Ali Baba - PubMed as a Graph


Attention: We will shutdown this service by March 31st, 2013. If you have any problems with this, please send us an email.

Update: Alibaba will soon move to a new server. We'll keep you posted.
  • Ali Baba helps you to search and visualize protein- and disease-centered information from PubMed.
  • Ali Baba displays the search result in form of a graph -- biological/medical objects such as proteins, diseases, or drugs are nodes; meaningful associations between them are edges.
  • Find out quickly about interacting proteins, genes with implications in diseases, tissue specificity of genes, and many more!
  • Ali Baba allows you to search for proteins by simply querying for UniProt IDs instead of typing a long list of synonyms.
  • Ali Baba is able to include pathways from KEGG -- new databases will be featured in the near future.
  • Ali Baba links all information to the underlying literature and databases -- this provides you with detailed information on selected aspects.
  • Ali Baba -- don't read abstracts, see them!


News

  • 2010-03-02: updated prefuse library, improved layout of radial view (prefuse)
  • 2010-02-22: resolved some bugs in graph visualization, improved edge highlighting
  • 2010-02-22: resolved bugs in XML parser
  • 2010-02-09: New relation filter: filter relations by interaction words
  • 2010-02-02: New relations filter: filter relations by involved entities
  • 2010-01-27: New abstracts filter: right-click on an abstract in abstracts panel -> hide this abstract...
  • 2010-01-07: Alibaba moved to a new server and runs stabler and faster than before
  • 2009-08-10: Added search function for evidence panel
  • 2009-08-03: Improved Entity-Class-Filter: Right-Click on class in TreeView->hide this class...
  • 2009-07-30: Fixed Confidence Filter
  • 2009-07-26: Alibaba GUI also works with Gnome now
  • 2009-07-15: Filter relations by annotation type ("Co-Occurrences only"/"Pattern based only")
  • 2009-07-15: Explore graph iteratively
  • 2009-07-02: Improved radial view
  • 2009-05-26: added new dictionaries for compounds, enzymes (source for both: KEGG DB as of 2009-04-15) and cells, tissues (source for both: MeSH DB as of 2009-04-15)
  • 2009-04-30: added new dictionaries for species (source: NCBI taxonomy tree as of 2009-03-02), drugs (source: DrugBank as of 2009-03-02 and MeSH DB as of 2009-04-15), Uniprot(source: Uniprot vers. 15.1)
  • 2009-03-15: Changed KEGG menu and visualisation to latest version of KEGG-ML
  • 2009-02-02: Fixed various bugs in text panel and graph visualisation
  • 2008-12-15: Improved highlighting of selected nodes and edges
  • 2008-11-15: Fixed minimum degree filter

View history





Screenshots

ScreenshotIs there a risk factor for treating G6PD-deficient malaria patients with primaquine? ScreenshotWhat are known or suspected genes that are associated with Parkinson's disease?
ScreenshotA patient with cough is treated with codeine. He becomes unresponsive after a while -- what is going on? ScreenshotA query for FADD shows parts of the apoptotic signaling pathway.
ScreenshotThe interferon gamma signaling pathway with some cellular locations. ScreenshotThe Wnt signaling pathway loaded into Ali Baba from KEGG.


Ali Baba is powered by



Team

  • Jörg Hakenberg: annotation pipeline, text mining and natural language processing components
  • Conrad Plake: application model and controller, annotation pipeline
  • Peter Palaga: pattern matching
  • Quang Long Nguyen: pattern optimization
  • Astrid Rheinländer: refining data sources and application view
  • Torsten Schiemann: application view, word sense disambiguation
  • Marcus Pankalla: PubMed retrieval, document indexing
  • Emre Kutbay: graph editing, DB storage, KEGG access
  • Kevin Arnoult: KEGG access
  • Ulf Leser: project leader and coordinator

Please send any comments or questions to JH and AR.



References

  • [PNLH09] Palaga, P., Nguyen, L., Leser, U. and Hakenberg, J. (2009).
    High-Performance Information Extraction with AliBaba.
    Extending Database Technology (EDBT), St. Petersburg, Russia.
    [Paper]
  • [HTG+09] Hakenberg, J., Tari, L., Gonzalez, G., Solt, I., Tikk, D., Rheinländer, A., Ngyuen, L. and Leser, U. (2009).
    Molecular event extraction from Link Grammar parse trees.
    BioNLP shared task 2009, Boulder, US.i
    [Paper]
  • [HPR+08] Hakenberg, J., Plake, C., Royer, L., Strobelt, H., Leser, U., and Schroeder, M. (2008).
    Gene mention normalization and interaction extraction with context models and sentence motifs.
    Genome Biol 9 Suppl 2: S.14.
    [Abstract]
  • [HPL08] Hakenberg, J., Plake, C., and Leser, U.
    Ali Baba: Text Mining for Systems Biology (to appear).
    In: Lodhi, H., and Muggleton, S.(eds). "Elements of Computational Systems Biology". Wiley & Sons, 2008.
  • [HSL07] Hakenberg, J., Schroeder, M., and Leser, U.
    Consensus pattern alignment to find protein-protein interactions in text.
    Proc. Second BioCreative Challenge Evaluation Workshop. Madrid, Spain (23-25 April 2007). ISBN 84-933255-6-2.
    [Paper] - [2nd BioCreAtIvE Workshop] - [BioCreAtIvE challenge evaluation]
  • [HPS+06a] Hakenberg, J., Plake, C., Schiemann, T., and Leser, U.
    Ali Baba - Visualizing biological networks from PubMed query results
    Poster at Data Integration in the Life Sciences, DILS 2006. Hinxton, UK (20-22 July 2006)
    [DILS'06]
  • [HPS+06b] Hakenberg, J., Plake, C., Schiemann, T., and Leser, U.
    Ali Baba: Accessing PubMed using graphs.
    German Conference on Bioinformatics, GCB'06. Tübingen, Germany (20-22 September 2006).
    [GCB'06]
  • [HLK+06] Hakenberg, J., Leser, U., Kisch, H., and Rebholz-Schuhmann, D.
    Collecting a Large Corpus from all of Medline.
    Proc. Second International Symposium on Semantic Mining in Biomedicine, SMBM, pp. 89-92. Jena, Germany (9-12 April 2006).
    [SMBM'06] - [Proceedings] - [Short paper]
  • [PSP+06] Plake, C., Schiemann, T., Pankalla, M., Hakenberg, J., and Leser, U.
    Ali Baba: PubMed as a graph.
    Bioinformatics, 22(19):2444-2445, 2006
    [Abstract] - [Full text]
  • [HPL+05] Hakenberg, J., Plake, C., Leser, U., Kisch, H., and Rebholz-Schuhmann, D.
    LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata.
    Proc Learning Language in Logic Workshop (LLL'05) at ICML 2005, pp. 38-45. Bonn, Germany (August 2005)
    [LLL'05] - [Paper]