GO-CAM Working Group Call 2018-07-31: Difference between revisions

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== Montreal Meeting - October 17- 19 ==
== Montreal Meeting - October 17- 19 ==
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Logistics]
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Logistics Montreal Logistics]
 
== GO Annotation Meetings ==
*Still will be Tuesdays at 8am PDT
*Proposed meeting schedule:
**1st Tuesday: Alliance Gene Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: ad hoc, as needed
*One Zoom URL for all - https://stanford.zoom.us/j/976175422


== Re-cap of Last Week's Call ==
== Re-cap of Last Week's Call ==
Line 11: Line 21:
===  Modeling Transcription in GO-CAM ===
===  Modeling Transcription in GO-CAM ===
*Sabrina - [http://noctua.berkeleybop.org/editor/graph/gomodel:5a5fc23a00000137 PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.']
*Sabrina - [http://noctua.berkeleybop.org/editor/graph/gomodel:5a5fc23a00000137 PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.']
== Screenshot of Model used for Discussion ==
[[File:Sabrina model 2017-07-24.png|800px|thumb|left]]
*The top part of the model shows alternative representations of the relation between the TF and transcription.
*The part_of relation is the agreed upon correct way to model the relationship between the TF and regulation of transcription.
*Note that this model is still under discussion and not the final version; this screenshot represented the model as of 2018-07-24.


=== Relations between Transcription Factor MFs and Regulation of Transcription BPs ===
=== Relations between Transcription Factor MFs and Regulation of Transcription BPs ===
Line 39: Line 43:
*The curator can model the unknown mechanism of regulation by saying that the TF is part_of regulation of transcription that is causally_upstream_of_or_within the positive or negative regulation of transcription that ultimately controls the expression of the gene.  The gene is then added as 'has input' to the most distal transcriptional regulatory process.
*The curator can model the unknown mechanism of regulation by saying that the TF is part_of regulation of transcription that is causally_upstream_of_or_within the positive or negative regulation of transcription that ultimately controls the expression of the gene.  The gene is then added as 'has input' to the most distal transcriptional regulatory process.


=== Relations between BP and input(s) ===
== Relations between BP and input(s) ==
*Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD
*Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD


=== Relations between BP and MF of transcriptional target ===
== Relations between BP and MF of transcriptional target ==
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002304 causally upstream of, positive effect]
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002304 causally upstream of, positive effect]
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002305 causally upstream of, negative effect]
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002305 causally upstream of, negative effect]


=Minutes=
== Root Node vs Existing Molecular Functions ==
*On call:
 
 
 
=== Root Node vs Existing Molecular Functions ===
*Curators should always try to construct models using the known MF of a gene product, even if that MF was not specifically demonstrated in the paper they are annotating.
*Curators should always try to construct models using the known MF of a gene product, even if that MF was not specifically demonstrated in the paper they are annotating.
*Associated evidence for that MF will always point back to the paper in which the MF was interrogated.  
*Associated evidence for that MF will always point back to the paper in which the MF was interrogated.  
*Creating models in this way will allow us to build on existing knowledge to create the most comprehensive and up-to-date model for a given BP.
*Creating models in this way will allow us to build on existing knowledge to create the most comprehensive and up-to-date model for a given BP.
*If a gene product has more than one MF, curators should use the biological context of the annotated process to select the most appropriate function(s) for that gene product.
*Proposal: if a gene product has more than one MF, curators should use either: 1) experimental data that supports the selection of one function vs another, 2) the common parent of the two functions, or 3) the biological context of the annotated process to select the most appropriate function(s) for that gene product.
 
**Examples: beta-catenin and PDIA6
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


=Minutes=
*On call: Bob, Chris, David, Dustin, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Laurent-Philippe, Marie-Claire, Pascale, Penelope, Ruth, Sabrina, Seth, Stacia, Suzi A, Suzi L,








[[Category: Annotation Working Group]]
[[Category:GO-CAM]]

Latest revision as of 05:48, 16 April 2019

Meeting URL

https://stanford.zoom.us/j/976175422

Agenda

Montreal Meeting - October 17- 19

GO Annotation Meetings

  • Still will be Tuesdays at 8am PDT
  • Proposed meeting schedule:
    • 1st Tuesday: Alliance Gene Function
    • 2nd Tuesday: GO Consortium
    • 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
    • 4th Tuesday: GO-CAM Working Group
    • 5th Tuesday: ad hoc, as needed
  • One Zoom URL for all - https://stanford.zoom.us/j/976175422

Re-cap of Last Week's Call

Modeling Transcription in GO-CAM

Relations between Transcription Factor MFs and Regulation of Transcription BPs

  • Transcription factor activity is 'part_of' regulation of transcription
  • This is consistent with the relations in the ontology and produces the correct annotations in the GPAD output file
  • A consequence of this is that any regulation terms needed for annotation will have to be instantiated in the ontology

General Rule for MFs and Regulation of BPs

  • MFs and BPs are linked by part_of (or other relations, e.g. acts upstream of, acts upstream of or within) but NOT by regulates relations

Relations between MF and Input(s)

  • has_input vs has_direct_input
  • Is there a meaningful distinction between these two relations for MF? What are we really trying to capture with MF inputs?
  • Proposal: review MF annotations using has_input
  • Right now, no changes to GO-CAM models (will continue to use has_input)

Direct vs Unknown Mechanism of Regulation

Capturing Unknown Mechanism of Regulation

  • If it is not known if the TF directly regulates the expression of a gene, then the input for the TF activity is left blank.
    • In this case, however, it is okay to use evidence from another experiment that might have shown different context (i.e. a different gene was regulated) as supporting evidence for the TF activity.
  • The curator can model the unknown mechanism of regulation by saying that the TF is part_of regulation of transcription that is causally_upstream_of_or_within the positive or negative regulation of transcription that ultimately controls the expression of the gene. The gene is then added as 'has input' to the most distal transcriptional regulatory process.

Relations between BP and input(s)

  • Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD

Relations between BP and MF of transcriptional target

Root Node vs Existing Molecular Functions

  • Curators should always try to construct models using the known MF of a gene product, even if that MF was not specifically demonstrated in the paper they are annotating.
  • Associated evidence for that MF will always point back to the paper in which the MF was interrogated.
  • Creating models in this way will allow us to build on existing knowledge to create the most comprehensive and up-to-date model for a given BP.
  • Proposal: if a gene product has more than one MF, curators should use either: 1) experimental data that supports the selection of one function vs another, 2) the common parent of the two functions, or 3) the biological context of the annotated process to select the most appropriate function(s) for that gene product.
    • Examples: beta-catenin and PDIA6

Minutes

  • On call: Bob, Chris, David, Dustin, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Laurent-Philippe, Marie-Claire, Pascale, Penelope, Ruth, Sabrina, Seth, Stacia, Suzi A, Suzi L,