Difference between revisions of "Annotation Conf. Call 2017-12-12"

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(HTP annotations)
 
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*[https://github.com/geneontology/go-site/blob/master/metadata/users.yaml users.yaml]
 
*[https://github.com/geneontology/go-site/blob/master/metadata/users.yaml users.yaml]
 
*[https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml groups.yaml]
 
*[https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml groups.yaml]
 +
**Some groups still need to be added, e.g. UniProt (GOA, Swiss-Prot)
 
*Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.  
 
*Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.  
 
*This means that:
 
*This means that:
Line 14: Line 15:
 
== github review ==
 
== github review ==
 
*go-annotation tracker is used for issues and project management related to the annotation working group
 
*go-annotation tracker is used for issues and project management related to the annotation working group
 +
*All curators who need to work on an issue should be listed in the Assignee field
 +
**Remove your name from the list when you've addressed or complete the work
 
*Types of issues:
 
*Types of issues:
 
**Annotation review
 
**Annotation review
Line 28: Line 31:
 
**Would like to move from using group labels to tracking submission via author
 
**Would like to move from using group labels to tracking submission via author
 
***is:issue author:vanaukenk  
 
***is:issue author:vanaukenk  
*All curators who need to work on an issue should be listed in the Assignee field
 
**Remove your name from the list when you've addressed or complete the work
 
 
*Notifications
 
*Notifications
 
**Not watching - will be notified when you are specifically mentioned (@yourname) or comment
 
**Not watching - will be notified when you are specifically mentioned (@yourname) or comment
Line 38: Line 39:
 
==== Canonical Wnt Signaling Pathway ====
 
==== Canonical Wnt Signaling Pathway ====
 
*[https://github.com/geneontology/go-annotation/issues/1714 Review annotations to beta catenin]
 
*[https://github.com/geneontology/go-annotation/issues/1714 Review annotations to beta catenin]
 +
**MGI review
 
*[https://github.com/geneontology/go-annotation/issues/1713 Review annotation to 'receptor ligand activity' (GO:0048018)]
 
*[https://github.com/geneontology/go-annotation/issues/1713 Review annotation to 'receptor ligand activity' (GO:0048018)]
 +
**Pending discussion with experts
 +
*Upgrade existing annotations to more specific pathway than 'Wnt signaling pathway' wherever possible
  
 
== HTP annotations ==
 
== HTP annotations ==
 
*Continue to check and update evidence codes as needed.
 
*Continue to check and update evidence codes as needed.
 +
*New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"
 +
https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit?ts=58d39700#gid=2144791301
 +
*https://github.com/geneontology/go-annotation/issues/1655
 +
*Generated by splitting out the experimental evidence codes and collating the papers with >40 lines of annotation per paper/per evidence code.
 +
*For most contributors, I have been able to do this directly from the GAF they submit to the GOC so that any DB-specific refs are included and any other sources that are incorporated into the anointed set.
 +
*For a few others, indicated on the sheet, had to download them from QuickGO.
 +
*Note: As they have been separated on evidence code, same paper may feature on separate lines.
 +
*Note: Only equivalent evidence codes to HTPs looked at (EXP, IDA, IEP, IGI, IMP).
  
 
== Progress Reports ==
 
== Progress Reports ==
*Due  
+
*Due this month
   
+
*http://wiki.geneontology.org/index.php/Grant_Progress_reports_2017
 +
 
 +
== Next Call ==
 +
*Tuesday, January 9th, 2018
 +
 
 +
== Upcoming Working Meetings ==
 +
*Docathon - Berkeley, January 22nd - 26th
 +
**Annotation, Pipelines
 +
*Ontology Editors - Denver, February 12th - 16th
 +
**github backlog
 +
**Please review old tickets and comment or close, as needed
 +
 
 +
= Minutes =
 +
*On call: David H., Edith, George, Giulia, Harold, Karen, Kevin, Kimberly, Midori, Paul T., Petra, Rob, Sabrina, Shur-Jen, Stacia, Stan, Tanya
 +
 
 +
== Infrastructure ==
 +
*Nearly all current curators and users are okay wrt the users.yaml file
 +
*UniProt will be sorting out this week how they should be represented
 +
 
 +
== github review ==
 +
*Reviewed tracker use, labels, assignees, watching
 +
*Need to confirm what is the best way to track issues according to group
 +
 
 +
== Annotation Review ==
 +
=== Signaling Project ===
 +
*MGI will review outstanding annotations for beta-catenin
 +
*Waiting to hear back from Ruth's group on the receptor ligand activity annotation
 +
*Will resume signaling workshop follow-up work next year
 +
 
 +
== HTP annotations ==
 +
*If they haven't already done so, curators need to review potential HTP annotations and update them in their local curation tool.
 +
*Guidelines for HTP evidence codes will be included in evidence code guidelines.
 +
*Need to confirm with Helen about final status of Google doc.
 +
 
 +
== Progress Reports ==
 +
*Due the end of this week.
 +
*Please put on the wiki.
 +
*Will confirm with PIs about exact date, formats.
 +
 
 +
== Next Call ==
 +
*Tuesday, January 9th, 2018
 +
 
 +
== Upcoming Working Meetings ==
 +
*Docathon - Berkeley, January 22nd - 26th
 +
**Annotation, Pipelines
 +
*Ontology Editors - Denver, February 12th - 16th
 +
**github backlog
 +
**Please review old tickets and comment or close, as needed
 +
**The week of the github review we will be asking curators to respond to older tickets as we review them.
  
 +
   
 
[[Category:Annotation Working Group]]
 
[[Category:Annotation Working Group]]

Latest revision as of 09:51, 12 December 2017

Meeting URL

Agenda

Infrastructure

  • Report on missing orcids and groups in users.yaml file
  • users.yaml
  • groups.yaml
    • Some groups still need to be added, e.g. UniProt (GOA, Swiss-Prot)
  • Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.
  • This means that:
    • 1) if the load fails the report may not be there (which is a good thing)
    • 2) there will times every day during regeneration when the report is not yet there

github review

  • go-annotation tracker is used for issues and project management related to the annotation working group
  • All curators who need to work on an issue should be listed in the Assignee field
    • Remove your name from the list when you've addressed or complete the work
  • Types of issues:
    • Annotation review
    • PAINT annotation/family review
    • Keyword mapping questions, e.g. InterPro2GO
    • Questions about annotation practice
    • Requests/proposals for annotation guidelines
  • Use of labels
    • Please always add a label to your issue
    • Trying to simplify the list of labels
    • Removed some that were overlapping, not applicable to this repo
    • Would like to move from using group labels to tracking submission via author
      • is:issue author:vanaukenk
  • Notifications
    • Not watching - will be notified when you are specifically mentioned (@yourname) or comment
    • Watching - will be notified of all activity

Annotation Review

Signaling Project

Canonical Wnt Signaling Pathway

HTP annotations

  • Continue to check and update evidence codes as needed.
  • New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"

https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit?ts=58d39700#gid=2144791301

  • https://github.com/geneontology/go-annotation/issues/1655
  • Generated by splitting out the experimental evidence codes and collating the papers with >40 lines of annotation per paper/per evidence code.
  • For most contributors, I have been able to do this directly from the GAF they submit to the GOC so that any DB-specific refs are included and any other sources that are incorporated into the anointed set.
  • For a few others, indicated on the sheet, had to download them from QuickGO.
  • Note: As they have been separated on evidence code, same paper may feature on separate lines.
  • Note: Only equivalent evidence codes to HTPs looked at (EXP, IDA, IEP, IGI, IMP).

Progress Reports

Next Call

  • Tuesday, January 9th, 2018

Upcoming Working Meetings

  • Docathon - Berkeley, January 22nd - 26th
    • Annotation, Pipelines
  • Ontology Editors - Denver, February 12th - 16th
    • github backlog
    • Please review old tickets and comment or close, as needed

Minutes

  • On call: David H., Edith, George, Giulia, Harold, Karen, Kevin, Kimberly, Midori, Paul T., Petra, Rob, Sabrina, Shur-Jen, Stacia, Stan, Tanya

Infrastructure

  • Nearly all current curators and users are okay wrt the users.yaml file
  • UniProt will be sorting out this week how they should be represented

github review

  • Reviewed tracker use, labels, assignees, watching
  • Need to confirm what is the best way to track issues according to group

Annotation Review

Signaling Project

  • MGI will review outstanding annotations for beta-catenin
  • Waiting to hear back from Ruth's group on the receptor ligand activity annotation
  • Will resume signaling workshop follow-up work next year

HTP annotations

  • If they haven't already done so, curators need to review potential HTP annotations and update them in their local curation tool.
  • Guidelines for HTP evidence codes will be included in evidence code guidelines.
  • Need to confirm with Helen about final status of Google doc.

Progress Reports

  • Due the end of this week.
  • Please put on the wiki.
  • Will confirm with PIs about exact date, formats.

Next Call

  • Tuesday, January 9th, 2018

Upcoming Working Meetings

  • Docathon - Berkeley, January 22nd - 26th
    • Annotation, Pipelines
  • Ontology Editors - Denver, February 12th - 16th
    • github backlog
    • Please review old tickets and comment or close, as needed
    • The week of the github review we will be asking curators to respond to older tickets as we review them.