Annotation Conf. Call 2017-02-14: Difference between revisions
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***See [http://link.springer.com/protocol/10.1007%2F978-1-4939-3743-1_17 Huntley and Lovering, 2016] and [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039540/ Huntley et al., 2014] | ***See [http://link.springer.com/protocol/10.1007%2F978-1-4939-3743-1_17 Huntley and Lovering, 2016] and [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039540/ 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 LEGO models, relations describe the context in which activities (GO MFs) occur and how activities relate to one another | ||
***[http://noctua.berkeleybop.org/editor/graph/gomodel:5323da1800000002 NEDD4 and the DNA damage response] | |||
=== New Relations for Modifying a Gene's Role in a Biological Process === | === New Relations for Modifying a Gene's Role in a Biological Process === | ||
[https://github.com/geneontology/go-annotation/issues/1517 Link to github Discussion] | [https://github.com/geneontology/go-annotation/issues/1517 Link to github Discussion] |
Revision as of 10:44, 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.
- We have talked about doing something like this for a long time, with the overall goal being a more accurate representation of biology.
- These relations will also allow us to better translate LEGO models into conventional GO annotations.
- The current proposal is to add:
- 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
- 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)