Regulates Meeting Minutes 4

1/23-24/2008 Revision 5.665

Continued on Chris' QC report. NO_target category. Also started to check valid part_of relationships in the 'regulates' file when we came across them.

• NO_TARGET: GO:0021821 "negative regulation of cell-glial cell adhesion involved in cerebral cortex lamination" MSG: cannot find regulated entity term
• NO_TARGET: GO:0021804 "negative regulation of cell adhesion in the ventricular zone" MSG: cannot find regulated entity term
• regulation of blood pressure part_of circulation

Noticed that if a term has the structure 'regulation of process x by y' and process y exists, then 'regulation of process x by y' is_a y.

Can we keep track of the cases where we make things univocal to send them to Larry Hunter? Mark these with a !.

1/28/2008 Revisions 5.669 and 5.671

• example of where regulation of regulation term is ok:

regulation of vasoconstriction

(vasoconstriction is a regulation of blood vessel size)

there's a bonafide process that regulates vasoconstriction, which, in itself regulates a biological quality

maybe revisit JAK kinase example

• pobably need to add parents to regulation of vasoconstriction/dilation to link to neuronal process - consult physiologists

• how about three way logical definitions:

for example negative regulation of microtubule depolymerization in axoneme

1/29/2008 Revisions 5.672

Fixed the following problems that were identified by David Miers test load into MGI.

Here are the parent/child terms in the current GO load that were identified as duplicates:

GO:0001928 is-a GO:0043254

GO:0001928 part-of GO:0043254 removed this relationship

GO:0007348 is-a GO:0009794

GO:0007348 part-of GO:0009794 removed this relationship

GO:0021940 is-a GO:0021936

GO:0021940 part-of GO:0021936 removed this relationship

GO:0021941 is-a GO:0021936

GO:0021941 part-of GO:0021936 removed this relationship

GO:0051580 is-a GO:0051588

GO:0051580 part-of GO:0051588 removed this relationship

GO:0051930 is-a GO:0051931

GO:0051930 part-of GO:0051931 removed this relationship

Continued with Chris' QC report. Thursday, work on the terms that contain the phrase 'mediated by'.

2/05/2008

Personnel: Tanya, Chris and David

• 4 options and time line: realize-neg-and-pos x include-P-F-links

• • Implementing the + and - relationships:

Positives:

It makes the intersection_of tags and the relationships consistent.

It makes the graph more expressive

It makes going forward using the reasoner easier.

Negatives:

It makes the graph more 'tangly'

In a conservative view, the graph stays with the same topology if we don't implement.

• • Do we realize the Process and Function links:

Will it break a lot of tools?

We should hold off on these for now, but make it clear that this is on the horizon. They will remain in the intersection tags. Chris will make a subdirectory of scratch and put very clearly named files in this subdirectory.(go/scratch/regulates_relations_examples with README!!)

We are comfortable with + and -, but no function to process links realized.

• Have we tested enough?

Tanya and David test every day as they work. This is a test of biological accuracy.

Only MGI has done a test load successfully, that we know of. We need to get the other reference genome MODS to test.

• Is everyone in GO comfortable with this?

No, but we plan to have a training tutorial and documentation in place well in advance of the release date.

We will make sure that everyone who edits the ontology has had training in how to create the new terms. (webex, skype, documentation)

• Or are they even paying attention?

Through the training sessions we establish above, we will be sure everyone is aware.

• Are the various software people at the MODs comfortable with the timeline?

By requiring that the MODS do a test load, we will be sure that the software people are comfortable.