MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'entrez'. Sat, 03 Sep 2011 02:58:37 +0100 http://www.medworm.com/index.php?rid=4139404&cid=t_119959_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F05%2Fwhat-the-world-needs-is-lists-of-entrez-database-fields%2F You know the problem. You want to qualify your NCBI/Entrez database search term using a field. For example: “autism[TIAB]“, to search PubMed for the word autism in either Title or Abstract. Problem – you can’t find a list of fields specific to that database. Now you can. Follow the links in this public Dropbox file, to see a CSV file containing name, full name and description of the fields for each Entrez database. Code to generate the files is listed below. This may or may not be the first in an occasional, irregular “what the world needs” series. #!/usr/bin/ruby require 'rubygems' require 'bio' require 'hpricot' require 'open-uri' Bio::NCBI.default_email = "me@me.com" ncbi = Bio::NCBI::REST.new ncbi.einfo.each do |db| puts "Processin... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4139404 Fri, 05 Nov 2010 04:31:55 +0100 4139404 http://www.medworm.com/index.php?rid=4013415&cid=t_119959_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F09%2F29%2Fpubmed-searching-experiments-in-javascript%2F Andrew asks: …anyone know of a tool that will take a pubmed query and plot the number of articles by year? I figured that this was a good excuse to improve my lowly Javascript skills by building a toy web application. First, video proof that I did get something to work, up to a point: Next, some code. I created a Sinatra application, with the directory structure shown. It’s fairly simple: one main file, app.rb, a “spinner” graphic to indicate loading operations, the jQuery and Highcharts Javascript libraries and one view, wrapped in a layout. Sinatra pubmed application file tree Next, the code in app.rb. It’s about as simple as it gets: require "rubygems" require "sinatra" require "haml" get "/" do haml :i... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4013415 Wed, 29 Sep 2010 03:32:43 +0100 4013415 http://www.medworm.com/index.php?rid=2442321&cid=t_119959_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F05%2F27%2Fquerying-ncbi-entrez-database-fields-using-ruby%2F Here’s a problem. You’d like to construct a complex query at NCBI Entrez using various fields. Example: “9606″[Taxonomy ID] to limit your search to Homo sapiens. Except – you don’t know which fields are available for the database that you want to query. EInfo can return an XML file with this information. Ruby + Hpricot eats XML for breakfast. Here’s an example using the GEO Datasets (gds) database. #!/usr/bin/ruby require 'rubygems' require 'hpricot' require 'open-uri' doc = Hpricot(open("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gds")) (doc/'//fieldlist/field').each do |f| puts "#{(f/'/name').inner_html},#{(f/'/fullname').inner_html},#{(f/'descr... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2442321 Wed, 27 May 2009 07:33:41 +0100 2442321 http://www.medworm.com/index.php?rid=1501550&cid=t_119959_105_f&fid=36987&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FIvorKovicMd%2F%7E3%2F307166493%2F Recently I wrote about PubReMiner, an online application designed to help you search PubMed. Now I present a similar and even more powerful application named GoPubMed. When you search PubMed the conventional way, via the Entrez system, two things happen. First your query is translated with identification of Medical Subject Headings (MeSH) terms and secondly this translated query is matched with words from all the abstracts. The second part is performed by term matching, which ultimately means that keyword synonyms are not used in the search. This way you can lose a lot of important articles. Finally, found abstracts are listed in the reverse chronological order. In most of the cases this is not what you want, and you are forced to manually go through all the abstracts to find those... Ivor Kovic, M.D. blogs http://www.medworm.com/rss/comments.php?id=1501550 Sun, 08 Jun 2008 05:11:25 +0100 1501550 http://www.medworm.com/index.php?rid=1466453&cid=t_119959_105_f&fid=36987&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FIvorKovicMd%2F%7E3%2F296848963%2F PubMed provides access to Medline, a premier bibliographic database that contains references to journal articles in the life sciences with a concentration on biomedicine. It is available via the NCBI Entrez retrieval system, which was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the U.S. National Institutes of Health (NIH).  PubMed is extremely popular among biomedical researchers, in part because it offers free access, contrary to other such search engines like Scopus and Web of Science. However, during the years I heard a lot of people complaining about PubMed. They do not like its interface and are not satisfied with search results it provides. A lot of these people never gave any thought about PubMed, nor d... Ivor Kovic, M.D. blogs http://www.medworm.com/rss/comments.php?id=1466453 Fri, 23 May 2008 23:28:53 +0100 1466453 http://www.medworm.com/index.php?rid=623759&cid=t_119959_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F117866118%2F Earlier this week, when I logged into my “MyNCBI” account, I got a message asking if I wanted to try out the beta site. Here is what I got when I clicked on “yes”. I actually don’t see the “leave beta” sign any more (maybe I clicked on it by mistake), but I presume others have seen the beta site as well. The current beta is a test for “the accuracy and speed of the improved search engine”. Apparently, it is just step 1 of an effort to develop new features and capabilities later this year. Click for larger image Update: Just read this on my NCBI news feed Entrez Beta was successfully tested and will soon replace the production system. The invitation to preview the site was removed, however, users may go directly to the site & new URL... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=623759 Sat, 19 May 2007 02:42:38 +0100 623759