Annotation Extension Relation Documentation Jamboree: Difference between revisions

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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''' ====

Revision as of 15:35, 6 June 2014


Documentation pages

http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation

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]

plus 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)