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Free PubMed Facelifts: Alternative Interfaces to an Essential Database
Posted Sunday, March 25, 2007 4:00 PM

Free Alternatives to PubMed



PubMed is pretty good on its own. But sometimes it would be nice to be able to produce different views of its information, to do some more complex data mining, or to add information from other databases to enrich your results.


The following is a list of alternative interfaces, mashups and mining tools for PubMed. It’s by no means complete. Some more comprehensive resources are given at the end of this article. The resources are listed alphabetically. Some of them are rather complicated to use. For example, Ali Baba (which is cool) requires a download and you must have Java operative on your computer. Be sure to have a look at PubFocus, which was highlighted in our January newsletter. PubReMiner and ReleMed are also worth trying.


According to Wikipedia, a mashup is a site that "combines content from more than one source into an integrated experience." See the same source for a good discussion of data mining. David Rothman, who writes an excellent blog for health librarians, has some interesting entries on alternative PubMed interfaces. PubMed is evolving, and you can get a good sense of where it may be going by checking out some of these useful tools.


Mark Rabnett

Hospital Librarian

St. Boniface General Hospital





Ali Baba: PubMed as a graph




Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. The resulting network is presented in graphical form, providing a quick overview of all information contained in the abstracts. Standard PubMed queries are supported. Ali Baba automatically retrieves all corresponding citations and parses them for


    * cells from the MeSH tree,

    * diseases from MeSH,

    * drugs from MedlinePlus: USDPI and MedMaster,

    * proteins/genes from the UniProt database,

    * species from NCBI Taxonomy,

    * tissues from MeSH, and

    * nutrients.


Ali Baba associates objects for the following types of relations with each other:


    * protein-protein interactions,

    * (sub)cellular location of proteins,

    * proteins/genes discussed with species,

    * proteins/genes discussed with tissues,

    * relations between drugs and diseases,

    * proteins/genes and diseases


The program is a bit tricky to install. To use Ali Baba the user must have Java 1.5 or higher on your computer.


For more information consult:

Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser

Ali Baba: PubMed as a graph.

Bioinformatics, 22(19):2444-2445, 2006







ClusterMed is a free demo that uses the Vivisimo Velocity Search Platform to organize PubMed results into hierarchical folders with meaningful categories, allowing researchers to hone in on the most relevant results quickly. The folders allow users to view categories, view related articles, and drill down through the topic hierarchy. Results can be clustered by topic, author, mesh headings and date. The blurb on this web site claims that users will be able reduce research time, improve research effectiveness and quickly view an overview on a new or peripheral research area.


For more information consult:

New ClusterMed Organizes PubMed Results

by Paula J. Hane

Information Today, April 5, 2004




ConceptLink: Visual Exploration of Medical Concepts




ConceptLink creates visual images for medical concepts. It allows the user to explore concept relationships visually. ConceptLink is also a visual interface for PubMed. It guides the user to construct search queries through concept maps generated instantly from user's queries. By visualizing the complex concept relationships and providing interactive functions for the user to explore concept relationships, ConceptLink can significantly improve a search and help the user understand the search results better.


For more information consult:

Lin X, Morton L.

Visual mapping for medical concepts.

AMIA Annu Symp Proc. 2003;:912.







eTBLAST is a new, free search engine developed by the University of Texas Southwestern Medical Center. The user inputs an abstract or paragraph, which is submitted to PubMed. Similar abstracts are then returned and ranked by weight. An advanced search option allows the user to give weight to particular keywords.


Results include a list of experts in the field, journals to submit to, and a history of publishing in this field. Be prepared for a long wait. The simple search takes some minutes, the advanced search results are emailed to the user.






GoPubMed allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits. First, it gives an overview of the literature abstracts by categorizing abstracts according to the GO and thus allowing users to quickly navigate through the abstracts by category. Second, it automatically shows general ontology terms related to the original query, which often do not even appear directly in the abstract. Third, it enables users to verify its classification because GO terms are highlighted in the abstracts and as each term is labelled with an accuracy percentage. Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org. Querying is currently limited to 100 papers per query.


For more information consult:

Doms A, Schroeder M.

GoPubMed: exploring PubMed with the Gene Ontology.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W783-6.







HubMed is an alternative search interface to the PubMed database, incorporating external web services and providing functions to improve the efficiency of literature search, browsing and retrieval. Users can create and visualize clusters of related articles, export citation data in multiple formats, receive daily updates of publications in their areas of interest, navigate links to full text and other related resources, retrieve data from formatted bibliography lists, navigate citation links and store annotated metadata for articles of interest. HubMed was the first to add the ability to save search strategies as RSS feeds, a feature now available in PubMed.


For more information consult:

Von Isenburg, Megan


J Med Libr Assoc. 2007 January; 95(1): 95–97.


Eaton AD.

HubMed: a web-based biomedical literature search interface.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W745-7.






LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process:


        * Genes: Names of genes and gene products.

        * Chemical Compounds: Names of chemical compounds and their aliases.

        * Diseases and Phenotypes: Names of diseases and phenotypes

        * Tissues and Organs: Names of tissues and organs


The LitMiner text-analysis application was developed to enable biologists to explore gene relationships in the published literature. The application features a suite of interfaces that enable users to search PubMed as well as local databases, to view document abstracts, to filter terms, to select gene name aliases, and to visualize the co-occurrences of genes in the literature. At each of these stages, LitMiner offers the functionality of a digital library. Documents that are accessible online are identified by an icon. Users can also order documents from their institutions library collection from within the application. In so doing, LitMiner aims to integrate digital library services into the research process of its users.


For more information consult:

Demaine J, Martin J, Wei L, de Bruijn B.

LitMiner: integration of library services within a bio-informatics application.

Biomed Digit Libr. 2006 Oct 19;3:11.








PubMed imposes an upper limit of 10,000 for downloading PMID list or citations; and MEDLINE files are too large for most off-the-shelf XML parsers. MedKit is a Java package to work around the limitations, as well as provide other useful functionalities, e.g. random sampling. Its four modules (querier, sampler, fetcher and parser) can work independently, or be pipelined in various combinations. MedKit can be used as a stand-alone GUI application, or integrated into other text-mining systems. Text mining researchers and others may download and use the toolkit free for non-commercial purposes.


For more information consult:

Ding J, Berleant D.

MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations.

Bioinformatics. 2005 Mar 1;21(5):694-5. Epub 2004 Oct 27.







PubFinder is designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine.


For more information consult:

Goetz T, von der Lieth CW.

PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W774-8.







PubFocus automates analysis of PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. In sum, PubFocus is a good alternative to PubMed. It provides statistical tools that can address the following questions:


1.         What are the publication trends in your field and the key articles?

2.         Which journals publish the best articles in your field?

3.         What does an author’s publication profile look like?


For more information consult:

Plikus MV, Zhang Z, Chuong CM.

PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm.

BMC Bioinformatics. 2006 Oct 2;7:424.



PubMed Assistant




A stand-alone Java program that helps biologists and medical workers get the most out of PubMed search. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, and clickable links to Google Scholar.


Beware of possible problems with the latest version of the Java Runtime Environment (J2SE 5.0 Update 10). On the author’s workstation PubMed Assistant failed to load.


For more information consult:

Ding J, Hughes LM, Berleant D, Fulmer AW, Wurtele ES.

PubMed Assistant: a biologist-friendly interface for enhanced PubMed search.

Bioinformatics. 2006 Feb 1;22(3):378-80. Epub 2005 Dec 6.



PubMed Gold




PubMed Gold is a PubMed interface that finds PDFs for PubMed citations by automatically searching Google. Links to free full text articles indexed by PubMed are also displayed with some citations.



PubMed Interact




PubMed Interact is a Web-based MEDLINE/PubMed search application that explores recent trends in Web development technologies like DOM tree manipulation and Ajax scripting methods. Users can control search parameters, refocus search strategies and modify search results easily. Many enhanced and interactive features occur at client-side and allow instant feedback without reloading or refreshing the page. PubMed Interact is a novel approach in the development of online tools for medical information research. The unique slider interface greatly simplifies applying basic limits to a PubMed search. A bit too simple for the serious searcher, but a useful tool for the casual seeker after information. An earlier version of PubMed Interact was called SLIM (Slider Interface for MEDLINE/PubMed).


For more information consult:

Muin M, Fontelo P, Ackerman M.

PubMed Interact: an interactive search application for MEDLINE/PubMed.

AMIA Annu Symp Proc. 2006;:1039.


Muin M, Fontelo P.

Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.

BMC Med Inform Decis Mak. 2006 Nov 3;6:36.



PubMed PubReMiner




PubReMiner is a tool that allows simple text-based query building and information gathering(mining) of PubMed. PubReMiner presents its results, gathered from abstracts, in frequency tables of journals, authors and words, which can be included/excluded in an iterative fashion.


Next to building efficient queries, PubReMiner can also be helpful in other areas: *Selecting a journal for your current work (by scanning the most often used journals of similar research)

*Finding experts in a research area (by viewing the authors associated with your query) *Determining the research interest of an author (by viewing the keywords associated with an author)







Browse PubMed citations with a modified version of the National Library of Medicine's MeSH Browser. PubWindows is most effective for broad-scope collection of citations in a specific subject area. This is an interesting introduction to medical subject headings for the novice, yet it has advanced features such as easy set up of RSS feeds based on subject searches. There is also the option to allow easy citation exporting in popular formats: RIS/EndNote, BibTex, RDF, MODS, RefWorks.







ReleMed is 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. PubMed generally gives the most recent articles first, searching for all the keywords you specify. ReleMed finds articles that show close relationships among the search terms, so that results are often more relevant. A relevancy bar helps you see at a glance how your results were analyzed. Extracts from the texts are clearly highlighted. Click on the record link at the end of each title. ReleMed also shrinks the displayed text, and hence the time spent scanning the articles.


For more information consult:

Siadaty MS, Shu J, Knaus WA.

ReleMed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.

BMC Med Inform Decis Mak. 2007 Jan 10;7:1.




XplorMed: eXploring Medline abstracts




As scientific literature databases like MEDLINE increase in size, so does the time required to search them. Scientists must frequently inspect long lists of references manually, often just reading the titles. XplorMed is a web tool that aids MEDLINE searching by summarizing the subjects contained in the results, thus allowing users to focus on subjects of interest. For further description of new features added to XplorMed during the last 2 years consult http://www.bork.embl-heidelberg.de/xplormed/.


For more information consult:

Perez-Iratxeta, Carolina, Perez, Antonio, Bork, Peer, Andrade, Miguel

Update on XplorMed: a web server for exploring scientific literature

Nucl. Acids Res. 2003 31: 3866-3868







Useful sources for alternative PubMed interfaces, mashups, and data mining tools


1. A Compendium of Free, Public Biomedical Text Mining Tools Available on the Web



2. The blog Journalology by Matt Hodgkinson provides a good, opinionated summary of many search tools.



3. MetaDB: A Metadatabase for the Biological Sciences (part of Neurotransmitter.net) provides a comprehensive list of alternative PubMed interfaces.





For more information, contact:
Information Centre
Neil John Maclean Health Sciences Library
Phone: (204) 789-3464
Fax: (204) 789-3922