annotation

Annotation related questions (e.g. evidence codes, ID mapping...).

How can I contribute to GO?

We welcome your contributions!

The GO project is constantly evolving, and we welcome feedback from all users. Research groups may contribute to the GOC by either providing suggestions for updating the ontology (e.g. requests for new terms) or by providing annotations, that is, associations between genes or gene products and ontology terms. Suggested edits are reviewed by the ontology editors and implemented where appropriate.

How do I submit annotations to GO?

We welcome your contributions!

We welcome annotation contributions from GOC and non-consortium members. It is important to contact the Gene Ontology Consortium (GOC) before annotation work is carried out; this will ensure that GOC mentors and trainers can be of assistance in producing data sets in agreement with the GOC annotation policies and format requirements. To learn more details, visit the page on Contributing GO annotations.

How do I annotate ESTs?

To make electronic GO annotation to ESTs, it is usual to BLAST the EST sequences against sequences that have been manually annotated and transfer the annotations from similar sequences, adding evidence code IEA.

Some useful tools for EST annotation:

How often does automatic annotation give results that are consistent with manual annotation?

I

n general, electronic annotations are rarely incorrect, as they are annotations to very high-level GO terms. For example, the GOA group at EBI reports:

How is annotation quality controlled to ensure consistency between databases?

The accuracy of GO annotations is a high priority for all members of the GO Consortium. Each member organization is responsible for keeping its own annotations accurate and up to date, and for correcting any errors. Users can report errors to the GO helpdesk; any comments on annotations will be forwarded to the appropriate contributing group.

What are the advantages and disadvantages of automatic annotation?

One advantage of automatic annotation is speed: wholly or partially automated methods facilitate the annotation of much larger sets of known or predicted gene products than can be produced manually. Automated annotation methods generally yields more broad (less detailed) annotations compared to manual annotation.

What are the advantages and disadvantages of manual annotation?

The most reliable annotations are those made manually by database curators based on primary and review literature. Manual annotations often cite experimental evidence that provides strong support for the association of a GO term with a gene product, and can be done at a very detailed level. The chief disadvantage of manual annotation is that it is labor-intensive, requiring a lot of time and effort from trained biologists.

Why are some gene products annotated to both a parent term and a child term?

This is done when there is explicit evidence to support separate annotations; usually it means that there is strong evidence for a more general annotation (parent term) and weaker evidence supporting a more specific annotation (child term).

From the GO annotation guide: