Annotation Conf. Call 2017-04-11: Difference between revisions
Jump to navigation
Jump to search
(→Agenda) |
|||
(38 intermediate revisions by 2 users not shown) | |||
Line 8: | Line 8: | ||
* [[2017 Corvallis GOC Meeting Agenda]] | * [[2017 Corvallis GOC Meeting Agenda]] | ||
** Please check the table at the bottom of the Agenda page and add your name, if not already there. Also please double-check the information associated with your entry. | ** Please check the table at the bottom of the Agenda page and add your name, if not already there. Also please double-check the information associated with your entry. | ||
== Jenkins Pipeline == | |||
*[https://github.com/geneontology/go-annotation/issues/1544 Redundant annotations coming from Function-Process inter-ontology links] | |||
== PAINT Annotation Queries/Disputes Now in Github == | |||
*Tracking PAINT-related annotation queries/disputes in github | |||
*[https://github.com/geneontology/go-annotation/issues/1546 Example] | |||
== Ontology Terms that Refer to Specific Gene Products == | == Ontology Terms that Refer to Specific Gene Products == | ||
*[https://github.com/geneontology/go-ontology/issues/13219 Ticket on geneontology/go-ontology] | *[https://github.com/geneontology/go-ontology/issues/13219 Ticket on geneontology/go-ontology] | ||
*Proposal is to remove ontology terms that refer to specific gene products | *Proposal is to remove ontology terms that refer to specific gene products | ||
== Proposed new Biological Process Annotation Qualifiers == | |||
*[https://github.com/geneontology/go-annotation/issues/1542 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 === | |||
*Held first call on 2017-03-21 | |||
**[https://docs.google.com/document/d/1Gd6cRQh67QZQ2_T7kQjqYMpkfJ_Wqm0baVpyMdFPRHs/edit Agenda/Minutes] | |||
**[https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0 Google spreadsheet documenting HTP experiments] | |||
=== Transcription Decision Tree === | |||
*Reminder to review latest version linked from [https://github.com/geneontology/go-annotation/issues/1463 github ticket] | |||
= Minutes = | = 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''' | |||
**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 | |||
*[https://github.com/geneontology/go-annotation/issues/1336 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''' | |||
*[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] | |||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Latest revision as of 13:45, 11 April 2017
Bluejeans URL
https://bluejeans.com/993661940
Agenda
GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017
- Logistics: https://sites.google.com/view/goc2017
- 2017 Corvallis GOC Meeting Agenda
- Please check the table at the bottom of the Agenda page and add your name, if not already there. Also please double-check the information associated with your entry.
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
- Ticket on geneontology/go-ontology
- Proposal is to remove 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
- Held first call on 2017-03-21
Transcription Decision Tree
- Reminder to review latest version linked from github ticket
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