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Dear GO Friends,

Having successfully implemented the 'regulates' relationships in the biological process (BP) ontology, we now plan to add 'regulates' relationships within the molecular function (MF) ontology and between the BP and MF ontologies.

These additions may have great impact on your tools and analyses because:

1) There will be inter-ontology links between MF and BP for the first time. 2) Loading scripts will need to be modified to take the inter-ontology links into account by Nov. 30, 2008. 3) GO analysis tools will need to be modified to take the new relationships into account by Nov. 30, 2008.


In detail, we will make the implied relationships between MF terms and the corresponding 'regulation of molecular function' BP terms explicit. For example:

regulation of kinase activity (BP) regulates kinase activity (MF)

Similarly, we will make implicit regulatory relationships between terms within the MF ontology explicit. For example:

kinase regulator activity (MF) regulates kinase activity (MF)

The former will be the first inter-ontology links in the GO vocabularies and may cause errors with loading or parsing scripts that do not allow inter-ontology links.

Adding these relationships improves the ability of the ontology to represent biology completely and accurately. The average GO user will benefit from these new links because they will be able to ask and answer more complex questions than they could previously. Users must understand what the different relationships mean and how the various GO tools utilize them. The addition of these links also has major implications for tools that ignore relationship types when summarizing annotations. For example, it is important to understand whether a query will return all children of a term regardless of its relationship to the parent or can whether the query can discriminate between relationship types. If your tool of choice lumps annotations to 'kinase regulator activity' together with the regulates parent 'kinase activity', users will retrieve gene products that function as kinase regulators (and not necessarily as kinases!) in a query for kinases. More sophisticated tools will allow users to customize queries to return results that better reflect their interests. For example, if tools are upgraded to take relationships into consideration and people want to look only for processes or functions and none of their regulates children, one can exclude the regulates children.

A test file with the BP-MF links can be found in:


We plan to implement these links in the live ontology on November 30, 2008.

Please provide feedback to us regarding this plan. We have created a wiki page [[1]] which will provide a more formal specification for software developers and database administrators. It will also provide answers to frequently asked questions and will be kept up to date with our progress.

On behalf of the GO Consortium,

Tanya Berardini David Hill Chris Mungall