Annotation Extension Relation:in absence of: Difference between revisions
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'''THIS RELATION IS DEPRECATED''' | |||
<pre style="color:#808080"> | |||
==Definition== | ==Definition== | ||
Identifies a | Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product. | ||
==Child terms== | ==Child terms== | ||
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[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex | [[ENTITY_UNION:0000005]] ! chemical, gene product, or complex | ||
=== DEPRECATION WARNING === | |||
The GO editors have agreed that this relation should be deprecated. There are two main reasons for this. | |||
* The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation is true. This can not be expressed in OWL. Annotation extensions using this relation will never fold. | |||
* The relation includes a hidden negation. This is problematic for a number of reasons, the most important of which is that burying negations in otherwise positive relationships can cause serious problems for inference. | |||
==Annotation Extension Usage Examples== | ==Annotation Extension Usage Examples== | ||
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---- | ---- | ||
</pre> | |||
Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation | Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation usage examples for each annotation extension relation] | ||
[[Category:annotation extension]] | [[Category:annotation extension]] | ||
Latest revision as of 11:06, 29 October 2019
THIS RELATION IS DEPRECATED
==Definition==
Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
==Child terms==
* None.
==Scope of use==
===Domain===
BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component)
===Range===
[[ENTITY_UNION:0000005]] ! chemical, gene product, or complex
=== DEPRECATION WARNING ===
The GO editors have agreed that this relation should be deprecated. There are two main reasons for this.
* The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation is true. This can not be expressed in OWL. Annotation extensions using this relation will never fold.
* The relation includes a hidden negation. This is problematic for a number of reasons, the most important of which is that burying negations in otherwise positive relationships can cause serious problems for inference.
==Annotation Extension Usage Examples==
'''Protein localization to component only occurs when substance is absent'''
SCAP (P97260) acts as a SREBP escort protein to localize SREBP from the ER to the Golgi ONLY in sterol-depleted conditions.
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| P97260
|GO:0090110 <span style="color:green">cargo loading into COPII-coated vesicle</span>
| PMID:15899885
| IDA
|
in_absence_of(CHEBI:15889 <span style="color:green">sterol</span>)
|}
{| class="wikitable" border="1"
|-
! Gene Name (col 2)
! Qualifier (col 4)
! GO ID (col 5)
! Reference (col 6)
! Evidence (col 7)
! Annotation Extension (col 16)
|-
| P97260
| colocalizes_with
| GO:0030127 <span style="color:green">COPII vesicle coat</span>
| PMID:15899885
| IDA
|
in_absence_of(CHEBI:15889 <span style="color:green">sterol</span>)
|}
----
Back to Annotation usage examples for each annotation extension relation