[gofriends] SECOND ANNOUNCEMENT: Introduction of New Relationship Types in GO (March 25, 2008)

[Tanya Berardini]

Please note that the name of the file to be used for testing has been
updated.

GO Consortium members:  Please let us know when you have successfully tested
loading the new files.

-------------

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.

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

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.

EXAMPLES OF CURRENT STANZAS

[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

[Term]

id: GO:0045596
name: negative regulation of cell differentiation
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate
or extent of cell differentiation." [GOC:go_curators]
subset: gosubset_prok
synonym: "down regulation of cell differentiation" EXACT []
synonym: "down-regulation of cell differentiation" EXACT []
synonym: "downregulation of cell differentiation" EXACT []
synonym: "inhibition of cell differentiation" NARROW []
is_a: GO:0045595 ! regulation of cell differentiation
is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051093 ! negative regulation of developmental process

EXAMPLES OF NEW STANZAS

[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
relationship: regulates GO:0006312 ! mitotic recombination
[Term]

id: GO:0045596
name: negative regulation of cell differentiation
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate
or extent of cell differentiation." [GOC:go_curators]
subset: gosubset_prok
synonym: "down regulation of cell differentiation" EXACT []
synonym: "down-regulation of cell differentiation" EXACT []
synonym: "downregulation of cell differentiation" EXACT []
synonym: "inhibition of cell differentiation" NARROW []
is_a: GO:0045595 ! regulation of cell differentiation
is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051093 ! negative regulation of developmental process
relationship: negatively_regulates GO:0030154 ! cell differentiation

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/regulates_relations_examples/go_regtest_withPosNeg_noPF_noXP.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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