Annotation Extension Relation Documentation Jamboree: Difference between revisions
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===Other=== | ===Other=== | ||
'''1. acts_on_population_of''' | ==== '''1. acts_on_population_of''' ==== | ||
Should this be a plural relationship? Pretty much everything else in GO is singular. | Should this be a plural relationship? Pretty much everything else in GO is singular. | ||
==== '''2. When to use has_input relationship and when to use has_regulation_target''' ==== | |||
'''2. When to use has_input relationship and when to use has_regulation_target''' | |||
has_regulation_target is limited to the domain GO:0065007 ! biological regulation | has_regulation_target is limited to the domain GO:0065007 ! biological regulation | ||
Line 51: | Line 50: | ||
Can has_input be used with the domain GO:0065007 ! biological regulation? | Can has_input be used with the domain GO:0065007 ! biological regulation? | ||
'''3. requires substance and other similar terms''' | ==== '''3. requires substance and other similar terms''' ==== | ||
* ''' | Some of these terms seem so similar it is hard to choose between them, especially true of the first 2 on this list | ||
* '''[[Annotation_Extension_Relation:requires_substance|requires_substance]]''' | |||
** Definition: The annotated gene product participates in a Biological Process or executes a Molecular Function only in presence of a substance | ** Definition: The annotated gene product participates in a Biological Process or executes a Molecular Function only in presence of a substance | ||
* ''' | * '''[[Annotation_Extension_Relation:activated_by|activated_by]]''' | ||
** Definition: Identifies a chemical | ** Definition: Identifies a chemical substance that increases the activity of the gene product. | ||
* [[Annotation_Extension_Relation:dependent_on|dependent_on]] NOTE Parent to requires_substance | |||
** Definition: Identifies a requirement under which the ontology term is observed to apply to the annotated gene product. | |||
* ''' | * '''[[Annotation_Extension_Relation:in_presence_of|in_presence_of]]''' | ||
** Definition: Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product. | ** Definition: Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product. | ||
* ''' | * '''has agent''' | ||
** Definition: | ** Definition: NO definition, usage: The relationship that links an entity with a process in which the entity participates in the process by serving as the continuant that is responsible for the execution of the process. Subsets: GO:cellular_component, cell_or_anatomical | ||
* '''[[Annotation_Extension_Relation:inhibited_by|inhibited_by]]''' | |||
** Definition: Identifies a chemical substance that decreases the activity of the gene product. | |||
* '''[[Annotation_Extension_Relation:in_absence_of|in_absence_of]]''' | |||
** 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. | |||
* ''' | * '''[[Annotation_Extension_Relation:independent_of|independent_of]]''' | ||
** Definition: Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product | |||
* | |||
* | |||
Not in current [http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html QuickGO visualisation] page (but on [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation] | ==== '''4. Not in current [http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html QuickGO visualisation] page (but on [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation]''' ==== | ||
* modified by | * modified by | ||
* requires_regulation_by | * requires_regulation_by | ||
** requires_direct_regulator | ** requires_direct_regulator | ||
* [[Annotation_Extension_Relation:requires_regulator|requires_regulator]] | |||
plus maybe a few more? | |||
Missing from [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation] but present on QuickGO visualisation page | ==== 5. Missing from [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation] but present on QuickGO visualisation page ==== | ||
* '''stabilizes''' | |||
* '''has agent''' | |||
===Examples needed=== | ===Examples needed=== |
Revision as of 15:33, 6 June 2014
Documentation pages
http://wiki.geneontology.org/index.php/Folding_and_Unfolding
Issues arising
Folded/Unfolded annotations
1. has_input relationship would annotations like these ever be folded?
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) |
---|---|---|---|---|---|
Q8WY54 | PPM1E | GO:0035690 cellular response to drugs | PMID:20801214 | IDA | has_input(CHEBI:6801 metformin) |
O14672 | ADAM10 | GO:0006509 membrane protein ectodomain proteolysis | PMID:18676862 | IMP | has_input(UNIPROT:Q29983 MICA) |
Other
1. acts_on_population_of
Should this be a plural relationship? Pretty much everything else in GO is singular.
2. When to use has_input relationship and when to use has_regulation_target
has_regulation_target is limited to the domain GO:0065007 ! biological regulation
Can has_input be used with the domain GO:0065007 ! biological regulation?
3. requires substance and other similar terms
Some of these terms seem so similar it is hard to choose between them, especially true of the first 2 on this list
- requires_substance
- Definition: The annotated gene product participates in a Biological Process or executes a Molecular Function only in presence of a substance
- activated_by
- Definition: Identifies a chemical substance that increases the activity of the gene product.
- dependent_on NOTE Parent to requires_substance
- Definition: Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
- in_presence_of
- Definition: Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
- has agent
- Definition: NO definition, usage: The relationship that links an entity with a process in which the entity participates in the process by serving as the continuant that is responsible for the execution of the process. Subsets: GO:cellular_component, cell_or_anatomical
- inhibited_by
- Definition: Identifies a chemical substance that decreases the activity of the gene product.
- in_absence_of
- 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.
- independent_of
- Definition: Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product
4. Not in current QuickGO visualisation page (but on [1]
- modified by
- requires_regulation_by
- requires_direct_regulator
- requires_regulator
plus maybe a few more?
5. Missing from [2] but present on QuickGO visualisation page
- stabilizes
- has agent
Examples needed
1. has_input
We need an example where the has_input ID is folded to be incorporated into the GO term. Preferably an example other than response to (has_input ID)