GO-CAM July 12th, 2017: Difference between revisions
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*Link to GPADs generated by Jim's code - much more complete, but still some issues with evidence; not species-specific files yet | *Link to GPADs generated by Jim's code - much more complete, but still some issues with evidence; not species-specific files yet | ||
**http://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/gpad | **http://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/gpad | ||
=== Handling evidence properly === | |||
*No progress to report this week | |||
=== Handling groups as output in the GPAD file === | |||
*Minerva needs to be updated so that users groups, as recorded in the users.yaml file, is included in the annotation output | |||
=== Creating biological processes to generate regulation annotations === | |||
*Needs more context, examples in documentation | |||
*See model 00366 | |||
*Creating a regulatory relationship between an MF and a BP currently requires creating an intervening regulatory BP | |||
**This is because an MF that regulates a process must always be part of some regulatory process | |||
**You will not get an annotation to a regulation BP term without adding the intervening regulatory BP | |||
=== Getting Correct Annotation Extensions === | |||
*See model 001088 | |||
*The cell type information needed to be moved from MF to terminal BP in the model to get the desired annotation extensions in the GPAD output | |||
*Need to be clear on what occurs_in means wrt modifying a BO | |||
*Saying that a BP occurs_in a CC means that that ''entire'' process occurs there | |||
*Is this consistent with how the occurs_in extension was used in conventional annotation? | |||
*More general question - how should anatomical and CC terms be used to qualify organism-level processes? | |||
*'''Action Item:''' We need a list of all of the relations and property chains and how they resolve. | |||
=== Curators should evaluate their workflow for areas where we can improve efficiency - high priority === | |||
*Submit tickets in geneontology/noctua | |||
*What's the development timeline here? | |||
*Note that many of these changes involve changing the fundamental graphics tool kit underlying the front end of Noctua - this will be a big endeavor | |||
=== Import existing CC and BP annotations === | |||
*The Cellular Component Companion exists | |||
*Accessed via clicking on the green box and scrolling down to 'Other operations' | |||
=== Documentation === | |||
*Google doc exists, but we still need updated SOPs for the mechanics of using the tool | |||
*Annotation guidelines, annotation philosophy still need fleshing out | |||
*One idea is to have an annotation documentation jamboree | |||
[[Category: | |||
[[Category:GO-CAM]] |
Latest revision as of 05:44, 16 April 2019
Zoom URL
https://stanford.zoom.us/j/679970729
Agenda
Update on Proposal for a Tabular Editing Interface
https://github.com/geneontology/noctua/issues/461
Priority list
- Viewing annotations in GPAD format
- Noctua ->Workbenches->Annotation Preview
- Noctua ->Model->Export GPAD
- Noctua->Jenkins (http://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/gpad)
- Handling evidence properly
- Complex model resolution to specify gene products along with evidence.
- evidence test: transferases - protein localization - differentiation
- Notch signaling - Part 1
- Karen's concerns regarding evidence usage and mapping
- Complex model resolution to specify gene products along with evidence.
- Handling groups as output in the GPAD file.
- Creating biological processes to generate regulation annotations.
- Generating a tabular interface
- Filtering GPAD annotations
- Regulation annotations when a named class exists
- Causal annotations to molecular functions
- Curators should evaluate their workflow for areas where we can improve efficiency - high priority
- Import existing CC and BP annotations
- Documentation
Minutes
- On call: David H, Harold, Jim, Karen, Kevin, Kimberly, Pascale, Sabrina, Sage, Seth, Stacia, Terry
- Regrets: Chris
Software Updates
Update on Proposal for a Tabular Editing Interface
- Hoping to port over a spreadsheet-like interface from IncaTools project
- Being used currently for editing DOS-DPs
- Needs to be able to communicate with minerva
- Part of the AGR project
- Three-week time frame (funding) for Noctua development
- Idea is to have a more P2GO-like, user friendly, intuitive annotation interface
- Simple design idea is to provide columns that match the fields of a GO annotation
- Will need input from curators familiar with the P2GO interface
- One question is whether the table editor should be write only or read-write
- Feedback so far is that, in the long run, curators would like read-write (i.e. full editing capability)
- What will be the relation between editing preformed in the graphical interface and the information stored in the table editor?
- Note that not all models will conform to a design pattern
Priority List
Viewing annotations in GPAD format
- GPAD export and Annotation Preview are consistent
- Are they the same? Seem to be
- Link to GPADs generated by Heiko's code - most simple annotations and extensions; there are species-specific files
- Link to GPADs generated by Jim's code - much more complete, but still some issues with evidence; not species-specific files yet
Handling evidence properly
- No progress to report this week
Handling groups as output in the GPAD file
- Minerva needs to be updated so that users groups, as recorded in the users.yaml file, is included in the annotation output
Creating biological processes to generate regulation annotations
- Needs more context, examples in documentation
- See model 00366
- Creating a regulatory relationship between an MF and a BP currently requires creating an intervening regulatory BP
- This is because an MF that regulates a process must always be part of some regulatory process
- You will not get an annotation to a regulation BP term without adding the intervening regulatory BP
Getting Correct Annotation Extensions
- See model 001088
- The cell type information needed to be moved from MF to terminal BP in the model to get the desired annotation extensions in the GPAD output
- Need to be clear on what occurs_in means wrt modifying a BO
- Saying that a BP occurs_in a CC means that that entire process occurs there
- Is this consistent with how the occurs_in extension was used in conventional annotation?
- More general question - how should anatomical and CC terms be used to qualify organism-level processes?
- Action Item: We need a list of all of the relations and property chains and how they resolve.
Curators should evaluate their workflow for areas where we can improve efficiency - high priority
- Submit tickets in geneontology/noctua
- What's the development timeline here?
- Note that many of these changes involve changing the fundamental graphics tool kit underlying the front end of Noctua - this will be a big endeavor
Import existing CC and BP annotations
- The Cellular Component Companion exists
- Accessed via clicking on the green box and scrolling down to 'Other operations'
Documentation
- Google doc exists, but we still need updated SOPs for the mechanics of using the tool
- Annotation guidelines, annotation philosophy still need fleshing out
- One idea is to have an annotation documentation jamboree