian - March 20, 2007 Author: The Krafty Librarian
A new tool
relemed, from the University of Virginia School of MedicineStill in its infancy, it tells you how relevant (and ranks results that way) a citation is to your search in MEDLINE, but it doesn't tell you how many results or allow advanced searching yet. In the meantime, try HubMed. And, of course, if sorting by date is fine with you, there's the gold standard of PubMed.
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The Rabid Librarian's Ravings in the Wind - March 15, 2007 Author: Eilir
Let the good times roll
We’ve just passed the midpoint to both the semester and the winter season …..that time of year when stir craziness beckons and we could all use a little break. For that reason, we have nothing but fun, footloose tools to talk about on this week’s BRAIN_blog! So in lieu of a trip to the Mexico, feast your eyes on these fabulous and fancy-free web search tools and go a little wild!
Various library entertainments…
New podcast!
Check out the BRAINcast web site this week to get an uncommonly good tour of the Learning Commons, find some common ground and share some good old common sense! Common cliches abound...
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BRAIN_blog - March 8, 2007 Author: Jenn
Relemed search engine
relemed search engine. This is basically a simple interface to Medline, and it returns results in relevance ranked order, rather than date. Search functionality isn't bad, with Boolean, nested logic searching, truncation, no automatic term mapping option and so on. If you find searching Medline a little on the daunting side, or you want a different display/results ranking, this is worth trying out. I'm not a medical search specialist, so if any of you out there are, and would care to comment, I'd love to hear from you.
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Phil Bradley - March 7, 2007 Author: philipbradley Tags: Subject specific
New Search Engine for Finding Articles in PubMed
Searching medical sites like PubMed can be intimidating at the best of times. When you’re trying to find articles related to two very distinctive concepts — say, spina bifida and autism — it can rapidly get frustrating. There’s a new search engine from the University of Virginia School of Medicine that searches PubMed for medical literature by assigning relevance to results in addition to just looking for keywords. relemed, as the engine is called, is available at http://www.relemed.com/ .
PubMed generally gives the most recent articles first, searching for all the keywords you specify. relemed fin...
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ResearchBuzz - March 5, 2007 Author: admin Tags: Science-Medical
Relemed
relemed search engine Search millions of biomedical articles for the most relevant answers
Covering the whole MEDLINE®, till January 17, 2007
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Sukhdev's World - January 25, 2007 Author: Sukhdev Singh
Relemed
relemed - "Search millions of biomedical articles for the most relevant answers. Covering the whole MEDLINE®, till January 17, 2007"
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Peter Scott's Library Blog - January 24, 2007 Author: Peter
Medline simplified - Relemed. We'd never have got ...
Medline simplified - relemed. We'd never have got here without Google.
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Libraries in the NHS - January 24, 2007 Author: Ben
Relemed
There is now yet another new search engine for Medline/PubMed. The relemed homepage states that it may be used to “Search millions of biomedical articles for the most relevant answers”. A recent article in BMC Medical Informatics and Decision Making titled “relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles” describes its search function and provides a couple of examples of searches. relemed supposedly retrieves higher specificity by searching for multiple terms only when they are in adjacent sentences, not simply when both are present in t...
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Librarians' Rx - January 23, 2007 Author: tchatter Tags: Resources Searching
