Annotation Conf. Call 2017-05-09: Difference between revisions
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= Agenda = | = Agenda = | ||
== Annotation and Ontology Proposals == | |||
=== Modification-Dependent Protein Binding === | |||
*Proposal from Pascale and Sylvain emailed | |||
*Would like to review and approve proposal on this call | |||
=== Transcription Decision Tree === | |||
*'''AI: Review annotation decision tree which is linked from the github ticket in go-annotation''' | |||
*[https://github.com/geneontology/go-annotation/issues/1463 github ticket 1463] | |||
== Annotation Guidelines == | == Annotation Guidelines == | ||
=== Review Annotation Guidelines for Cellular Component (CC) Annotations === | === Review Annotation Guidelines for Cellular Component (CC) Annotations === | ||
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***ZP3 (zona pellucida glycoprotein of oocyte) to 'outer acrosomal membrane' (of sperm cell) | ***ZP3 (zona pellucida glycoprotein of oocyte) to 'outer acrosomal membrane' (of sperm cell) | ||
**What if you don't know whether a subcellular location is a site of molecular activity? | **What if you don't know whether a subcellular location is a site of molecular activity? | ||
=== Use of colocalizes_with Qualifier === | === Use of colocalizes_with Qualifier === | ||
*[http://geneontology.org/page/go-annotation-conventions#colocal Current documentation]: | *[http://geneontology.org/page/go-annotation-conventions#colocal Current documentation]: | ||
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pole body and the contractile ring (evidence from GFP fusion). Clp1p is annotated to spindle pole body; GO:0005816 and contractile | pole body and the contractile ring (evidence from GFP fusion). Clp1p is annotated to spindle pole body; GO:0005816 and contractile | ||
ring; GO:0005826, using the colocalizes_with qualifier in both cases. | ring; GO:0005826, using the colocalizes_with qualifier in both cases. | ||
= Minutes = | = Minutes = |
Revision as of 13:26, 8 May 2017
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Agenda
Annotation and Ontology Proposals
Modification-Dependent Protein Binding
- Proposal from Pascale and Sylvain emailed
- Would like to review and approve proposal on this call
Transcription Decision Tree
- AI: Review annotation decision tree which is linked from the github ticket in go-annotation
- github ticket 1463
Annotation Guidelines
Review Annotation Guidelines for Cellular Component (CC) Annotations
- Many gene products can be found in multiple places within the cells in which they are expressed
- Soluble secreted proteins and transmembrane proteins can be found in a number of different cytoplasmic compartments (ER, Golgi, vesicles) as they traverse the secretory pathway
- Internalized receptors can be found in endocytic vesicles
- Transcriptional regulators can shuttle between the cytoplasm and the nucleus
- Secreted ligands can be found in the extracellular space and the external side of a plasma membrane when they are bound to their receptor
- The curation guidelines for CC annotation are to annotate the gene product to the cellular/extracellular location where it is believed to be active
- For some gene products this will be very clear
- There are some cases where receptors found at the plasma membrane are also found to be involved in signaling pathways that occur at other locations
- PACAP1 receptor - endocytic vesicle
- Trk - Golgi
- Is it appropriate to annotate a membrane protein that is a ligand for a signalling pathway in another cell to a location that is in that other cell?
- ZP3 (zona pellucida glycoprotein of oocyte) to 'outer acrosomal membrane' (of sperm cell)
- What if you don't know whether a subcellular location is a site of molecular activity?
Use of colocalizes_with Qualifier
Gene products that are transiently or peripherally associated with an organelle or complex may be annotated to the relevant cellular component term, using the colocalizes_with qualifier. This qualifier may also be used in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member. Example (from Schizosaccharomyces pombe): Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p is annotated to spindle pole body; GO:0005816 and contractile ring; GO:0005826, using the colocalizes_with qualifier in both cases.