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Table 3 Some currently available web-based tools that allow users to carry out post-processing of PubMed queries.

From: Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

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