Annotation Extension Relation Documentation Jamboree

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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

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

Issues arising

Folded/Unfolded annotations

1. has_input relationship

i) would annotations like these ever be folded into new GO terms in the GO?

ii) should we document how these would be folded by users based on the relationship applied?

iii) should the AE associated with cellular response to drugs use the relationship in_presence_of rather than has_input?

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: 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. happens during place in RO

happens_during is is_a ends_during, but not is_a starts_during (when imported from go-trunk). This seems odd.


consistency issues in the response to ontology domain

When applying the term GO:0035690 cellular response to drug what relationship to use in C16?

Currently have:

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 drug PMID:20801214 IDA has_input(CHEBI:6801 metformin)
Q9NW64 RBM22 GO:0035690 cellular response to drug PMID:21122810 IDA in_presence_of(CHEBI:9516)thapsigargin)
Q5QJU3 ACER2 GO:0035690 cellular response to drug PMID:20628055 IEP has_direct_input(CHEBI:42588)4-hydroxyphenyl retinamide)

Note I don't like the IEP annotation but this is the only has_direct_input example, has_input is used more frequently

4. Not in current QuickGO visualisation page (but on [1]

(We should think about obsoleting these as they are annotating in the reverse direction, which we agreed not to do at the Bar Harbor meeting). 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)