Ontology meeting 2023-01-30: Difference between revisions
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(Created page with "=Editors discussion items= ==Announcements== ===Annotation reviews at MGI=== * Li (@LiNiMGI) will be replacing Harold for annotation tickets review. * The group-contacts.csv file has been updated: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv ===GOC consortium=== * April 27th-29th, Padua, Italy * If you plan to attend, please register ASAP. geneontology.ticketleap.com/goc2023 password: goc2023 ===Update missing MetaCyc2GO mappings...") |
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* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul | |||
* '''Present:''' Pascale, Harold, Raymond, Val, Edith, Jim, Tanya, Karen, Kimberly, David, Chris, Peter, Paul | |||
* '''Regrets: ''' | |||
* | |||
* | =Announcements= | ||
==GOC consortium== | |||
* April 27th-29th, Padua, Italy | * April 27th-29th, Padua, Italy | ||
* If you plan to attend, please register ASAP. | * If you plan to attend, please register ASAP. | ||
geneontology.ticketleap.com/goc2023 | geneontology.ticketleap.com/goc2023 | ||
password: goc2023 | password: goc2023 | ||
==Annotation reviews at MGI== | |||
* Li (@LiNiMGI) will be replacing Harold for annotation tickets review. | |||
* The group-contacts.csv file has been updated: | |||
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv | |||
=Editors discussion items= | |||
===Update missing MetaCyc2GO mappings for SGD YeastPathways | ==introduce Molecular Event class to GOPlus== | ||
Close? | |||
https://github.com/geneontology/go-ontology/issues/19960 | |||
=Script to download annotations= | |||
https://github.com/geneontology/simple-report-system | |||
# Create New issue | |||
# Paste GO term(s) (1 or many) | |||
# Select report using the labels: | |||
#* "direct_ann_to_list_of_terms": all direct EXP annotations to the terms entered | |||
#* "reg_ann_to_list_of_terms": all EXP annotations to the term entered, plus all children (including regulates children) | |||
# Navigate to the [https://github.com/geneontology/simple-report-system/tree/main/reports reports] (can also go via the [https://github.com/geneontology/simple-report-system simple-report-system link] at the top | |||
# Select the report that corresponds to the ticket number | |||
# Copy to clipboard - best to do it from "edit" mode (for Pascale - mac + firefox) | |||
# Make a copy of the [https://docs.google.com/spreadsheets/d/1z496xuif_6RrooHLW4kKl0ob-GiZ_JPc0qd7Vv19RyE/edit#gid=0 New Annotation Review Template] | |||
# Paste annotations | |||
#* Results: copying from edit mode versus 'normal': https://docs.google.com/spreadsheets/d/1Tbnpc-rDzIgjacEc6vs5eHU6EU2zvQTJjilF3HstrCE/edit#gid=0 | |||
# Sort by Assigned by, then by reference | |||
* NOTE: If you dont add the label AT ISSUE CREATION it doesnt work (to be confirmed) | |||
* It might be nice to get another report: number of EXP, IEA, Others, for a list of GOIDs, showing 0 for terms with no annotations | |||
==Update missing MetaCyc2GO mappings for SGD YeastPathways== | |||
Jim, Chris | Jim, Chris | ||
https://github.com/geneontology/go-ontology/issues/24597 | https://github.com/geneontology/go-ontology/issues/24597 | ||
Line 22: | Line 51: | ||
====Obsolete BPs "regulation MF"==== | ====Obsolete BPs "regulation MF"==== | ||
https://github.com/geneontology/go-ontology/projects/34?add_cards_query=is%3Aopen | https://github.com/geneontology/go-ontology/projects/34?add_cards_query=is%3Aopen | ||
=Tickets by ontology editors= | =Tickets by ontology editors= |
Latest revision as of 09:51, 31 January 2023
- Group members: Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
- Present: Pascale, Harold, Raymond, Val, Edith, Jim, Tanya, Karen, Kimberly, David, Chris, Peter, Paul
- Regrets:
Announcements
GOC consortium
- April 27th-29th, Padua, Italy
- If you plan to attend, please register ASAP.
geneontology.ticketleap.com/goc2023
password: goc2023
Annotation reviews at MGI
- Li (@LiNiMGI) will be replacing Harold for annotation tickets review.
- The group-contacts.csv file has been updated:
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv
Editors discussion items
introduce Molecular Event class to GOPlus
Close? https://github.com/geneontology/go-ontology/issues/19960
Script to download annotations
https://github.com/geneontology/simple-report-system
- Create New issue
- Paste GO term(s) (1 or many)
- Select report using the labels:
- "direct_ann_to_list_of_terms": all direct EXP annotations to the terms entered
- "reg_ann_to_list_of_terms": all EXP annotations to the term entered, plus all children (including regulates children)
- Navigate to the reports (can also go via the simple-report-system link at the top
- Select the report that corresponds to the ticket number
- Copy to clipboard - best to do it from "edit" mode (for Pascale - mac + firefox)
- Make a copy of the New Annotation Review Template
- Paste annotations
- Results: copying from edit mode versus 'normal': https://docs.google.com/spreadsheets/d/1Tbnpc-rDzIgjacEc6vs5eHU6EU2zvQTJjilF3HstrCE/edit#gid=0
- Sort by Assigned by, then by reference
- NOTE: If you dont add the label AT ISSUE CREATION it doesnt work (to be confirmed)
- It might be nice to get another report: number of EXP, IEA, Others, for a list of GOIDs, showing 0 for terms with no annotations
Update missing MetaCyc2GO mappings for SGD YeastPathways
Jim, Chris https://github.com/geneontology/go-ontology/issues/24597
Bulk updates
Obsoleting large sets of terms
Obsolete BPs "regulation MF"
https://github.com/geneontology/go-ontology/projects/34?add_cards_query=is%3Aopen