|
|
Slim Gene Ontology
Background: Hierarchy, NLI Related: Examples Description: The Gene Ontology describes gene products in terms of their associated biological processes, cellular components and molecular functions. The Generic Slim Gene Ontology is a subset of the whole Gene Ontology. The slim version gives a broad overview and leaves out specific/fine grained terms. This example stores the slim version of the Gene Ontology (goslim_generic_obo) that can be downloaded from www.geneontology.org/GO.slims.shtml. Download (see below) includes populated database. Follow these steps to import a new slim version of the Gene Ontology into DBD: 1. Run dbd.exe 2. Create a new database file and save with desired name (ie go.dbd). 3. Increase db size from 256000 (1Mb) to 512000 (2Mb). 4. Import data by selecting File Menu option "Import Slim Gene Ontology...". Click OK in dialog box prompting user to increase db memory. Select file in dialog box and click OK. 5. After a few seconds, a dialog box reports import status. Click OK. 6. Expand tree nodes starting from db\item\gene_ontology as shown in figures. A term (gene product) can have subClasses and parts. The directory named heirarchy stores root classes.  NLI Script (; Get gene ontology term whose id is GO:0008150) (get * id GO:0008150) (; Get gene ontology term whose name is chromosome) (get * name 'chromosome) Notes: Download Application, Database and Slim Gene Ontology File: go_dbd.zip (333 KB) |