Sites that Augment the Standard PubMed Search Service

• MESHy unanticipated knowledge discovery through statistical ranking of MeSH term pairs          http://tools.bat.ina.certh.gr/meshy/

• PIE 

  searching PubMed literature for protein interaction information http://www.ncbi.nlm.nih.gov/CBBresearch/Wilbur/IRET/PIE/

• PolySearch
  The typical query supported by PolySearch is "Given X, find all Y's" where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites.
• Jane(Journal/Author Name Estimator)
  helps identify the journals and authors related to any input text.
• EAGL
• Reference.MD
  searching/browsing for biomedical concepts and their links to information taken from MeSH, UMLS, Drugs@FDA, FDA AERS.
• BioText
  for searching full-text of Open Access articles. Allows for searching and browsing figures and their captions.
• PubReMiner
  performs detailed analysis of PubMed search results, similar in some ways to our Anne O'Tate tool. For any given PubMed query, it computes frequency tables for publication years, authors, journals, words, or MeSH that can be used to refine the query.
• EBIMed
  analyses PubMed abstracts to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts.
• MEDIE
  an intelligent search engine to retrieve biomedical correlations from MEDLINE. You can find abstracts/sentences in MEDLINE by specifying semantics of correlations; for example, "What activates p53" and "What causes colon cancer".
• ADAM
  Another Database of Abbreviations in Medline.
• Acromine
  acronym dictionary automatically constructed from the whole of MEDLINE.
• Stanford Abbreviations server.
  an online dictionary of abbreviations in PubMed articles.
• PubMed Gold
  finds PDFs for PubMed citations by automatically searching Google.
• PubMed Assistant
  a biologist-friendly interface for enhanced PubMed search
• ReleMed
  ranks MEDLINE articles by relevance
• PubFinder
  a tool for improving retrieval rate of relevant PubMed abstracts
• PubNet
  publication network graph utility
• PubFocus
  semantic PubMed/MEDLINE citation analytics
• Alibaba
  PubMed as a graph
• MedKit
  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.
• SLIM
  Slider Interface for MEDLINE/PubMed searches (BETA)
• MEVA
  upload the result of a PubMed query to MEVA and get a summary of selected MEDLINE fields like MeSH and author names.
• BIOWIZARD
  allows everyone in the scientific community to rank and discuss PubMed articles.
• GoPubMed
  your query is submitted to PubMed and the resulting abstracts are classified using Gene Ontology terms.
• HubMed
  an alternative interface to MEDLINE.
• TWEASE
  finds individual sentences for matches to your query, not the MEDLINE abstract as a whole.
• eTBlast
  input an entire paragraph and it returns MEDLINE abstracts that are similar to it.
• ExpertMapper
  a tool to help identify a medical expert on a given topic.
• FABLE
  finds MEDLINE articles that mention human genes and proteins more thoroughly than other systems.
• Pubcrawler
  alerting service that searches custom queries in PubMed or Genbank automatically and notifies the user by email when new relevant papers or sequences appear in the literature.
• Vivisimo
  demo site that searches PubMed (or the Web) and arranges the output into clusters of articles that are most thematically similar to each other.
• BioEx
  consists of three components at this point - a) definition question answering system (QA), b) image-based question answering (ImageQA), c) information retrieval system (IR).
• BioIE
  a rule-based system that extracts informative sentences from the biomedical literature.
• askMEDLINE
  a free-text, natural language query tool for MEDLINE/PubMed.
• PICO
  (Patient, Intervention, Comparison, Outcome) search interface, a method of searching MEDLINE/PubMed that encourages the creation of a well-formulated search.
• Visual MeSH
  browser to assist searchers in choosing appropriate MeSH terms.
• Xplormed
  to assist browsing articles by topics using chains of word associations.
• AkwanMed
  enhanced PubMed search interface which ranks articles by relevance
• ConceptLink
  makes concept maps of related MeSH terms.
• Ask HERMES,  computational system that automatically analyzes large sets of documents pertaining to specific questions and generates short text from them as output. http://www.askhermes.org/.