GoPubMed

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Introduction

See PubMed Alternative Interfaces, PubReMiner and Semantic search

GoPubMed is a knowledge-based semantic browsing tool for the life sciences. The Gene Ontology (GO) and Medical Subject Headings (MeSH) serve as a "Table of contents" to structure the millions of articles in MEDLINE. The search engine allows its users to find relevant search results in biomedical texts significantly faster than by using PubMed alone. The technology used in GoPubMed is applied to texts in order to mine them. Developed at the Technical University of Dresden by Michael Schroeder and Transinsight, GoPubMed has been called one of the first web 2.0 and semantic search engines.

What GoPubMed does to expand a search query is add 'ontologies' or categories to how articles are displayed. As mentioned, the Medical Subject Headings (MeSH) and the Gene Ontology (GO) are used by GoPubMed to identify the interrelatedness of articles. The statistics feature is a semanto-bibliometric analysis of search results. After conducting your search, see the “Statistics” tab to view bar graphs, charts and visual representations of top authors, top countries, top cities, top journals, and so on.

• GoPubMed versus PubReMiner for analyzing PubMed search results: a head to head comparison

Sorting results

Results in GoPubMed can be filtered by:

• “what” – which contains the terms and knowledge base concepts related to your query
• “who” - authors contributing to the articles
• “where” – where the authors and institutions for the article are located, as well as a limit to specific journals or high impact factor journals as a group and
• “when” – the year the articles were published.

Alternative, data-mining tools

• Ali Baba - PubMed as a Graph - http://alibaba.informatik.hu-berlin.de/
• Biblimed - http://www.biblimed.fr/
• ClusterMed - http://clustermed.info/
• ConceptLink - http://project.cis.drexel.edu/conceptlink/
• eTBLAST - http://etest.vbi.vt.edu/etblast3/
• FABLE - http://fable.chop.edu/
• GoPubMed - http://gopubmed.com/
• HubMed - http://www.hubmed.org/
• Interact - http://pmi.nlm.nih.gov/interact
• LigerCat - http://ligercat.ubio.org/
• MedMiner - http://discover.nci.nih.gov/textmining/main.jsp (Genomics and Bioinformatics Group at NCI)
• Medstory - http://www.medstory.com/Home.html
• MedSum - http://webtools.mf.uni-lj.si/public/medsum.html
• MeshPubMed - http://www.meshpubmed.org
• Novoseek - http://www.novoseek.com/
• PubFocus - http://www.pubfocus.com/
• PubGet - http://pubget.com/
• PMinstant - http://pminstant.com/
• PubAnatomy - http://brainarray.mbni.med.umich.edu/Brainarray/prototype/PubAnatomy/
• PubMed On Tap (for iPhone) - http://www.referencesontap.com/
• PubMedReMiner - http://bioinfo.amc.uva.nl/human-genetics/pubreminer/
• Quertle - http://www.quertle.info/v2/
• ReleMed - http://www.relemed.com/
• SLIM v.2 - http://pmi.nlm.nih.gov/slim/
• XplorMed - http://www.ogic.ca/projects/xplormed/

References