[Go] Attn DB admins : Introduction of New Relationship Types in GO (March 25, 2008)

[Chris Mungall]

Hi all

I'm contacting you because your name is listed as being one of the  
technical contacts for a database that is affiliated with the GO  
consortium[*].

As previously announced on the gofriends list, the Gene Ontology is  
introducing 3 new relations: regulates, negatively_regulates and  
positively_regulates. This requires no changes to the logic of any  
software or databases that use the GO. However, any special purpose  
code or configurations for rendering relations as icons, images or  
short symbols may need changed.

If you wish to use the same SVGs as oboedit or the same pngs/gifs as  
AmiGO, you can download any of the icons here:
http://obofoundry.org/ro/icons/

See the email below for full details

If you had not previously received notice of this change and need  
more time to test let me know, otherwise the new relations will go  
live this week.

Let me know if you have any other questions

--
Chris

[*] See:
http://wiki.geneontology.org/index.php/External_Database_Contact_Info


Begin forwarded message:

> From: "Tanya Berardini" <tberardi at acoma.Stanford.EDU>
> Date: February 26, 2008 2:04:24 PM PST
> To: "GO LIST" <go at genome.stanford.edu>, gofriends at genome.stanford.edu
> Subject: [gofriends] SECOND ANNOUNCEMENT: Introduction of New  
> Relationship Types in GO (March 25, 2008)
>
> 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