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Formal description and reconstruction of biological pathways is complex task. To simplify this task we introduced solitaire game as a metaphor for user interface (Figure 1.12). Here:
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the desk � a BioUML diagram
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solitaire game � reconstructed biological pathway
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cards � biological objects (genes, proteins, lipids, etc.)
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packs of cards � different biological databases (for example, Ensembl, UniProt, ChEBI, etc)
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Figure 1.12
. Solitaire game as a metaphor for reconstruction of biological pathways.
To support this metaphor BioUML workbench provides following functionality:
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different databases � �packs of cards� - (Ensembl, UniProt, ChEBI, IntAct, GeneOntology, Reactome, BioModels) can be installed locally or can be available via Internet from BioUML server
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convenient user interface for installation of these databases on client side (
Load database dialog
). For this purpose user should specify server to use and select the databases to be installed.
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composite database module � allows to specify what databases will be used for reconstruction. User can create his own database (�sandbox�) where his diagrams and user added information will be stored. Composite database module is described formally using XML. Composite module editor provides user interface for its editing.
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when user add some component on a diagram he can select from which database corresponding biological object will be selected;
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full text search engine allows to search information in different databases for specified biological object type (gene, protein, etc.) using several corresponding database simultaneously. Then user can select one or more found objects and put them on diagram;
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graph search engine allows to find biologically related objects (participating in the same reaction or semantic relation) in the databases and put them into diagram.
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See also:
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