Meeting Minutes 3:Stanford

From GO Wiki
Jump to navigation Jump to search

Implementation Meeting 14 January, 2008

David Hill, Tanya Berardini, Chris Mungall all at TAIR (Carnegie)

Tried to pull out all 'biological qualities' from the regulation of BQ terms in order to see if they map to existing PATO terms. Initial mapping attempts were unsuccessful.

Looked at Chris' error report:


UNEXPECTED: finding terms that are children of ROBQ for which the BQ is not expected to be found in GO but the term really does exist in GO, the question then is, should they be is_a children of ROBQ or not?

OK: ignore

HIERARCHY: term has both ROMF and ROBP as is-a parents

will also detect cases where just one is_a parent to the regulation upper term but it is the wrong kind (i.e. a reg of MF sub-term that only traces up to ROBP)

MISSING_LINK: terms that should be under biological regulation via a direct is_a path but are not

NP: no parse, this category probably includes terms that D and T have already looked at and decided were ok types of a legitimate regulates parent, Chris will modify this code to discriminate between the ones already checked and those that haven't been.

Working with the following file:


reasoner run on Chris' machine in batch mode, then saved, then had intersection tags removed

rough outline of steps:

loaded in OBOEdit 2.0

ran reasoner

Edit -> assert implied links

Reviewed and accepted the removal of redundant links.

Save in OBO 1.2 format.

substitute part_of for regulates/positively regulates/negatively regulates (switch back to part_of since regulates is not yet live to the community)

remove interontology links from process to function (like regulation of MF is part_of MF)

ACTION ITEM: (D and T, to be reviewed by Jen and Midori)

Create email for announcement of 'regulates' relationship implementation.

ACTION ITEM: update documentation for regulation terms, regulates relationships

Draft letter, regulates announcement

Subject: new relationship types in GO

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.


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.



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



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

We strongly suggest that you test your loading scripts to ensure that your database doesn't go down in flames. There is a test OBO 1.2 file available at:


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


The GOC regulates working group

Meeting Minutes, Day 2, 15 January 2008

David Hill, Tanya Berardini, Chris Mungall at TAIR (Carnegie)

Reviewed diff between regulation-nugo-fixed.obo and current gene_ontology_edit.obo. All proposed new relationships are ok. Confirmed that redundant links have been removed.

Put up draft letter for 'regulates' premiere for review.

Skype conversation with Midori and Jen to bring them up-to-date on yesterday's progress.

Removed TypeDefs for 'regulates' relationships from .obo file before committing changes.

Chris reran analysis and file processing scripts on latest gene_ontology_edit.obo file and we committed this to the repository after sanity check. Revision 5.647.

   969 new links
   302 deleted links

Worked through Chris' QC report after the rerun on new, committed file:

new QC report name: /scratch/regulation-report.txt




NO_TARGET: almost all ROBQ and ROMF children or ones that were ok subchildren of higher level ROBPs: 383 (STARTED)

NP (NO PARSE): appear to be subclasses of 'regulation' terms that are not named 'regulation of %':1091


Issues with new file:
Regulation of receptor activity has now inherited a regulation of some type of binding because receptor activity is_a binding. However the regulation of the receptor is not always a regulation of the binding, so we needed to go through and delete those.

Other discussions:
We talked about the relationships between function and process due to the ability of a regulates term to be both a RoMF and RoBP. We decided we will need both part_of and has_part relationships for the MF to BP links

Second error report: scratch/regulation-unimplied-links.txt

These represent cases where the regulates hierarchy doesn't match the process hierarchy.