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Some currently available web-based tools that allow users to carry out post-processing of PubMed queries. |
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| Type |
Site |
URL |
Features |
|
|
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| 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 |
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| PubReMiner [24] |
http://bioinfo.amc.uva.nl/human-genetics/pubreminer/ |
Categories include words, MeSH, authors, journals, year, substances and country |
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| PubMed Assistant [25] |
http://metnet.vrac.iastate.edu/browser/ |
Lists MeSH and chemicals, with link-outs to PubMed, Google and Google Scholar |
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| 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 |
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| 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 |
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Smalheiser et al. Journal of Biomedical Discovery and Collaboration 2008 3:2 doi:10.1186/1747-5333-3-2 |
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