Search tools
From BioUML platform
Revision as of 15:53, 17 June 2013 by Stanislav Loskutnikov (Talk | contribs)
BioUML provides 3 types of search engine for working with databases:
- data search (filter) - this search engine maps database content into Java objects and filters these Java objects according filtering condition for each property, for example, name="TP53" or "*acid". Regular expressions can be used for text values. This search engine works quite slowly because it scans all the database objects of the corresponding type (for example, gene, protein or substance).
- full text search - the search engine uses Lucene full text search engine. For this purpose the database content is also mapped into Java objects and then these Java objects are indexed by Lucene. In most cases an element can be found by its name, title, description or other specific fields. Due to the index usage this search engine is much faster than the data search using filters. The simplest way to use the search functionality is via the Search tab of the information box.
- graph search - this search engine finds interacting pathway components and displays the result as an editable graph. To start a search the user should specify the start node on the diagram and search the conditions: what type of interactions should be found and the depth of search. The graph search supports interactive search and incremental graph layout, so the user can select any node on the graph and find other biological objects in the database that interact with it. These objects will be shown in tabular form. The user can add these nodes and corresponding edges to the diagram. The graph layout will locate new nodes and edges automatically preserving location of previous diagram elements.
