Annotation Conf. Call 2017-07-25: Difference between revisions
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*Need feedback on GO Slim and ribbon display on gene pages | *Need feedback on GO Slim and ribbon display on gene pages | ||
*Mary Dolan will provide an overview of the methodology used to generate the slim | *Mary Dolan will provide an overview of the methodology used to generate the slim | ||
Alliance JIRA ticket, curators comment here: https://agr-jira.atlassian.net/browse/AGR-470 | |||
== Signaling Project == | == Signaling Project == | ||
*Update on what pathways have been claimed | *Update on what pathways have been claimed | ||
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= Minutes = | = Minutes = | ||
*On call: David H., Edith, Emily, Giulia, Mary, Midori, Pascale, Paul T., Penelope, Rob, Sabrina, Sage, Shur-Jen, Stacia, Stan, Tanya | *On call: David H., Edith, Emily, Giulia, Harold, Helen, Jim, Mary, Midori, Pascale, Paul T., Penelope, Petra, Rob, Ruth, Sabrina, Sage, Shur-Jen, Stacia, Stan, Sylvain, Tanya, Tom | ||
== Annotation Guidelines for Modified-Protein Binding == | |||
*Discussion began at USC meeting in November 2016 | |||
*Question: How to correctly annotate when binding to a protein is modification-dependent? | |||
**For example, a protein binding ubiquitin vs protein binding that depends on ubiquitin modification | |||
*Solution: create new terms, using the most common types of protein binding that reflect the dependency | |||
**Less frequent modifications would be annotated to the parent term, modification-dependent protein binding | |||
*Comments on term usage have been added to the terms in the ontology | |||
**For example, [http://amigo.geneontology.org/amigo/term/GO:0140034 methylation-dependent protein binding] | |||
*Full documentation will be added to the go-annotation github repository | |||
*Sylvain reviewed annotation errors | |||
**For example, targets of post-translational modifications should not be added to the BP term for the modification | |||
*Annotations that may have been affected by these terms are recorded in the github ticket for this issue | |||
**Curators can review these annotations to make sure that we didn't lose information by merging into the parent term, protein binding | |||
== GO Slims == | |||
*Mary presented slides on construction of AGR GO slim | |||
*Started with experimental annotations for all organisms included in AGR + human | |||
*Select terms based on number of annotations, depth in DAG, information content using an algorithm | |||
**Select terms | |||
***Tended to select terms that had between 200 - 1000 annotations (don't want terms with 30000 annotations) | |||
***Selected terms that are generally 4-7 levels down in the DAG - note that we can always select a parent if a child term is too specific and doesn't have many annotations | |||
**Eliminate parent-child terms | |||
**Then manually analyze the list | |||
***Analyze what terms are in and out | |||
***Analyze what genes are in and out | |||
****It might be worthwhile to include an 'Other' category to capture the genes that don't currently map to a slim | |||
****In AGR, the ribbon display is the main way, right now, that GO annotations will be displayed | |||
**Gene products can fall into more than one bucket of the slim | |||
*Map selected terms onto the graph view of GO terms to see what is/is not included | |||
*Mary also has a view that shows the breakdown of annotations based on contributing group | |||
*Question about terms in F list | |||
**How many reflect the overall function vs part of the mechanism of the function | |||
***For example, metal ion binding - what types of gene products are annotated to these terms? Transporters? Others? | |||
*Mary will make slides available here on the wiki | |||
*Relevant github tickets: | |||
**[https://github.com/geneontology/go-ontology/issues/13013 Slim needed for AGR ribbon view] | |||
**[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim] | |||
*Alliance JIRA ticket: | |||
**https://agr-jira.atlassian.net/browse/AGR-470 | |||
*The AGR slim will be available to all as part of the ontology | |||
*What are the plans, if any, for integrating the AGR slim with the generic GO slim? | |||
*Overall workload - not too time-consuming to generate a slim, much of this can be automated | |||
**Manual review takes a bit more time but is not unbearable (An hour or so for reviewing the whole slim) | |||
*The slim could also be used also to compare what annotations are used in PAINT propagation | |||
== Signaling Project == | |||
*Overview | |||
**Signaling projects are being tracked in [https://github.com/geneontology/go-annotation/projects/4 github go-annotation projects page] | |||
**This high-level page is for tracking tasks that need to be done, not for in-depth discussion of specific issues | |||
**So far, three pathways have been claimed: | |||
***Canonical Wnt | |||
***MAPK | |||
***GPCR | |||
***Ca2+-mediated fertilization | |||
**Reviewed workflow for canonical Wnt signaling | |||
***Review annotations | |||
***Review ontology term definitions, parentage | |||
****For example, where does the pathway start and end? What regulates the pathway? | |||
***Create a GO-CAM model | |||
**For canonical Wnt signaling, spreadsheets and docs are all in [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGM05zSU90VndEYTA GO's Google drive] | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 12:01, 25 July 2017
Meeting URL - NOTE CHANGE TO ZOOM
Agenda
Annotation Guidelines for Modified-Protein Binding
- Pascale and Sylvain will present the guidelines for annotating to modified-protein binding terms
GO Slims
- AGR is including a GO slim on the gene pages
- Launch date for AGR 1.0 is October 2017
- Need feedback on GO Slim and ribbon display on gene pages
- Mary Dolan will provide an overview of the methodology used to generate the slim
Alliance JIRA ticket, curators comment here: https://agr-jira.atlassian.net/browse/AGR-470
Signaling Project
- Update on what pathways have been claimed
- Wnt - Giulia, Helen, Kimberly
- Update on progress to date, github tickets
- MAPK - David H.
- Examining gene products annotated to the process with no experimental support for known MFs
- Thinking about how to define the beginning and parts of the pathway
- Ca2+ Signaling
- Fertilization - Penelope
- GPCR - Pascale, Petra
- Some ontology tickets have been addressed
- Needs global annotation review
- Needs GO-CAM model
- Reminder - discussion on specific github tickets, not on project page
- MAPK - David H.
Minutes
- On call: David H., Edith, Emily, Giulia, Harold, Helen, Jim, Mary, Midori, Pascale, Paul T., Penelope, Petra, Rob, Ruth, Sabrina, Sage, Shur-Jen, Stacia, Stan, Sylvain, Tanya, Tom
Annotation Guidelines for Modified-Protein Binding
- Discussion began at USC meeting in November 2016
- Question: How to correctly annotate when binding to a protein is modification-dependent?
- For example, a protein binding ubiquitin vs protein binding that depends on ubiquitin modification
- Solution: create new terms, using the most common types of protein binding that reflect the dependency
- Less frequent modifications would be annotated to the parent term, modification-dependent protein binding
- Comments on term usage have been added to the terms in the ontology
- For example, methylation-dependent protein binding
- Full documentation will be added to the go-annotation github repository
- Sylvain reviewed annotation errors
- For example, targets of post-translational modifications should not be added to the BP term for the modification
- Annotations that may have been affected by these terms are recorded in the github ticket for this issue
- Curators can review these annotations to make sure that we didn't lose information by merging into the parent term, protein binding
GO Slims
- Mary presented slides on construction of AGR GO slim
- Started with experimental annotations for all organisms included in AGR + human
- Select terms based on number of annotations, depth in DAG, information content using an algorithm
- Select terms
- Tended to select terms that had between 200 - 1000 annotations (don't want terms with 30000 annotations)
- Selected terms that are generally 4-7 levels down in the DAG - note that we can always select a parent if a child term is too specific and doesn't have many annotations
- Eliminate parent-child terms
- Then manually analyze the list
- Analyze what terms are in and out
- Analyze what genes are in and out
- It might be worthwhile to include an 'Other' category to capture the genes that don't currently map to a slim
- In AGR, the ribbon display is the main way, right now, that GO annotations will be displayed
- Gene products can fall into more than one bucket of the slim
- Select terms
- Map selected terms onto the graph view of GO terms to see what is/is not included
- Mary also has a view that shows the breakdown of annotations based on contributing group
- Question about terms in F list
- How many reflect the overall function vs part of the mechanism of the function
- For example, metal ion binding - what types of gene products are annotated to these terms? Transporters? Others?
- How many reflect the overall function vs part of the mechanism of the function
- Mary will make slides available here on the wiki
- Relevant github tickets:
- Alliance JIRA ticket:
- The AGR slim will be available to all as part of the ontology
- What are the plans, if any, for integrating the AGR slim with the generic GO slim?
- Overall workload - not too time-consuming to generate a slim, much of this can be automated
- Manual review takes a bit more time but is not unbearable (An hour or so for reviewing the whole slim)
- The slim could also be used also to compare what annotations are used in PAINT propagation
Signaling Project
- Overview
- Signaling projects are being tracked in github go-annotation projects page
- This high-level page is for tracking tasks that need to be done, not for in-depth discussion of specific issues
- So far, three pathways have been claimed:
- Canonical Wnt
- MAPK
- GPCR
- Ca2+-mediated fertilization
- Reviewed workflow for canonical Wnt signaling
- Review annotations
- Review ontology term definitions, parentage
- For example, where does the pathway start and end? What regulates the pathway?
- Create a GO-CAM model
- For canonical Wnt signaling, spreadsheets and docs are all in GO's Google drive