Pubmed Front Ends

[July 3, 2011]

Using Pubmed Directly

The primary source for abstracts of medical research is the National Insitute of Health (NIH) pubmed site found at http://pubmed.org. The PMID labels in most of the posts on this site reference abstracts there. One can simply enter words into the Pubmed search box at the top of the Pubmed screen or special keywords can be used to direct the search. For example, enter this into the pubmed search box:


prostate cancer


to find papers on prostate cancer. One can also use tags (see [this list]) like this:


free full text[sb] "Zlotta AR"[Au] 1999[dp]


which would find all papers whose full text is freely available on the net, authored by Alexandre R. Zlotta and the date published is 1999. Here is another example. This one finds all comparative studies on prostatectomy.


Comparative Study[Publication Type] prostatectomy


A different interface, also available at the Pubmed site, is the Advanced Pubmed Interface which allows one to build a query using drop downs without the need to memorize the various codes such as [Author].

NCBI also provides a number of useful tutorial videos on the use of certain Pubmed features.

Every paper in Pubmed is assigned a pubmed id which can be used to retrieve the abstract:


15313934[uid]

Papers reporting on research that is funded by the US National Institute of Health not only appear in abstract form on Pubmed but their full text also appears in Pubmed Central and a link from the abstract to the full free text is given. (Papers that appear in Pubmed Central have both a Pubmed Id and a Pubmed Central Id. There exists a page that gives one id if you know the other [here].)

Pubmed Front Ends

A number of web sites that act as front ends to pubmed have also arisen and summaries of them are given in this University of Manitoba article.

The direct list of sites mentioned in that article is given here (http://lib.bioinfo.pl is not mentioned in the University of Manitoba article):

Unbound Medicine, also
not mentioned there has the usual search box plus an interesting Best Evidence search and an Advanced search with boxes for author, date of publication, etc.

Ali Baba produces attractive graphics relating various keywords associated with your search and allows you to refine search by them. You must have the Java runtime installed to use this.

Vivisimo returns results clustered by topic. Choose Pubmed from drop down list near search button. Also works on Web and a number of other sources. More info on vivisimo can be found in this http://demos.vivisimo.com/clustermed
article including the use of visimo to search for clinical trials.

eTblast allows one to enter an entire abstract and get similar articles. Slow.

gopubmed will list the entire abstract of each returned result saving one having to click on each in turn. Its main feature is actually its ability to handle gene ontologies (GO). Page 12 of this survey also has a description.

hubmed allows one to narrow searches to articles with free full text on the net. After performing search click on Free near top. It can also display the citation for an article in different formats. Page 12 of this survey also has a description.

litminer is specialized for search for Genes, Chemical Compounds, Diseases and Phenotypes and Tissues and Organs.

Pubfocus uses journal impact factor and volume of forward references to enhance searches. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies.

Pubmed Assistant is a java program that provides a convenient interface to pubmed.

Pubmed Gold can limit search to articles with free full text.

Pubmed Interact is a forms-based Pubmed interface being test out by NIH, the provider of pubmed.

PubReMiner has a novel way of letting you successively narrow your searches.

PubWindows allows one to browse Medical Subject Headings (MeSH).

Relemed retrieves same or similar set of articles as a pubmed search but sorts them differently by relevance.

Xplormed returns pubmed results sorted into MeSH categories. Page 12 of this survey also has a description.

Linking to Pubmed

The shortest link using the pubmed site itself is


http://pubmed.org/17720304


The http://pmid.us site makes it even easier to create links to pubmed articles using only the PMID. For example,


http://pmid.us/17720304


which generates and jumps to a link of this form:


http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&dopt=AbstractPlus&list_uids=17720304


The http://bioinfo.pl site also has an easy linking format:


http://bioinfo.pl/pmid:17720304


This takes you to a bioinfo page with the abstract with a link to the original pubmed version below it.

Weekly Summaries

. Amedeo and Cancer Updates provide periodic summaries of prostate cancer articles found on Pubmed. Links to both of these can be found at the top of this blog in small letters just above the revolving news.

Google

. Google Scholar is not a front end to PubMed but many readers may wish to try it anyways. Just plain google is also very useful. Also, if you know a Pubmed ID then just enter pubmed into google to get to pubmed and in the pubmed search bar enter something like 15313934[uid] where you replace the number with the ID of interest to you.

Other Search

. Readers interested in search may also wish to check out this post about Banana Slug which is a front end to google that adds a random word to your search.

Bioinformatics Tools

. A more general list of bioinformatic sites in HTML and PDF form includes pubmed tools in the Information Retrieval and Clustering section.