Adding a GO database in Scaffold

Please refer to this link for more details: 

How do I add organism-specific GOA databases to Scaffold – Proteome Software Technical Help Center

Option 1 (preferred method)

1. Access the UniProt FTP server, also available from the link (UniProt FTP server (ebi.ac.uk)).
2. Select the specific organism you are working with and open the corresponding folder. NOTE: If you do not see your organism listed on the main page click on the Proteomes folder to bring up a vast collection of organism-specific proteomes. 
3. IMPORTANT: Scaffold can only read data contained in the file with the extension GAF.GZ. 
4. Right click the organism-specific file with gaf.gz extension that you are interested in adding and select Copy Link Location.
5. Follow this pathway: Edit > Edit Annotation Options... Here you will see any databases that have been added (NCBI is added automatically).
6. Select Add. Here you have the option the add the All Proteomes and Human Only UniProt databases.
7. Select Other Web Site... from the dropdown menu and paste the copied link into the box.
8. Give your database a name and choose a folder <D:\Person Lab GO files> to save your GOA database. Click Add.
9. Your database should appear under Database Name. NOTE: Currently selected database is highlighted in green.
10. Once your database is selected GO terms can be applied. You can add go terms to an experiment from a selected database by clicking Experiment >Add or Edit Annotations... This dialog allows you to add either GO or Pathway annotations.
11. Choose the appropriate GO term source from the dropdown menu next to the GO Terms button. Then click OK.
12. Here you have the option to select the terms displayed, adjust the default, and add the selected terms. Simply selecting OK here will apply the default set of GO terms to your experiment file.
13. If two or more samples have been loaded, Scaffold can find enriched terms using the PSEA-Quant algorithm. More information can be found here: Gene Ontology: Custom Annotations in Scaffold – Proteome Software Technical Help Center

Option 2

Navigate to (https://www.ebi.ac.uk/GOA/downloads) and on the right side is a box of “Latest statistics”.

Click the organism of interest e.g., human.

Click “download the GOA for Human” link.

Click the “goa_human.gaf.gz” file. This will download the file.

Copy the file to the <D:\Person Lab GO files> folder.

Unzip the file here.

In the Scaffold software:

Edit > Edit Annotation Options

Select Add.

Source: Other file.

Choose: navigate to <D:\Person Lab GO files> folder and select the .gaf file of choice.

Name: type in the organism’s name.

Add.

Your database should appear under Database Name.

The currently selected database is highlighted in green.

Once your database is selected GO terms can be applied by clicking:

Experiment >Add or Edit Annotations.

This dialog allows you to add either GO or Pathway annotations.

Choose the appropriate GO term source from the dropdown menu next to the GO Terms button.

Click OK.

You have the option to select the terms displayed, adjust the default and add the selected terms. Simply selecting OK here will apply the default set of GO terms to your experiment file.

If two or more samples have been loaded, Scaffold can find enriched terms using the PSEA-Quant algorithm. More information can be found in the User Guide