1. Progress on Annotation extension relations32
GO editors agreed on C16 relations
QuickGO graph of relations much less flat 51

2. Progress on Annotation extension relations
David OS transferred all C16 relations Wiki pages to GitHub and created new pages
Rachael and Ruth checked all GitHub pages
Edited where formatting errors existed
Raised tickets for RO file edits required
Identified pages without usage examples
David OS edited RO files and reloaded to GitHub

3. Example GitHub page

4. Example GitHub page

5. Use of relations slated for deprecation
David OS created file of AE annotations
Each annotation row unrolled to give a single AE relation per line (to enable sorting)
Rachael and Ruth looked at use of dependent_on and in_presence_of (over 4000 annotations) and extracted examples of use/misuse
Rama organised AE annotation calls (Rama, Petra, Ruth, Rachael provided examples)
for majority of cases alternative ways of capturing were agreed
In some cases it was agreed that the example was outside range of GO

6. Consistent use of relations
86,600 AE annotations
Ruth, Rachael, Rama reviewed relation use in all annotations
Status of term
No relations
No. annotations
Mostly correct use
20+
>55000
Slated for deprecation 7
~5116
edits required*
~21 ?
not yet in use (May 2015) 15
*Difficult to assess all but some are obvious from just looking:
e.g. 113 MF/BPs part_of (CL or Uberon) should be occurs_in

7. Edits required
...some are obvious from just looking

8. Deprecated terms?
Around 5000 annotations (~6% of extended annotations)
Revise where possible?
What about annotations outside of scope?
Continue to display?
dependent_on ✔
in_absence_of ?
independent_of ✔
in_presence_of ?
localization_dependent_on ✔
requires_substance ✔
requires_sequence_feature ✔
agreed previously
? still to be decided

9. Completion of GitHub page examples
61 relationships
# relationship
GitHub page
Usage example
Folding example
13 * - 25 ✔ 23
Some of the ‘completed’ examples need further discussion
*Causally_upstream_of
no GitHub page, is this controversial?

10. Relations still to be discussed/resolved
dependent_on – decided to deprecate at last call
part_of (GO ID) – use with GO IDs to be revised
in_absence_of
in_presence_of
regulates_o_occurs_in – confusing usage, see later
Petra’s example to be modeled in Noctua

11. Discussions from calls
Many annotations using controversial relations, e.g. dependent_on could be
expressed using a different relation or GO term
Exists_during
-> rename to ‘during’ to avoid confusion?
Requires_substance
-> we should not be recording cofactors, these should be in the definition
of the GO term
-> can use activated_by for activators (needs to be allowed for AE)
Independent_of
-> term is deprecated, but can we capture this type of concept in other ways?
-> we should not make negative terms, e.g. parkin-independent mitophagy

12. Discussions from calls cont’d
In_presence_of/dependent_on
-> we should avoid recording experimental assay details
-> if cofactor, this should be in GO term definition
-> GitHub
In_absence_of (to be discussed further)
annotations: nucleus in_absence_of cAMP
cytosol in_presence_of cAMP
PMID:
“We report here that GtaC exhibits rapid nucleocytoplasmic shuttling in response
to periodic cAMP waves.” p1329

13. regulates_o_occurs_in
label: regulates process that occurs in
Local domain: GO: : regulation of biological process
Definition: A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.
Usage: Use this relation to link a regulatory process or function to the structure that the regulated process or function occurs in.
Currently no examples available on GitHub page
Would expect this to just relate to BPs that involve whole cell processes
Regulation of apoptosis
Regulation of action potential
Regulation of mitotic cell cycle
Some groups using ‘occurs_in’ rather than regulates_o_occurs_in
Regulation of transcription
Regulation of signaling

14. regulates_o_occurs_in cont’d
MGI guidelines
If you are describing the regulatory process, then you should use the
conventional relations (e.g. occurs_in)
If you are describing the GO process or function that is the target of the
regulation, then you should use the chain relation (e.g. regulates_o_occurs_in)
'regulation of transcription, DNA dependent' occurs_in 'fibroblast'
means that the regulatory process occurs in a fibroblast
‘regulation of transcription, DNA dependent' regulates_o_occurs_in 'fibroblast' means that the 'transcription, DNA dependent' occurs in a fibroblast

15. Re-annotation? Terms slated for deprecation Inconsistently used terms
>5000 annotations
Inconsistently used terms
? annotations
Annotations to deprecated terms (e.g. during, not_exists_during)
only 50 left!