obsolete property

Class: term

Read-only Boolean value that indicates whether a GO term is obsolete

Description

obsolete is a read-only property of the term class. obsolete is a Boolean value that indicates if the GO term is obsolete (1) or not obsolete (0).

Values

1 — Obsolete

0 — Not obsolete

Use the obsolete property to determine whether a term object is obsolete, or to access or filter term objects by obsolete value.

Examples

Example 87. Using the obsolete Property to Determine the Obsolete Status of a term Object

1. Download the current version of the Gene Ontology database from the Web into a geneont object in the MATLAB^® software.

   GeneontObj = geneont('LIVE', true)

   The MATLAB software creates a geneont object and displays the number of term objects associated with the geneont object.

   Gene Ontology object with 27769 Terms.

2. Display the obsolete status of the term object in the third and seventh positions in the geneont object, GO

   GeneontObj.terms(3).obsolete
   
   ans =
   
        0
   
   GeneontObj.terms(7).obsolete
   
   ans =
   
        1

Tip

If you know the GO identifier (for example, 8) of a term object, instead of its index or position number (for example, 7), you can use the following syntax to display the obsolete status of a term object:

GeneontObj(8).terms.obsolete

For help converting the index or position number of a term object to its GO identifier, see the term.id property.

Example 88. Filtering term Objects by Obsolete Status

1. Download the current version of the Gene Ontology database from the Web into a geneont object in the MATLAB software.

   GeneontObj = geneont('LIVE', true)

   The MATLAB software creates a geneont object and displays the number of term objects associated with the geneont object.

   Gene Ontology object with 27769 Terms.

2. Display the structure array containing 27,786 term objects associated with the geneont object.

   GeneontObj.terms
   
   27786x1 struct array with fields:
       id
       name
       ontology
       definition
       comment
       synonym
       is_a
       part_of
       obsolete
   

3. Create a cell array of logicals that list the obsolete property for each term in the geneont object.

   obsolescence = get(GeneontObj.terms,'obsolete');

4. Create a logical mask from the cell array that identifies all the nonobsolete terms.

   mask = ~cell2mat(obsolescence);

5. Apply the logical mask to all the terms in the GeneontObj geneont object to return a structure containing only terms that are not obsolete.

   nonobsolete_terms = GeneontObj.terms(mask)
   
   26424x1 struct array with fields:
       id
       name
       ontology
       definition
       comment
       synonym
       is_a
       part_of
       obsolete
   

   There are 26,424 terms that are not obsolete.