Annotation Conf. Call 2017-12-12: Difference between revisions
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= Agenda = | = Agenda = | ||
== Infrastructure == | |||
*[http://skyhook.berkeleybop.org/snapshot/metadata/users-and-groups-report.txt Report on missing orcids and groups in users.yaml file] | |||
*[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] | |||
**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 == | == 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: | |||
**Annotation review | **Annotation review | ||
**PAINT family review | **PAINT annotation/family review | ||
**Keyword mapping questions | **Keyword mapping questions, e.g. InterPro2GO | ||
**Questions about annotation practice | **Questions about annotation practice | ||
** | **Requests/proposals for annotation guidelines | ||
**Requests for documentation | ***Requests for [https://github.com/geneontology/go-site/tree/master/metadata/rules annotation rules] | ||
***Requests for documentation | |||
*Use of labels | *Use of labels | ||
**Please always add a label to your issue | |||
**Trying to simplify the list of labels | **Trying to simplify the list of labels | ||
**Removed some that were overlapping, not applicable to this repo | **Removed some that were overlapping, not applicable to this repo | ||
**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 | ||
* | *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 ==== | |||
*[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)] | |||
**Pending discussion with experts | |||
*Upgrade existing annotations to more specific pathway than 'Wnt signaling pathway' wherever possible | |||
== 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 == | |||
*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 12:51, 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
- Requests for annotation rules
- Requests for documentation
- 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
- Review annotations to beta catenin
- MGI review
- 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
- 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://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.