GO annotation fields required for correct display

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GO annotations are most completely represented by the gene association file format used by GO Consortium members, detailed here.

However, for a web-based display of annotation data it is understandable when groups to decide to restrict their display to the most essential and useful GO annotation fields required by their users. However, we would ask that such displays do include the mininimal fields which are essential to be able to properly interpret a GO annotation statement.


Column No. Column Name Requirement Further Detail
1. DB Optional
2. DB_Object_ID Essential can be mapped to corresponding sequence identifiers
3. DB_Object_Symbol Optional
4. Qualifier Essential Notably annotations using the 'NOT' qualifier
5. GO term ID and/or name Essential
6. DB:Reference Essential? Recommended? this is an integral part of the annotation format. Without the reference, the annotation becomes untraceable and causes problems for users of the displayed annotation set who would like to verify the statement
7. Evidence Essential
8. With(or)From Recommended Provides important supporting information, especially required to add meaning to annotations describing interactions
9. Aspect Optional
10. DB_Object_Name Optional
11. DB_Object_Synonym Optional
12. DB_Object_Type Optional
13. Taxon Optional
14. Date Recommended
15. Assigned_by Essential
16. Annotation Extension Optional
17. Gene Product Form ID Optional

COMMENTS

1. In addition, should external websites be encouraged to provide a link to the GO Consortium? Rachael

2. we could also suggest that if external websites would like to be notified of any changes to these recommendations, then to send us an email? We would then be able to build up a picture of who displays our annotations, which may be useful for grant reporting purposes. Edimmer 11:12, 2 February 2011 (UTC)

3. Suggested change to the second part of the intro to this statement: The display of annotation data by some web-based databases is often restrict to the most essential and useful GO annotation fields required by their users. However, the GOC expects the display of all GO data to include the mininimal fields which are essential to enable appropriate interpretion of a GO annotation statement, and also to provide recognition of the data source. Ruth]

4. Should also state that websites providing users with a way of filtering and viewing GO annotations or terms should take into account the GO structure. i.e. therefore when a user is looking for annotations to 'nucleus', should bring back annotations not only to the directly searched term, but also to descendants (nucleolus, nuclear membrane). GO managers call feedback.

Examples of external website displays

1. Ensembl e.g. Stat6


Displays GO ID, GO term name, Evidence code, 'with' field information (only seems to be for Compara annotations, incomplete for other IEA methods, ISS and IPI).

2. NCBI e.g. Stat6

Displays GO term name, evidence code, PMID link