Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

What is Ali Baba?

Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts.

You can use any query you would usually use with PubMed. Ali Baba automatically retrieves all corresponding citations and parses them for

  • cells from the MeSH tree,
  • compounds from the KEGG database,
  • diseases from MeSH,
  • drugs from MeSH,
  • enzymes from KEGG,
  • nutrients,
  • proteins/genes from the UniProt database,
  • reactions from KEGG,
  • species from NCBI Taxonomy, and
  • tissues from MeSH.

Ali Baba associates objects for the following types of relations with each other:

  • protein-protein interactions,
  • (sub)cellular location of proteins,
  • proteins/genes discussed with drugs,
  • proteins/genes discussed with species,
  • proteins/genes discussed with tissues,
  • relations between drugs and diseases,
  • proteins/genes and diseases,
  • nutrients associated with proteins, diseases, or tissues.