Alibaba - 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
- 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
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
- JavaTM Web Start Technology
monq.jfa
visualization toolkit
JavaTM Web Start TechnologyTeam
- 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 UL (leser at informatik dot hu-berlin dot de) and AR (rheinlae at informatik dot hu-berlin dot de).