comparison variant_effect_predictor/Bio/EnsEMBL/OntologyTerm.pm @ 0:1f6dce3d34e0

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author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
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1 =head1 LICENSE
2
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
4 Genome Research Limited. All rights reserved.
5
6 This software is distributed under a modified Apache license.
7 For license details, please see
8
9 http://www.ensembl.org/info/about/code_licence.html
10
11 =head1 CONTACT
12
13 Please email comments or questions to the public Ensembl
14 developers list at <dev@ensembl.org>.
15
16 Questions may also be sent to the Ensembl help desk at
17 <helpdesk@ensembl.org>.
18
19 =cut
20
21 =head1 NAME
22
23 Bio::EnsEMBL::OntologyTerm
24
25 =head1 DESCRIPTION
26
27 An ontology term object, (most often) created by
28 Bio::EnsEMBL::DBSQL::GOTermAdaptor and used in querying for
29 transcripts, genes, and translations using the relevant adaptors and
30 methods.
31
32 =head1 METHODS
33
34 =cut
35
36 package Bio::EnsEMBL::OntologyTerm;
37
38 use strict;
39 use warnings;
40
41 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
42
43 use base qw( Bio::EnsEMBL::Storable );
44
45 =head2 new
46
47 Arg [-ACCESSION] : String
48 The accession of the ontology term.
49
50 Arg [-ONTOLOGY] : String
51 The ontology that the term belongs to.
52
53 Arg [-NAMESPACE] : String
54 The namespace of the ontology term.
55
56 Arg [-NAME] : String
57 The name of the ontology term.
58
59 Arg [-SUBSETS] : (optional) Listref of strings
60 The subsets within the ontology to which this
61 term belongs.
62
63 Arg [-DEFINITION] : (optional) String
64 The definition of the ontology term.
65
66 Arg [-SYNONYMS] : (optional) Listref of strings
67 The synonyms of this term.
68
69 Arg : Further arguments required for parent class
70 Bio::EnsEMBL::Storable.
71
72 Description : Creates an ontology term object.
73
74 Example :
75
76 my $term = Bio::EnsEMBL::OntologyTerm->new(
77 '-accession' => 'GO:0021785',
78 '-ontology' => 'GO',
79 '-namespace' => 'biological_process',
80 '-name' => 'branchiomotor neuron axon guidance',
81 '-definition' => 'The process in which a branchiomotor '
82 . 'neuron growth cone is directed to a specific target site. '
83 . 'Branchiomotor neurons are located in the hindbrain and '
84 . 'innervate branchial arch-derived muscles that control jaw '
85 . 'movements, facial expression, the larynx, and the pharynx.',
86 '-synonyms' => [ 'BMN axon guidance',
87 'branchial motor axon guidance',
88 'special visceral motor neuron axon guidance' ]
89
90 # ... other arguments required by Bio::EnsEMBL::Storable.
91 );
92
93 Return type : Bio::EnsEMBL::OntologyTerm
94
95 =cut
96
97 sub new {
98 my $proto = shift(@_);
99
100 my $this = $proto->SUPER::new(@_);
101
102 my ( $accession, $ontology, $namespace, $name, $definition, $subsets )
103 = rearrange( [ 'ACCESSION', 'ONTOLOGY', 'NAMESPACE', 'NAME',
104 'DEFINITION', 'SUBSETS' ],
105 @_ );
106
107 $this->{'accession'} = $accession;
108 $this->{'ontology'} = $ontology;
109 $this->{'namespace'} = $namespace;
110 $this->{'name'} = $name;
111 $this->{'definition'} = $definition;
112 $this->{'subsets'} = [ @{$subsets} ];
113
114 $this->{'child_terms_fetched'} = 0;
115 $this->{'parent_terms_fetched'} = 0;
116
117 return $this;
118 }
119
120 =head2 accession
121
122 Arg : None
123
124 Description : Returns the accession for the ontology term in question.
125
126 Example : my $accession = $term->accession();
127
128 Return type : String
129
130 =cut
131
132 sub accession {
133 my ($this) = @_;
134 return $this->{'accession'};
135 }
136
137 =head2 ontology
138
139 Arg : None
140
141 Description : Returns the ontology for the ontology term in question.
142
143 Example : my $ontology = $term->ontology();
144
145 Return type : String
146
147 =cut
148
149 sub ontology {
150 my ($this) = @_;
151 return $this->{'ontology'};
152 }
153
154 =head2 namespace
155
156 Arg : None
157
158 Description : Returns the namespace for the ontology term in question.
159
160 Example : my $acc = $term->namespace();
161
162 Return type : String
163
164 =cut
165
166 sub namespace {
167 my ($this) = @_;
168 return $this->{'namespace'};
169 }
170
171 =head2 name
172
173 Arg : None
174
175 Description : Returns the name for the ontology term in question.
176
177 Example : my $name = $term->name();
178
179 Return type : String
180
181 =cut
182
183 sub name {
184 my ($this) = @_;
185 return $this->{'name'};
186 }
187
188 =head2 definition
189
190 Arg : None
191
192 Description : Returns the definition for the ontology term in question.
193
194 Example : my $definition = $term->definition();
195
196 Return type : String
197
198 =cut
199
200 sub definition {
201 my ($this) = @_;
202 return $this->{'definition'};
203 }
204
205 =head2 synonyms
206
207 Arg : None
208
209 Description : Returns the list of synonyms defined for this term
210 (if any).
211
212 Example : my @synonyms = @{ $term->synonyms() };
213
214 Return type : Listref of strings
215
216 =cut
217
218 sub synonyms {
219 my ($this) = @_;
220
221 if ( !exists( $this->{'synonyms'} ) ) {
222 $this->{'synonyms'} =
223 $this->adaptor()->_fetch_synonyms_by_dbID( $this->dbID() );
224 }
225
226 return $this->{'synonyms'};
227 }
228
229 =head2 subsets
230
231 Arg : None
232
233 Description : Returns a list of subsets that this term is part
234 of. The list might be empty.
235
236 Example : my @subsets = @{ $term->subsets() };
237
238 Return type : listref of strings
239
240 =cut
241
242 sub subsets {
243 my ($this) = @_;
244 return $this->{'subsets'};
245 }
246
247 =head2 children
248
249 Arg : (optional) List of strings
250 The type of relations to retrieve children for.
251
252 Description : Returns the children terms of this ontology term.
253
254 Example : my @children =
255 @{ $term->children( 'is_a', 'part_of' ) };
256
257 Return type : listref of Bio::EnsEMBL::OntologyTerm
258
259 =cut
260
261 sub children {
262 my ( $this, @relations ) = @_;
263
264 my @terms = @{ $this->adaptor()->fetch_all_by_parent_term($this) };
265
266 if (@relations) {
267 @terms = ();
268 foreach my $relation (@relations) {
269 if ( exists( $this->{'children'}{$relation} ) ) {
270 push( @terms, @{ $this->{'children'}{$relation} } );
271 }
272 }
273 }
274
275 return \@terms;
276 }
277
278 =head2 descendants
279
280 Arg : None
281
282 Description : Returns the complete set of 'is_a' and 'part_of'
283 descendant terms of this ontology term, down to
284 and including any leaf terms.
285
286 Example : my @descendants = @{ $term->descendants() };
287
288 Return type : listref of Bio::EnsEMBL::OntologyTerm
289
290 =cut
291
292 sub descendants {
293 my ($this) = @_;
294 return $this->adaptor()->fetch_all_by_ancestor_term($this);
295 }
296
297 =head2 parents
298
299 Arg : (optional) List of strings
300 The type of relations to retrieve parents for.
301
302 Description : Returns the parent terms of this ontology term.
303
304 Example : my @parents =
305 @{ $term->parents( 'is_a', 'part_of' ) };
306
307 Return type : listref of Bio::EnsEMBL::OntologyTerm
308
309 =cut
310
311 sub parents {
312 my ( $this, @relations ) = @_;
313
314 my @terms = @{ $this->adaptor()->fetch_all_by_child_term($this) };
315
316 if (@relations) {
317 @terms = ();
318 foreach my $relation (@relations) {
319 if ( exists( $this->{'parents'}{$relation} ) ) {
320 push( @terms, @{ $this->{'parents'}{$relation} } );
321 }
322 }
323 }
324
325 return \@terms;
326 }
327
328 =head2 ancestors
329
330 Arg : None
331
332 Description : Returns the complete set of 'is_a' and 'part_of'
333 ancestor terms of this ontology term, up to and
334 including the root term.
335
336 Example : my @ancestors = @{ $term->ancestors() };
337
338 Return type : listref of Bio::EnsEMBL::OntologyTerm
339
340 =cut
341
342 sub ancestors {
343 my ($this) = @_;
344 return $this->adaptor()->fetch_all_by_descendant_term($this);
345 }
346
347 1;