Annotation Extension Relation Documentation Jamboree
Documentation pages
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]
- modified by
- requires_regulation_by
- requires_direct_regulator
- requires_regulator
(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)