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  Other PubMed Search Engines Resource Guide

There is more than one way to search the medical literature (PubMed) stored at the National Library of Medicine.  Entrez is the search engine created by NLM to search PubMed, but just like there are multiple search engines to search the Internet (Google, Netscape, etc.) there are multiple engines that can be used to search PubMed.  As different groups and people have needed different things from the literature, they have created front-ends or 3rd party tools to search the medical literature.  Some of these PubMed interfaces are useful if your specific needs correspond to those of the search tool.

NOTE:  Many of these interfaces are developed by small groups of people working from a university department or lab.  As such, there is no guarantee of continued funding so any of these sites could stop working or charge fees in the future.

• Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba (screen shots of graphs here) visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts. This is a downloadable program using Java 1.5 or higher - installation instructions.
• Anne O'Tate searches PubMed (including some limits) and allows overviews of the results based on important words, topics (MeSH), year, affiliations or journal. Entry link on Arrowsmith page.
• Arrowsmith identifies meaningful links between two sets of Medline articles.  The program generates a list of words and phrases found in both sets of articles that can be displayed by relevance or restricted to certain semantic categories.
• askMedline is a free-text, natural language search interface for Medline developed by the National Library of Medicine (NLM).
• Author-ity searches for authors based on a probabilistic similarity metric which attempts to disambiguate all papers into distinct authors. Entry link on Arrowsmith page.
• Authoratory analyzed PubMed data to create a database of contact information, collaborators, research areas, funding sources, and affiliation so you can search for experts in a field or find out more about others in your field.
• BabelMeSH allows Medline searching in Arabic, Chinese, English, French, German, Italian, Japanese, Portuguese, Russian or Spanish. Developed by NLM.
• BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature.  Used for text-mining, especially for annotation of microarray data and protein databases.
• BioWizard allows basic PubMed searching, but it is most useful for providing user submitted ratings and discussions about articles.  Articles can be viewed by subject areas and ranking.
• BITOLA, Biomedical Discovery Support System, helps biomedical researchers discover potentially new relations between biomedical concepts, combining MeSH (Medical Subject Headings) and gene information (from HUGO and OMIM and NCBI).
• Chilibot search PubMed for relationships between proteins, genes or keywords.
• ConceptLink creates visual images for medical concepts that act as an interface to PubMed and can help guide the construction of search queries.
• DailyUpdates from LeadDiscovery uses special strategies to search PubMEd for potential drug development research.  Newsfeeds or email alerts are available.
• eTBLAST searches PubMed, plus NASA, IOP, and CRISP, using input that can range from keywords to a whole abstract of text.  Search results are ranked by similarity and can be further refined by checking relevant abstracts and redoing the search with the new text words.  The interface then provides the options of finding an expert or journal, or viewing publication history on the subject.
• FABLE (Fast Automated Biomedical Literature Extraction) mines the biomedical literature for information about human genes and proteins. Article Finder identifies biomedical research articles that mention genes and proteins of interest. Search terms are normalized by default, so that searching for "p53" will identify articles that mention "TP53", "P53", "tumor suppressor protein p53", and any other known synonym used to describe the p53 gene. Gene Lister identifies sets of genes that are mentioned in articles containing one or more keyword search terms of interest. Searching for "Mendel AND peas" will identify all genes mentioned in articles that contain both of the words "Mendel" and also "peas"
• GoPubMed uses Gene Ontology (a controlled vocabulary) to organize and refine the results of a PubMed search.  Lots of extra features such as exporting citations of bibliographic software and linking to Wikipedia articles.  Most useful for molecular biology searching.  Related to MeshPubMed
• HAPI (High-density Array Pattern Interpreter) provides a method for interpreting the conceptual similarities of a cluster or group of genes and linking them through keyword hierarchies based on MEDLINE indexing.
• HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organizing and gathering information from the biomedical literature. Searches can be conducted using the full range of operators available in Entrez/PubMed; when using the default search options, results will be identical to those of a PubMed search.  Special features of HubMed include date- or relevance-ranked search results; web feeds for regular updates of published literature matching any search; clustering and graphical display of related articles; expansion of query terms; direct export of citation metadata in many formats; linking of keywords to external sources of information; manual categorization (tagging) and storage of interesting articles.
• iHOP uses genes and proteins as hyperlinks between sentences and abstracts to navigate the scientific literature.  Over 30,000 genes can be searched and connected via similar concepts.
• Interact is an NLM developed interface that looks like SLIM but allows for more interactions with the results of your search, including deleting articles and adding citations from related articles.  Abstracts and related articles boxes can be opened and closed without jumping to a PubMed search.
• ISI Web of Knowledge PubMed VCU allows you to search PubMed concurrently with Web of Science and other databases.  Use pull-down menu in green top band to choose 'CrossSearch' then click on 'Go'. 
• JournalReview.org is an online journal club that allows discussion and ranking of articles in a wide variety of medical specialties.  Some basic PubMed searching can be done.
• MedGene, from the Institute of Proteomics at Harvard Medical School, looks for relationships between genes and diseases based on co-citations in Medline records.
• MEDLINE via CSA Databases VCU searches MEDLINE from 1997 to the present only, but allows concurrent searching with a number of biological databases like Genetics Abstracts, BioEngineering Abstracts, Human Genome Abstracts, Medical and Pharmaceutical Biotechnology Abstracts, TOXLINE, etc.
• MedMiner (from the Genomics and Bioinformatics Group at NCI) is a text-mining system that extracts relevant sentences in the literature based on a gene, gene-gene or gene-drug query.
• MedMOLE (Mining On-Line Expert on Medline) searches and retrieves Medline articles and performs text-mining analysis to improve the comprehension of microarray experimental results by grouping co-regulated genes.
• Medstory searches articles on the web, NIH grants, clinical trials and news articles as well as PubMed.  Ranked lists of subjects associated with your topic can be used to refine your search.
• MeshPubMed uses MeSH (Medical Subject Headings from the National Library of Medicine) to organize and refine the results of a PubMed search.  Results are placed in a hierarchy based on MeSH terms so you choose only the terms relevant to your query.
• PICO searching from NLM is a specialty interface where Patient/Problem, Intervention, Compare to, and Outcome factors are entered to search MEDLINE.
• PubFocus performs statistical analysis of Medline results based on journal rank and citation information to provide a list of articles ranked by relevancy.  Information on publishing trends can also be established.
• PubNet creates network graphs based on user-specified nodes for one or two PubMed queries.  These graphs visualize the degree and variety of relationships between authors and collaborators.
• PubReMiner searches PubMed and displays results in frequency tables that list year, author, keyword and MeSH heading.  You can add terms from the frequency tables to refine your search and then send the search to PubMed to see the final results list.
• RefWorks VCU, the web-based citation management tool used at VCU can be used to search databases or online catalogs and then download citations directly to your account.  Under the 'Search' menu choose 'Online Catalog or Database'.  Then change the database using the drop down menu - PubMed is first on the list.
• ReleMed retrieves the most relevant recent references published about a problem or a combination of conditions.  The first articles returned in response to a query have close relationships between the search terms.
• SLIM (Slider Interface for MEDLINE) is an NLM sponsored system to allow easy selection of limits and parameters: date, journal subset, age group, methodology filter, level of MeSH mapping, Human/English limits, and number of citations to display.  Not intended for comprehensive searching.
• XplorMed refines a PubMed search by analyzing word chains in abstracts and using your choice of chains to further limit the search. Also from OHRI in Canada, is Kfinder, which uses your abstract text to suggest keywords and MeSH headings as well as authors that have written papers with those subject terms (and links to PubMed abstracts).