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[Gofriends] SECOND ANNOUNCEMENT: Additional inter- and intra-ontology 'regulates' links in the GO coming

Tanya Berardini tberardi at acoma.stanford.edu
Tue Oct 28 14:08:28 PDT 2008


SECOND ANNOUNCEMENT

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. The target date for these additions is February 9, 2009.

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

   1. There will be inter-ontology links between BP and MF for the first
   time.
   2. Loading scripts will need to be modified to take the inter-ontology
   links into account by Feb. 9, 2009.
   3. GO analysis tools will need to be modified to take the new
   relationships into account by Feb. 9, 2009.

-- 

Specifically, we will make the implicit regulatory relationships between
'regulation of molecular function' BP terms and the corresponding MF terms
explicit. For example:

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

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

   - calcium channel regulator activity (MF) *regulates* calcium channel
   activity (MF)

The former will be the first inter-ontology links in the GO vocabularies.
Note that if software has been constructed with the assumption that there
are no inter-ontology links, then this software may break when presented
with the new ontology.

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 discriminate between
relationship types. If your tool of choice lumps annotations to 'calcium
channel regulator activity' together with the regulates parent 'calcium
channel activity', a query for calcium channels will also retrieve gene
products that function as calcium channel regulators (and not necessarily as
channels!). More sophisticated tools will allow users to customize queries
to return results that better reflect their interests. For example, tools
that are upgraded to take relationships into consideration will allow users
to look for processes or functions, and specify whether to include or
exclude their regulates children.

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

http://www.geneontology.org/scratch/regulates_relations_examples/go_regtest_withPosNeg_withPF_noXP.obo

We will provide a test file with both BP-MF and MF-MF shortly.

As noted, we plan to implement these links in the live ontology on February
9, 2009.

Please provide feedback to us regarding this plan. We have created a wiki
page

http://wiki.geneontology.org/index.php/FP-regulates

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



-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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