2016 Los Angeles GOC Meeting Agenda: Difference between revisions
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=Agenda= | =Agenda= | ||
== Regulation relations == | |||
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. | |||
DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators (David H & Val?) where we can show application to LEGO models. | |||
== Genetic entities in GO annotation == | |||
* What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation? | |||
* What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how? | |||
==Conference Calls== | ==Conference Calls== | ||
*Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST | *Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST | ||
Revision as of 12:42, 27 September 2016
Agenda
Regulation relations
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators (David H & Val?) where we can show application to LEGO models.
Genetic entities in GO annotation
- What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation?
- What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how?
Conference Calls
- Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST
- These areas of annotation, and ontology development, are, or have been, converging for some time now and we think it would be a better use of everyone's time to have one weekly call where we discuss any annotation- or ontology-related issues
Annotation Issues - Conventional Annotations
- Modified protein binding: GO terms & annotations are very inconsistent.
- Recent github issues:
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020 ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320
Annotation Issues - LEGO Annotations (Sunday AM?)
- How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?
- Are we going to allow Noctua to make annotations to the root nodes of the ontology? This would be useful for contextual annotations that are to otherwise root nodes. However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information.
- MGI's experience roundtripping with Noctua Models (DPH)
Production
New data flow (Chris)