Annotation Conf. Call 2017-02-14: Difference between revisions
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*Note the differences between the relations for GAF/GPAD and the relations used in LEGO models due to the nature of what is being related, i.e. gene to GO term in the former and GO term to another GO term in LEGO. | *Note the differences between the relations for GAF/GPAD and the relations used in LEGO models due to the nature of what is being related, i.e. gene to GO term in the former and GO term to another GO term in LEGO. | ||
**Example translation: | **Example translation: | ||
***LEGO 'causally upstream of' | ***LEGO: 'causally upstream of' | ||
***GAF/GPAD 'acts upstream of' | ***GAF/GPAD: 'acts upstream of' | ||
*For discussion: | *For discussion: | ||
**Use of 'within' vs 'involved_in' | **Use of 'within' vs 'involved_in' |
Revision as of 11:02, 14 February 2017
Bluejeans URL
Agenda
Meeting Reminder
- Next Consortium Meeting: June 1-3, 2017 in Corvallis, Oregon
- Noctua Workshop on June 4th
- Reactome Workshop on June 5th
Qualifiers and Relations in GO
- Qualifiers are used in GAF and GPAD
- Modify the meaning of the association between a gene/gene product and GO term
- colocalizes_with
- contributes_to
- NOT
- Documentation on Qualifier Use
- Relations are used in GPAD, Annotation Extensions, and LEGO models
- In GPAD, the explicit relations between a gene/gene product and GO terms are ontology-specific:
- involved_in a BP
- enables a MF
- part_of a CC
- Annotation extension relations 'extend' the meaning of the GO term, providing additional biological context
- For example, nucleus part_of(body wall muscle cell) or protein localization to nucleus has_input(pcf2)
- See Huntley and Lovering, 2016 and Huntley et al., 2014
- In LEGO models, relations describe the context in which activities (GO MFs) occur and how activities relate to one another
- In GPAD, the explicit relations between a gene/gene product and GO terms are ontology-specific:
New Relations for Modifying a Gene's Role in a Biological Process
- This issue is about adding more relations to the list that curators currently use to describe the relationship between a gene/gene product and a BP GO term, again, with the overall goal being a more accurate representation of biology.
- We have talked about doing something like this for some time wrt conventional annotations, and we need them to translate LEGO annotations back to GPAD/GAF formats.
- The current proposal is to add the following relations to the 'qualifier' column of GAF and GPAD to better describe the relationship between a gene product and a GO term:
- acts_upstream_of_or_within
- acts_upstream_of
- involved_in_regulation_of
- involved_in_or_involved_in_regulation_of
- involved_in
- involved_in_regulation_of
- involved_in_negative_regulation_of
- involved_in_positive_regulation_of
- acts_upstream_of
- acts_upstream_of_or_within
- Note the differences between the relations for GAF/GPAD and the relations used in LEGO models due to the nature of what is being related, i.e. gene to GO term in the former and GO term to another GO term in LEGO.
- Example translation:
- LEGO: 'causally upstream of'
- GAF/GPAD: 'acts upstream of'
- Example translation:
- For discussion:
- Use of 'within' vs 'involved_in'
- Definitions
- Formal definitions exist, but curators would like guidance on how experimental results inform selection of a given relation
- LEGO GPAD outputs
- How will LEGO annotations translate back to GPAD annotations, specifically wrt regulates relations?
- Where can curators view all of the relations used in GO, their definitions, and usage statements and examples?
- See email thread from last week with subject: documentation for AE
- GO website
- Annotation Documentation
- Ontology browser
- GO wiki
- github
- Google docs
- OLS
- Protege
- GO website
Jenkins Jobs
- GOC-OWL Inference Pipeline
- Currently suspended?
February 28th Call
- Discussion of LEGO Models
- Sabrina (ZFIN)
- Midori (PomBase)