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Table 3 Some currently available web-based tools that allow users to carry out post-processing of PubMed queries.
| Type | Site | URL | Features |
|---|---|---|---|
| TYPE 1: extract relationships and allow for 1) graphical visualization or navigation; or 2) refining queries | AliBaba [15] | http://alibaba.informatik.hu-berlin.de/ | Extract relationships between biological objects and map them into a graphical network |
| BioIE [16] | http://umber.sbs.man.ac.uk/dbbrowser/bioie/ | Extract informative sentences from retrieved results | |
| Chilibot [17] | http://www.chilibot.net/ | Extract biological relationships from search results | |
| ConceptLink [18] | http://project.cis.drexel.edu/conceptlink | Extract relationships between medical concepts and allow graphical visualization | |
| PubNet [29] | http://pubnet.gersteinlab.org/ | Extract several relationships from the search results and then map them into networks | |
| XplorMed [20] | http://www.bork.embl-heidelberg.de/xplormed/ | Extract dependency relations among words and allow users to refine queries using these words | |
| TYPE 2: organize results by ontologies or hierarchies | GoPubMed [21] | http://www.gopubmed.org/ | Sort PubMed query results through Gene Ontology and MeSH hierarchy |
| MEVA [22] | http://www.med-ai.com/meva/index.html | Summarize search results according to MeSH hierarchy | |
| FABLE [23] | http://fable.chop.edu/ | Tag gene and protein occurrences in text | |
| PubReMiner [24] | http://bioinfo.amc.uva.nl/human-genetics/pubreminer/ | Categories include words, MeSH, authors, journals, year, substances and country | |
| PubMed Assistant [25] | http://metnet.vrac.iastate.edu/browser/ | Lists MeSH and chemicals, with link-outs to PubMed, Google and Google Scholar | |
| TYPE 3: cluster articles into categories | Vivísimo ClusterMed [26] | http://clustermed.info/ | Cluster articles into several categories |
| HubMed [27] | http://www.hubmed.org | Cluster related articles and allow for graphical visualization | |
| TYPE 4: rank articles | PubFocus [28] | http://www.pubfocus.com/ | Rank articles by the journal impact factor and volume of forward references |
| ReleMed [29] | http://www.relemed.com/ | Rank articles by relevance |
