term

Data structure containing information about Gene Ontology (GO) term

Description

A term object is a data structure containing information about a Gene Ontology (GO) term. You can explore and traverse Gene Ontology terms using “is_a” and “part_of” relationships.

A term object has handle copy semantics. To learn how this affects your use of the class, see Copying Objects in the MATLAB^® Programming Fundamentals documentation.

Creation

A term object is part of the terms property of a Gene Ontology object. Create a Gene Ontology object using the geneont command.

Properties

definition — Definition of the GO term

character vector

This property is read-only.

Definition of the GO term. specified as a character vector.

Tip

If you know the GO identifier (for example, 314) of a term object, instead of its index or position number (for example, 287), you can use the following syntax to display the definition of a term object:

GeneontObj(314).terms.definition

For an example, see Investigate Gene Ontology Term Properties.

Data Types: char

id — GO identifier of GO term

numeric scalar

This property is read-only.

GO identifier of GO term, specified as a numeric scalar.

Tip

You can use the num2goid function to convert id to a GO ID character vector formatted as a 7-digit number preceded by the prefix GO:, which is the standard used by the Gene Ontology database.

Tip

You can use the id property for a GO term as input to methods of a geneont object, such as getancestors, getdescendants, and getrelatives.

Data Types: single | double

is_a — GO identifiers of GO terms that have an “is a” relationship with this GO term

numeric array

This property is read-only.

GO identifiers of GO terms that have an “is a” relationship with this GO term, specified as a numeric array.

Tip

You can also use the getancestors method of a geneont object with the 'Relationtype' property set to 'is_a' to determine term objects with an “is a” relationship.

Tip

If you know the GO identifier (for example, 42321) of a term object, instead of its index or position number (for example, 18703), you can use the following syntax to display the is_a property of a term object:

GeneontObj(42321).terms.is_a

For an example, see Investigate Gene Ontology Term Properties.

Data Types: single | double

name — Name of GO term

character vector

This property is read-only.

Name of GO term, specified as a character vector.

Data Types: char | string

obsolete — Indication that term is obsolete

logical value

This property is read-only.

Indication that term is obsolete, specified as a logical value.

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 an example, see Investigate Gene Ontology Term Properties.

Data Types: logical

ontology — Ontology of GO term

'molecular function' | 'biological process' | 'cellular component'

This property is read-only.

Ontology of GO term, specified as one of these values:

• 'molecular function'

• 'biological process'

• 'cellular component'

Use the ontology property to determine the ontology of term objects, or to access or filter term objects by ontology.

Tip

If you know the GO identifier (for example, 179) of a term object, instead of its index or position number (for example, 155), you can use the following syntax to display the ontology of a term object:

GeneontObj(179).terms.ontology

For an example, see Investigate Gene Ontology Term Properties.

Data Types: char

part_of — GO identifiers of GO terms that have a “part of” relationship with this GO term

numeric array

This property is read-only.

GO identifiers of GO terms that have a “part of” relationship with this GO term, specified as a numeric array.

Tip

You can also use the getancestors method of a geneont object with the 'Relationtype' property set to 'part_of' to determine term objects with a “part of” relationship.

Tip

If you know the GO identifier (for example, 42321) of a term object, instead of its index or position number (for example, 18703), you can use the following syntax to display the part_of property of a term object:

GeneontObj(42321).terms.part_of

For an example, see Investigate Gene Ontology Term Properties.

Data Types: single | double

synonym — GO terms that are synonyms of this GO term

two-column cell array

This property is read-only.

GO terms that are synonyms of this GO term, specified as a two-column cell array. The first column contains a character vector specifying the type of synonym, such as 'exact_synonym', 'related_synonym', 'broad_synonym', 'narrow_synonym', or 'alt_id'. The second column contains the GO identifier of the synonymous term or a character vector describing the synonymous term.

Tip

If you know the GO identifier (for example, 398) of a term object, instead of its index or position number (for example, 352), you can use the following syntax to display the synonym of a term object:

GeneontObj(398).terms.synonym

For an example, see Investigate Gene Ontology Term Properties.

Data Types: cell

Examples

Investigate Gene Ontology Term Properties

Investigate some of a properties of Gene ontology (GO) term object. First download the current Gene Ontology database into a geneont object.

GeneontObj = geneont('LIVE', true)

Gene Ontology object with 47331 Terms.

Investigate Ontology

Display the ontology of the term object in the 155th position in GeneontObj.

GeneontObj.terms(155).ontology

ans = 
'biological process'

Create a cell array of character vectors that list the ontology property for each term in GeneontObj.

ontologies = get(GeneontObj.terms,'ontology');
size(ontologies)

ans = 1×2

       47331           1

Create a logical mask that identifies all the terms with an ontology property of 'cellular component'.

mask = strcmp(ontologies,'cellular component');

Apply the logical mask to all the terms in GeneontObj to return a structure containing only terms with an ontology property of 'cellular component'.

cell_comp_terms = GeneontObj.terms(mask);
size(cell_comp_terms)

ans = 1×2

        4470           1

Investigate Names

Display the name property of the term object in the 157th position in GeneontObj.

GeneontObj.terms(157).name

ans = 
'obsolete activation of MAPKK (pseudohyphal growth)'

Find the index or position number of the term object whose name property is 'membrane'.

membrane_index = find(strcmp(get(GeneontObj.terms,'name'),'membrane'))

membrane_index = 9883

Use this index or position number and the id property to determine the GO identifier of the term object.

membrane_goid = GeneontObj.terms(membrane_index).id

membrane_goid = 16020

Use this GO identifier as input to the getrelatives method to find the GO identifiers of other term objects that are immediate relatives of the term object whose name property is 'membrane'.

relative_ids = getrelatives(GeneontObj,membrane_goid)

relative_ids = 23×1

        5628
        5642
        5886
       16020
       19867
       19898
       31090
       31224
       34045
       34357
      ⋮

List the name properties of these term objects.

lst = GeneontObj(relative_ids).terms;
get(lst,'name')

ans = 23×1 cell
    {'prospore membrane'                                            }
    {'annulate lamellae'                                            }
    {'plasma membrane'                                              }
    {'membrane'                                                     }
    {'outer membrane'                                               }
    {'extrinsic component of membrane'                              }
    {'organelle membrane'                                           }
    {'intrinsic component of membrane'                              }
    {'phagophore assembly site membrane'                            }
    {'photosynthetic membrane'                                      }
    {'ascus membrane'                                               }
    {'nuclear outer membrane-endoplasmic reticulum membrane network'}
    {'coated membrane'                                              }
    {'prospore membrane leading edge'                               }
    {'respirasome'                                                  }
    {'leaflet of membrane bilayer'                                  }
    {'side of membrane'                                             }
    {'plasma membrane region'                                       }
    {'membrane protein complex'                                     }
    {'membrane microdomain'                                         }
    {'cellular anatomical entity'                                   }
    {'pathogen-containing vacuole membrane'                         }
    {'spore inner membrane'                                         }

Investigate part_of and is_a Relationships

Display the term objects to which the term object in the 18,703rd position has an “is a” relationship.

GeneontObj.terms(18703).is_a

ans = 30282

Display the term objects to which the term object in the 18,703rd position has a “part of” relationship.

GeneontObj.terms(18703).part_of

ans = 43931

Investigate Synonyms

Display the term objects that are synonymous to the term object in the third position in GeneontObj.

synonyms = GeneontObj.terms(3).synonym

synonyms = 3×2 cell
    {'alt_id' }    {'GO:0019952'                                   }
    {'alt_id' }    {'GO:0050876'                                   }
    {'synonym'}    {'"reproductive physiological process" EXACT []'}

Display the text of the third synonym.

synonyms(3,2)

ans = 1×1 cell array
    {'"reproductive physiological process" EXACT []'}

Display the term objects that are synonymous to the term object in the 352nd position of GeneontObj.

GeneontObj.terms(352).synonym

ans = 1×2 cell
    {'synonym'}    {'"histone proline isomerization" EXACT []'}

Investigate Obsolete Status

Display the obsolete status of the term object in the third and seventh positions of GeneontObj.

GeneontObj.terms(3).obsolete

ans = logical
   0

GeneontObj.terms(7).obsolete

ans = logical
   1

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

obsolescence = get(GeneontObj.terms,'obsolete');
sum(cell2mat(obsolescence))

ans = 3718

The number of obsolete terms is 3718.

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

mask = ~cell2mat(obsolescence);

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

nonobsolete_terms = GeneontObj.terms(mask)

  43613×1 struct array with fields:

    id
    name
    ontology
    definition
    comment
    synonym
    is_a
    part_of
    obsolete

Version History

Introduced before R2006a