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[gofriends] Introduction of new relationship types in GO

Tanya Berardini tberardi at acoma.Stanford.EDU
Wed Jan 23 11:18:44 PST 2008


Dear GO Community:

We are pleased to announce that The Gene Ontology Consortium will
introduce three new relationship types -- regulates,
negatively_regulates and positively_regulates -- into the Biological
Process ontology.

For some time now, the GO content developers have been aware that
regulatory processes are not necessarily integral to the processes (as
previously indicated by the use of the 'part_of' relation) that they
regulate. Nevertheless, regulatory processes have been represented as
part_of the processes they regulate. We have long intended to replace
these part_of relationships with a new relationship type called
'regulates'. We are now in a position to make this replacement.

Ontology developers have thoroughly reviewed the relationships
involving regulatory processes and their targets to ensure internal
consistency. If a term 'regulation of process X' exists in the
ontology, it must be a valid subtype of 'regulation of biological
process', and must have a part_of relationship (which will be
transformed into one of the 'regulates' relationships) with 'process
X' or be a valid subtype of another regulatory process.

We have also introduced two new high-level regulation terms,
'regulation of molecular function' (for example, 'regulation of
cyclase activity') and 'regulation of biological quality' (for
example, 'regulation of blood pressure'), to represent processes that
regulate the activity of gene products and processes that regulate
measurable biological attributes, respectively. Regulation of
molecular function terms have been aligned with the corresponding
terms in the molecular function ontology, and we are working to align
regulation of biological quality terms with PATO.

WE PLAN TO REPLACE THE CURRENT 'part_of' RELATIONSHIPS IN THE ONTOLOGY
WITH THE NEW 'regulates' RELATIONSHIPS ON MARCH 25,2008.

Concurrent with this replacement, we will also introduce new
'intersection_of' tags into the OBO stanzas of the regulation terms;
these tags can be safely ignored by software with no negative
consequences.

Software developers should ensure that their procedures for loading
the ontologies into their resources are compatible with these changes
by this date. Below is an example of a current OBO 1.2 stanza for a
regulates term and a new stanza with the regulates relationship in
place.

CURRENT STANZA

[Term]
id: GO:0000019
name: regulation of mitotic recombination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA
recombination during mitosis." [GOC:go_curators]
narrow_synonym: "regulation of recombination within rDNA repeats" []
is_a: GO:0000018 ! regulation of DNA recombination
relationship: part_of GO:0006312 ! mitotic recombination


NEW STANZA

[Term]
id: GO:0000019
name: regulation of mitotic recombination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA
recombination during mitosis." [GOC:go_curators]
synonym: "regulation of recombination within rDNA repeats" NARROW []
is_a: GO:0000018 ! regulation of DNA recombination
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006312 ! mitotic recombination
relationship: regulates GO:0006312 ! mitotic recombination

The regulates relationship is transitive over both the is_a and
part_of relationships.

is_a transitivity:  If process B exists in the GO biological process
ontology and it is an is_a child of process A then any process that
regulates process B also regulates process A.

part_of transitivity:  If process Y exists in the GO biological
process ontology and it is a part_of child of process X then any
process that regulates process Y also regulates process X.

We strongly suggest that you test your loading scripts to ensure that
your database loads execute correctly. There is a test OBO 1.2 file
available at:

go/scratch/gene_ontology_with_regulates_relations_test.obo

Please feel free to contact us with any questions or concerns about this change.

Sincerely,

Tanya Berardini
David Hill
Chris Mungall
on behalf of the GO Consortium

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