Difference between revisions of "Annotation Conf. Call 2017-04-11"

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(Redundant F-P Links)
 
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= Minutes =
 
= Minutes =
*On call: Alice, Chris, Emily, George, Guilia, Helen, Judy, Midori, Moni, Pascale, Petra, Rachael, Shur-Jen, Stan, Tanya, Terry, Suzi, Stacia
+
*On call: Alice, Chris, Emily, George, Guilia, Helen, Judy, Li, Midori, Moni, Pascale, Petra, Rachael, Shur-Jen, Stan, Tanya, Terry, Suzi, Stacia
  
 
== Call Agendas on Github ==
 
== Call Agendas on Github ==
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== Redundant F-P Links ==
 
== Redundant F-P Links ==
*'''AI:''' Create a new ticket, since the existing one has veered in several directions and is a bit confusing
 
 
*F-P links were always intended to just create annotations, using the same evidence code, for terms linked via the ontology
 
*F-P links were always intended to just create annotations, using the same evidence code, for terms linked via the ontology
 
**Some groups could not handle the inter-ontology links, so the annotations were generated
 
**Some groups could not handle the inter-ontology links, so the annotations were generated
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*Multiple annotations can indicate confidence in a given area of the ontology
 
*Multiple annotations can indicate confidence in a given area of the ontology
 
*Redundancy should not affect enrichment analysis
 
*Redundancy should not affect enrichment analysis
*'''AI:''' Need to have better documentation about what will be generated by the inference pipelines
+
*'''AI:Need to have better documentation about what will be generated by the inference pipelines'''
 +
**See [https://github.com/geneontology/go-site/pull/333 github ticket on go-site]
 
*Also note we still have the related issue of getting different annotations between Jenkins run remotely vs locally
 
*Also note we still have the related issue of getting different annotations between Jenkins run remotely vs locally
 +
*[https://github.com/geneontology/go-annotation/issues/1336 github ticket 1336]
  
 
== PAINT Annotation Disputes Tracked Centrally in Github ==
 
== PAINT Annotation Disputes Tracked Centrally in Github ==
*Previously, these issues where tracked in SourceForge
+
*Previously, these issues were tracked in SourceForge
 
*Please create tickets on github geneontology/go-annotation
 
*Please create tickets on github geneontology/go-annotation
 
*Does this create extra work for Protein2GO users?
 
*Does this create extra work for Protein2GO users?
 
*Goal is trying to create a centralized place where PAINT GO annotations queries/disputes can be tracked
 
*Goal is trying to create a centralized place where PAINT GO annotations queries/disputes can be tracked
 
*Annotation queries can come from within GO or outside (e.g. users)
 
*Annotation queries can come from within GO or outside (e.g. users)
 +
*Is it worthwhile to record all annotation queries/disputes in github for the sake of internal documentation?
 +
 +
== Gene Product-Specific GO Terms ==
 +
*Pascale generated a list of gene product-specific terms
 +
*Can these terms be deleted and merged into the appropriate parent?
 +
*'''AI:Pascale will go ahead with the deletions and merges'''
 +
*[https://github.com/geneontology/go-ontology/issues/13219 github ticket 13219]
 +
 +
== Use of New Biological Process Qualifiers ==
 +
*'''AI: Construct queries to generate list of genes/gene products annotated to: 1) regulation term and no MF and/or 2) process term and regulation of the process'''
 +
*[https://github.com/geneontology/go-annotation/issues/1542 github ticket 1542]
 +
 +
== Working Groups ==
 +
=== HTP Experiments ===
 +
*Goal is to define what is meant by HTP experiments
 +
**Google docs for first meeting minutes with discussion and ideas on what is HTP
 +
**Google spreadsheet for listing some papers that have been curated and/or identified as HTP papers
 +
*'''AI: Please take a look at the Google spreadsheet and add any papers from your group that would be relevant to the discussion.'''
 +
*Aiming to have a proposal for the June consortium meeting
 +
*Marcus has created a high throughput evidence code and will review ECO for these codes
 +
*The number of annotations is not as critical as the type of methodology used to perform the experiments
 +
*Need to use ECO codes consistently with other annotation groups, e.g. phenotype curators
 +
*[https://github.com/geneontology/go-annotation/issues/1469 github ticket 1469]
 +
 +
=== 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]
  
  

Latest revision as of 10:45, 11 April 2017

Bluejeans URL

https://bluejeans.com/993661940

Agenda

GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017

Jenkins Pipeline

PAINT Annotation Queries/Disputes Now in Github

  • Tracking PAINT-related annotation queries/disputes in github
  • Example

Ontology Terms that Refer to Specific Gene Products

Proposed new Biological Process Annotation Qualifiers

  • Use of Regulation Terms
  • Gene products annotated to regulation term but no MF annotation
  • Gene products annotated to both a process and regulation of that process

Working Groups

HTP Experiments

Transcription Decision Tree

Minutes

  • On call: Alice, Chris, Emily, George, Guilia, Helen, Judy, Li, Midori, Moni, Pascale, Petra, Rachael, Shur-Jen, Stan, Tanya, Terry, Suzi, Stacia

Call Agendas on Github

  • Will post meeting agenda on github so we can coordinate tickets with actionable items from calls/meetings

GOC Meeting - Corvallis, Oregon, June

  • Register on Pankaj's Google site
  • Also, please add your name to the table at the bottom of the agenda wiki page
  • Agenda is currently a bit free-form, please add your items and the PIs will review and structure
  • Next ontology editors call, editors will discuss what to present in Oregon

Redundant F-P Links

  • F-P links were always intended to just create annotations, using the same evidence code, for terms linked via the ontology
    • Some groups could not handle the inter-ontology links, so the annotations were generated
  • Some duplicates do get generated
    • MGI removes exact duplicates
  • PomBase noticed that less specific terms were being generated
  • Should this be corrected in the code that generates the F-P propagated term?
    • Suzi - yes
  • Some groups do make redundant annotations, even if to a less granular term
  • Multiple annotations can indicate confidence in a given area of the ontology
  • Redundancy should not affect enrichment analysis
  • AI:Need to have better documentation about what will be generated by the inference pipelines
  • Also note we still have the related issue of getting different annotations between Jenkins run remotely vs locally
  • github ticket 1336

PAINT Annotation Disputes Tracked Centrally in Github

  • Previously, these issues were tracked in SourceForge
  • Please create tickets on github geneontology/go-annotation
  • Does this create extra work for Protein2GO users?
  • Goal is trying to create a centralized place where PAINT GO annotations queries/disputes can be tracked
  • Annotation queries can come from within GO or outside (e.g. users)
  • Is it worthwhile to record all annotation queries/disputes in github for the sake of internal documentation?

Gene Product-Specific GO Terms

  • Pascale generated a list of gene product-specific terms
  • Can these terms be deleted and merged into the appropriate parent?
  • AI:Pascale will go ahead with the deletions and merges
  • github ticket 13219

Use of New Biological Process Qualifiers

  • AI: Construct queries to generate list of genes/gene products annotated to: 1) regulation term and no MF and/or 2) process term and regulation of the process
  • github ticket 1542

Working Groups

HTP Experiments

  • Goal is to define what is meant by HTP experiments
    • Google docs for first meeting minutes with discussion and ideas on what is HTP
    • Google spreadsheet for listing some papers that have been curated and/or identified as HTP papers
  • AI: Please take a look at the Google spreadsheet and add any papers from your group that would be relevant to the discussion.
  • Aiming to have a proposal for the June consortium meeting
  • Marcus has created a high throughput evidence code and will review ECO for these codes
  • The number of annotations is not as critical as the type of methodology used to perform the experiments
  • Need to use ECO codes consistently with other annotation groups, e.g. phenotype curators
  • github ticket 1469

Transcription Decision Tree

  • AI: Review annotation decision tree which is linked from the github ticket in go-annotation
  • github ticket 1463