Bioinformatics Toolbox™

geneont - Create `geneont object`

Syntax

GeneontObj = geneont GeneontObj = geneont('File', FileValue) GeneontObj = geneont('Live', LiveValue) GeneontObj = geneont('Live', LiveValue, 'ToFile', ToFileValue)

Arguments

`FileValue`	String specifying the file name of an OBO-formatted file that is on the MATLAB^® search path.
`LiveValue`	Controls the creation of the most up-to-date geneont object. Enter `true` to create `GeneontObj`, a geneont object, from the most recent version of the Gene Ontology database. Default is `false`.
`ToFileValue`	String specifying a file name or path and file name to which to save the contents of the current version of the Gene Ontology database.

Return Values

GeneontObj MATLAB object containing gene ontology information.

Description

GeneontObj = geneont creates GeneontObj, a geneont object, from the gene_ontology.obo file in the MATLAB current directory.

GeneontObj = geneont('File', FileValue) creates GeneontObj, a geneont object, from FileValue, a string specifying the file name of an OBO-formatted file that is on the MATLAB search path.

GeneontObj = geneont('Live', LiveValue) controls the creation of GeneontObj, a geneont object, from the current version of the Gene Ontology database, which is the file at:

http://www.geneontology.org/ontology/gene_ontology.obo

Choices are true or false (default).

Note The full Gene Ontology database may take several minutes to download when you run this function using the 'Live' property.

GeneontObj = geneont('Live', LiveValue, 'ToFile', ToFileValue), when LiveValue is true, creates GeneontObj, a geneont object, from the most recent version of the Gene Ontology database, which is the file at:

http://www.geneontology.org/ontology/gene_ontology.obo

and saves the contents of this file to ToFileValue, a string specifying a file name or a path and file name.

Examples

Download the current version of the Gene Ontology database from the Web into a geneont object in the MATLAB software.
```
GO = geneont('LIVE', true)
```
The MATLAB software creates a geneont object and displays the number of terms in the database.
```
Gene Ontology object with 24316 Terms.
```

Display information about the geneont object.

get(GO)

default_namespace: 'gene_ontology'
                 date: '12:06:2007 19:30'
       format_version: '1.0'
              version: '4.256'
            subsetdef: {5x1 cell}
                Terms: [24316x1 geneont.term]

Search for all GO terms in the geneont object that contain the string ribosome in the field name and create a MATLAB structure containing those terms.

comparison = regexpi(get(GO.Terms,'name'),'ribosome');
indices = find(~cellfun('isempty',comparison));
terms_with_ribosmome = GO.Term(indices)

22x1 struct array with fields:
    id
    name
    ontology
    definition
    comment
    synonym
    is_a
    part_of
    obsolete