AliBaba: PubMed as a graph

Bioinformatics. 2006 Oct 1;22(19):2444-5. doi: 10.1093/bioinformatics/btl408. Epub 2006 Jul 26.


The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and 'hidden' in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance.


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abstracting and Indexing / methods*
  • Algorithms*
  • Computer Graphics*
  • Database Management Systems
  • Information Storage and Retrieval / methods
  • Natural Language Processing*
  • Periodicals as Topic*
  • Software*
  • User-Computer Interface*
  • Vocabulary, Controlled