The manuscript describes some of the changes of the GO ontology and annotations, from the experience of the UniProt annotation team.

It also describes some of the quality checks performed in the UniProt GO annotation process, especially related to taxon restrictions in the GO

Major compulsory revisions

1. The title and abstract only mention the content about GO changes, but does not include any mention to the quality assurance. I'd suggest either to concentrate on GO changes in the manuscript only, or to mention the quality checks in the title and abstract (provided they are related to the general subject of the paper)

2. It is not clear which is the target audience of the paper. Is it written to those developing applications that use GO annotations or for the end users of those applications? How do changes affect this target audicence? (can you provide some examples?)

3. Which are the policies of the GOC regarding ontology and annotation version controlling? And the UniProt GO annotations? Are annotations syncronised with a verticular version of the GO ontology?

4. Where can users find the changes that "are planned and announced by GOC" or the UniProt GOA? (as mentioned in the Introduction)

5. Can you clarify what "changing submissions" refer to? (in Introduction)

6. What are the practical implications of obsolete terms? If annotations and ontology are in sync, users should not find any obsolete term at all.

7. The manuscript describes both the GOC and the curators as the ones suggesting changes to the terms. Is there any mechanism for GO users to suggest or remove GO terms?

8. Can you explain what GO projections are (in Changes in submitted annotation sets)

9. It is not clear to me what caution comments curated in UniProtKB (in Annotation blacklist) are. Can you provide some example?

Minor essential revisions

1. Consider adding a brief description at the end of the "true-path-rule" in the "Development of ontologies" section to explain why re-annotation with a specific term does not remove more general terms.

Discretionary revisions
None

Level of interest: An article whose findings are important to those with closely related research interests

Quality of written English: Acceptable

Statistical review: No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests: I declare that I have no competing interests

The authors have addressed all my previous comments but only partially the first one.

Minor Essential Revisions

The manuscript has two main sections 'Changes to ontologies and annotations' and 'Quality assurance', with lengths of 7'5 and 5 pages respectively. Nevertheless neither the title nor the abstract mention the second section on quality assurance.

Level of interest: An article whose findings are important to those with closely related research interests

Quality of written English: Acceptable

Statistical review: No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests: I declare that I have no competing interests