Ali Baba - PubMed as a graph

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

2008-03-17: Added support for regulatory pathways from KEGG with original KEGG layout
2007-12-12: Switched to the new 2008 version of MeSH (cells, tissues, diseases)
2007-11-01: Ali Baba now also searches for drugs from DrugBank
2007-10-01: Web services provided to the BCMS project by Biotec TU Dresden and Ali Baba
2007-09-18: Save graphs as images: File|Save as image...
2007-07-04: Ali Baba features an automated query expansion for proteins
2007-06-18: Query Ali Baba using UniProt IDs instead of keywords

About Ali Baba

Screenshots

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

Ali Baba is powered by

monq.jfa, developed at EMBL-EBI, Rebholz-Group
visualization toolkit
database
NCBI citation index and search
Java^TM Web Start Technology

Team

Jörg Hakenberg: annotation pipeline, text mining and natural language processing components
Conrad Plake: application model and controller, annotation pipeline
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.

References

[1] Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser
Ali Baba: PubMed as a graph.
Bioinformatics, 22(19):2444-2445, 2006
[Abstract] - [Full text]
[2] Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
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]
[3] Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser
Ali Baba: Accessing PubMed using graphs.
German Conference on Bioinformatics, GCB'06. Tübingen, Germany (20-22 September 2006).
[GCB'06]
[4] Jörg Hakenberg, Michael Schroeder, Ulf Leser
Consensus pattern alignment to find protein-protein interactions in text.
Proc. of the Second BioCreative Challenge Evaluation Workshop. Madrid, Spain (23-25 April 2007). ISBN 84-933255-6-2 (accepted for presentation and proceedings).
[Paper] - [2nd BioCreAtIvE Workshop] - [BioCreAtIvE challenge evaluation]
[5] Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
Collecting a Large Corpus from all of Medline.
Proc. of the Second International Symposium on Semantic Mining in Biomedicine, SMBM, pp. 89-92. Jena, Germany (9-12 April 2006).
[SMBM'06] - [Proceedings] - [Short paper]
[6] Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
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]

Humboldt-Universität zu Berlin - Faculty of Mathematics and Natural Sciences II - Department of Computer Science - Knowledge Management in Bioinformatics - Ali Baba

Last changes: December 12 2007 JH