How to submit genome annotations using the VectorBase Community Annotation Pipeline

1. Instructions for using the
VectorBase Community Annotation system
Rob Bruggner
August 2007

2. VectorBase User Login Page
You need to be logged in to submit data to VectorBase. Go to the quot;Userquot; section,
enter your user name and password, and click quot;Log In.quot;

3. VectorBase User Home Page
After logging in, click on the quot;Contribute Manual Annotationquot; link to be taken to the
manual annotation submission page.

4. Contribute Manual Annotation Page
The Contribute Manual Annotation page gives the user a general overview of how
to submit manual annotation to VectorBase. Click on the Read more about the
process and submit data here link to go to the Gene Submission Page.

5. Manual Annotation Submission Page
Download the gene submission form and directions by clicking on the document
icons.

6. Gene Submission Form
Fill out the gene submission form as described by the directions.

7. Upload the completed gene submission form
After filling out the gene submission form, select the the organism that your
submitting data for, select the completed submission form for upload, and click
quot;Submit.quot;

8. A preview of uploaded data
After submitting your gene sequence, you'll be shown a preview of your uploaded
data. The translated portion of your transcript, as specified in the submission form,
will be shown in parallel with the submitted transcript sequence. Additionally, any
submitted publications or controlled vocabulary terms will also be shown. Use this
data preview page to make sure your data has been uploaded properly before
submitting your data for curator review.

9. Submit uploaded data
If you've described a transcript's functionality using Gene Ontology Terms and that
functionality is further described in a paper that's also being submitted, please
associate the paper with the corresponding terms.
If your data looks correct, click on the quot;Submit Dataquot; button at the bottom of the
preview page to submit your gene model(s) for curator review. NOTE: If you are
submitting a large amount of models simultaneously, the submission process could
take several minutes. Please do not close the browser window while submitting
your data.

10. Data submission report
After your data is submitted to VectorBase, you will be presented with a report
indicating if there were any problems with the submission of your data. If problems
did occur during data submission, please contact a VectorBase curator for
assistance.

11. Recently Submitted Data
If you return to the Community Annotaiton Submission page, you'll see recently
submitted data listed on the right.

12. Display of Gene Model in Contig View
After your gene model has been reviewed and approved by a VectorBase curator,
the model will become immediately visible in the quot;Manual Annotationquot; DAS track in
the VectorBase genome browser contig view.