GO-CAM May 24th, 2017: Difference between revisions
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= Minutes = | = Minutes = | ||
*On call: Chris, Karen, Kimberly, Moni, Pascale, Seth, Suzi | *On call: Chris, Karen, Kimberly, Moni, Pascale, Paul T., Seth, Suzi | ||
== Software Updates == | == Software Updates == | ||
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**Curators can now annotate with the reasoner on and this should catch mistakes | **Curators can now annotate with the reasoner on and this should catch mistakes | ||
**Ultimately working towards real-time error checking | **Ultimately working towards real-time error checking | ||
**If using undone/redo DON'T USE THE REASONER | **If using undone/redo DON'T USE THE REASONER right now - still some troubleshooting to be done here | ||
**Removed GAF output option from Noctua | **Removed GAF output option from Noctua | ||
*Human readable GPAD output | *Human readable GPAD output | ||
Line 31: | Line 31: | ||
**See Annotation preview under Workbenches menu | **See Annotation preview under Workbenches menu | ||
**Will live update as curators edit their models | **Will live update as curators edit their models | ||
*Added visual compactor | |||
**Individuals will map into approx. 700x700 square, essentially a screen view | |||
**This helps keep individuals closer together | |||
**One caveat - individuals can get stacked | |||
**Can individuals connected together get stacked? | |||
***There are a number of possible variations to this display - can talk more about the options here | |||
**Exploding specific box(es) would be useful; there is a ticket for this | |||
*Ability to have different views of annotation sets | |||
**Annotations from a specific paper | |||
**Annotations for a specific gene (this might need some filtering options) | |||
*Model searching - in Noctua | |||
**Search by gene, GO term, paper | |||
*Browse function in Noctua | |||
**An alpha version of faceted searching in AmiGO | |||
== Direction for these Calls == | |||
*Use these calls to prioritize | |||
**High priority vs showstoppers - what are the differences? | |||
*What do we need to do to get everyone using Noctua? | |||
*Handling evidence properly - high priority | |||
*Generating a tabular interface - high priority | |||
*Curators should evaluate their workflow for areas where we can improve efficiency - high priority | |||
*Efficiency of adding evidence - not high priority, but would improve workflow | |||
*Import existing CC and BP annotations - high priority | |||
**GP buddy works on CC | |||
**There are issues to work out wrt importing annotations and making sure we are consistent with an instance-level representation | |||
*Constraining relations - not a showstopper, but would make workflow easier | |||
*Documentation - high priority | |||
== Other Considerations == | |||
*How is Noctua modeling changing our annotations? | |||
*What is the best way to assess this? | |||
**Changes to annotations, e.g. more precise MF representation | |||
**Improved representation of causal relations in BPs | |||
**Changes to enrichment analysis | |||
[[Category: LEGO]] | [[Category: LEGO]] |
Latest revision as of 12:00, 24 May 2017
Bluejeans URL
https://bluejeans.com/969313231
Agenda
Recent Software Updates
- New fast reasoner: Arachne
- Export GPAD menu option now using reasoner (ie Jim's code; Heiko's is retired)
- Readable GPAD ("labelified-GPAD") progress
Review of github Tickets
Minutes
- On call: Chris, Karen, Kimberly, Moni, Pascale, Paul T., Seth, Suzi
Software Updates
- Updated relations available in Noctua (e.g. directly positively regulates)
- Also updated existing models
- Incorporated SynGO models files generated by David OS
- JSON -> OWL
- New reasoner
- Incorporated Jim B.'s Arachne reasoner into Noctua
- Much faster than ELK
- Curators can now annotate with the reasoner on and this should catch mistakes
- Ultimately working towards real-time error checking
- If using undone/redo DON'T USE THE REASONER right now - still some troubleshooting to be done here
- Removed GAF output option from Noctua
- Human readable GPAD output
- First version is available for use
- See Annotation preview under Workbenches menu
- Will live update as curators edit their models
- Added visual compactor
- Individuals will map into approx. 700x700 square, essentially a screen view
- This helps keep individuals closer together
- One caveat - individuals can get stacked
- Can individuals connected together get stacked?
- There are a number of possible variations to this display - can talk more about the options here
- Exploding specific box(es) would be useful; there is a ticket for this
- Ability to have different views of annotation sets
- Annotations from a specific paper
- Annotations for a specific gene (this might need some filtering options)
- Model searching - in Noctua
- Search by gene, GO term, paper
- Browse function in Noctua
- An alpha version of faceted searching in AmiGO
Direction for these Calls
- Use these calls to prioritize
- High priority vs showstoppers - what are the differences?
- What do we need to do to get everyone using Noctua?
- Handling evidence properly - high priority
- Generating a tabular interface - high priority
- Curators should evaluate their workflow for areas where we can improve efficiency - high priority
- Efficiency of adding evidence - not high priority, but would improve workflow
- Import existing CC and BP annotations - high priority
- GP buddy works on CC
- There are issues to work out wrt importing annotations and making sure we are consistent with an instance-level representation
- Constraining relations - not a showstopper, but would make workflow easier
- Documentation - high priority
Other Considerations
- How is Noctua modeling changing our annotations?
- What is the best way to assess this?
- Changes to annotations, e.g. more precise MF representation
- Improved representation of causal relations in BPs
- Changes to enrichment analysis