This exercise gives you a taste of manual annotation, culminating in reading a paper and annotating a protein. Working through the following tutorial should help you get a grasp on the tools available to annotators. It is based on the Gene Ontology Annotation (GOA) Tutorial by Evelyn Camon.
The first part of this tutorial uses the AmiGO browser, developed by the Gene Ontology Consortium, which accesses the GO database and allows users to search both Gene Ontology terms and the gene products and genes annotated to those terms.
Open up an AmiGO window.
You can navigate the tree in the same way as DAG-Edit, by clicking on the 
and 
icons at the start of each line. 
means that the term on that line has no children. Greyed out terms are obsolete, meaning that they are deprecated and should no longer be used. The Graphical View link on the right allows you to view the selected tree in pictorial form.
Each instance of a term gets one horizontal line.
The 
and 
icons represent the relationship of the term to its parent, either is a and part of the parent term.
The GO term identifier and term name can be clicked to get a more detailed view of the term, including the definition and all genes and gene products annotated to the term. Mousing over the term brings up a floating box showing the term definition.
Following the term ID and name is a number in parentheses. This is the total number of genes manually annotated to this term and its children. Electronic annotations (evidence code IEA) are not shown for two reasons: there are large numbers of these annotations, and they are deemed lower quality as they have not been checked by a human.
Terms may be followed by the 
icon. Clicking this icon will bring you to a pie chart which displays the percentage of gene products annotated to each term below that selected.
Open the node biological process, then open physiological process, then secretion
How many of the children of secretion have no children of their own?
How many annotations (non-IEA) does acid secretion have to it?
Clicking on a term name or ID opens the term detail page.
The term detail page shows all the information available about the term: the term name and ID, any synonyms it might have, the term definition, its position in the GO structure, references to external databases, and the gene products associated with that term. Note that children of the selected term are not shown.
Open the node protein secretion and click on the term cytokine secretion. It will open in a new window.
What are the parents of cytokine secretion and what relationships does it have to them?
Click on the parent term protein secretion to retrieve the information about it.
Beneath the term information are the annotations, the genes or gene products assigned the selected term.
The first column is the gene or gene product identifier; clicking on the name will take you to the AmiGO gene product detail page, which shows the information held in the GO database about that gene product, including all its GO annotations and the peptide sequence (if available).
The second column indicates whether the object is a gene or a protein.
The third column is the data source that submitted the annotation (e.g. FlyBase, SGD, UniProt), and clicking on this takes you to the detail page at the source's website.
The fourth column is the evidence code for the association; when underlined, clicking on the evidence code brings up the source reference used to make the association.
The final column has the full name of the gene product where available.
You can choose to view the annotations to the term itself or to the term and its children.
Go back to the cytokine secretion term detail page. From the drop-down menu on the right, choose get All associations with terms and click submit.
How many gene products are annotated directly to cytokine secretion and how many are annotated to its child terms?
Which databases have made these annotations?
Note the filtering menus in the light grey box. You can also choose to filter annotations by the database that supplied them, by the evidence code used in the annotation and by species.
Change the view so that gene associations from mouse (M. musculus) are displayed.
Which databases have submitted mouse gene annotations?
Shut the popup window and return to the main page. To reset the filters, you will need to choose All from the species filter list and click Set Filters.
At the top of the page there is a search box. GO terms or associated gene products can be searched by checking the "terms" or "gene products" boxes respectively.
Perform a search for gene products containing the text 'grim'.
The results list displays all gene products containing the text "grim", the name of the external database which the gene product is from, all GO terms to which the product has been associated and the types of evidence linking the gene product to that term, and the aspect - function, process, component - that the GO term describes.
How many GO terms is the FlyBase gene product "Buffy" associated with?
Do a search for your favourite gene product.
Does this gene product already have a GO association?
Perform a search for GO terms containing the text rough endoplasmic reticulum.
Each row of the results table contains one GO term, its aspect and the definition, where available. Clicking the term will bring up the detailed view. Clicking the icon to the left of the term name (ringed in red) will show your term placed in the GO tree.
The paper you will be reading later concerns proteins ERF1 and ERF3. What information can you find out about them?