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,
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:
(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.
Jörg Hakenberg Conrad Plake Quang Long Nguyen Astrid Rheinländer Torsten Schiemann Marcus Pankalla Emre Kutbay Kevin Arnoult Ulf Leser
Palaga, P., Nguyen, L., Leser, U. and Hakenberg, J. (2009). High-Performance Information Extraction with AliBaba. Extending Database Technology (EDBT), St. Petersburg, Russia.
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.
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.
Hakenberg, J., Plake, C., and Leser, U. Ali Baba: Text Mining for Systems Biology (2008). In: Lodhi, H., and Muggleton, S.(eds). "Elements of Computational Systems Biology". Wiley & Sons.
Hakenberg, J., Schroeder, M., and Leser, U. (2007). Consensus pattern alignment to find protein-protein interactions in text. Proc. Second BioCreative Challenge Evaluation Workshop. Madrid, Spain.
Hakenberg, J., Plake, C., Schiemann, T., and Leser, U. (2006). Ali Baba - Visualizing biological networks from PubMed query results Poster at Data Integration in the Life Sciences, DILS 2006. Hinxton, UK.
Hakenberg, J., Plake, C., Schiemann, T., and Leser, U. (2006). Ali Baba: Accessing PubMed using graphs. German Conference on Bioinformatics, GCB'06. Tübingen, Germany.
Hakenberg, J., Leser, U., Kisch, H., and Rebholz-Schuhmann, D. (2006). Collecting a Large Corpus from all of Medline. Proc. Second International Symposium on Semantic Mining in Biomedicine, SMBM, pp. 89-92. Jena, Germany.
Plake, C., Schiemann, T., Pankalla, M., Hakenberg, J., and Leser, U. (2006). Ali Baba: PubMed as a graph. Bioinformatics, 22(19):2444-2445, 2006.
Hakenberg, J., Plake, C., Leser, U., Kisch, H., and Rebholz-Schuhmann, D. (2005). 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.