13 JULY 2010 RefGen Phone Conference (Archived): Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 26: Line 26:


Becky and Susan responded to the accompanying SourceForge item, felt that binding captured the function sufficiently.
Becky and Susan responded to the accompanying SourceForge item, felt that binding captured the function sufficiently.
'''SourceForge Items'''
Quite a few SF items related to Wnt project; curators, please keep an eye on these and comment, as needed.


==GO camp action items==
==GO camp action items==

Revision as of 14:13, 13 July 2010

Present

wnt project

Ontology Issues

Canonical vs Non-Canonical Wnt Signaling

Varsha: Split into canonical or non-canonical?

Stan: Yes, authors usually make that distinction in the papers.

Molecular Function for Wnts

Varsha: email that Ruth sent to Ref Genome list

Ruth wanted to have a better way of describing the molecular function of Wnts, e.g. Wnt ligand activity?

What do people think about that?

What functions would be suggested?

Some type of signaling activity other than just binding to the receptor.

Susan: Is Ruth striving to describe the class of protein rather than the actual function? Does the molecular function extend beyond the binding?

Becky and Susan responded to the accompanying SourceForge item, felt that binding captured the function sufficiently.

SourceForge Items

Quite a few SF items related to Wnt project; curators, please keep an eye on these and comment, as needed.

GO camp action items

  • Send final guidelines to Rachael/Pascale for inclusion on the GO wiki

Binding group action items

  • Unresolved issues to be discussed by binding group

1. Annotation of 'NOT' binding a specific protein: new GO term or column 16 (consider IntAct guidelines on this)?

2. Automate annotation to specific binding term from known functions of protein, eg transcription factor binding, based on evidence that protein is transcription factor, or domain implied? Or not create this type of term?

3. Transferring cross species information by ISS and inclusion of non in-vivo targets in column 8 or 16.

4. How specific to make substrate/product target information?

5. Will CHEBI IDs in function ontology propagate to process terms?

6. Existing GO to follow new has_part relationships implying substrate binding

  • Unresolved issues to be discussed by other groups:

1. Incorporation of IMEX data being discussed

2. Col 16 relationship ontology (has_input=substrate)

Response group action items

1. Update definition of response to terms to indicate that we are capturing mediators (wording needs to be worked out)

Protein complexes group action items

1. Long term goal is to annotate complexes; details and requirements need to be clarified.

Downstream Process group action items

1. What is the process term for a specific transcription factor? (i.e. 'transcription' or 'regulation of transcription'?) ACTION: transcription ontology revision

2. Define the start and end of signaling processes. ACTION: signaling working group

3. Is a ligand part of the pathway? Can it also regulate the pathway? Is there a difference between intra- and inter-cellular pathways regarding the ligand?

4. Some MODs keep legacy annotations (i.e. correct annotations to downstream processes), but some prefer to remove them, is this a problem? ACTION: all

5. Form a working group to look into phenotype/development/IMP issues. How should we annotate to development terms?

6. Regarding the survey question 2, whether to annotate ubiquitin ligases to regulation of histone methylation, Val will give reasons why she would like to annotate to regulation of histone methylation. The ontology may need altering to reflect the step-by-step nature of this pathway. ACTION: Val/Sylvain/Ontology editors

Quality control checks

1. High level ‘response to’ terms should not directly be used for annotation

2. Avoid annotations to GO: MF by IPI (except for ‘protein binding’ and children)

3. Check for less-granular and more-granular annotation from the same path (soft check)

PAINT-generated GAF files