GO-CAM August 23, 2017: Difference between revisions
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== Modeling in Noctua == | == Modeling in Noctua == | ||
*We discussed what the current modeling statements in Noctua actually mean | *We discussed what the current modeling statements in Noctua actually mean | ||
* | *For example, the model currently requires that a molecular_function is associated with a cellular component | ||
*Is it possible to make a different statement in Noctua | *Is it possible to make a different type of statement in Noctua, or GO in general? | ||
**For example, a TF is observed in the cytoplasm, but it does not execute its MF there | **For example, a TF is observed in the cytoplasm, but it does not execute its MF there | ||
*Curators should read Paul T.'s [https://www.ncbi.nlm.nih.gov/pubmed/27812932 chapter about representation of function in the GO Handbook] | |||
*Can different localizations be annotated using different CC qualifiers? | |||
*Counter-argument | |||
**Shouldn't GO just be focused on capturing where activities occur? | |||
**Adding more relations to CC could potentially generate another point for annotation inconsistency and noise | |||
*One question: when would curators make an annotation to a CC and when not? | |||
**If you don't know anything about a protein but its localization, curators would typically make that CC | |||
*There is a distinction between saying a protein localizes to a CC and likely functions there vs a protein localizes to a CC and we don't know if it actually has a function there | |||
*This is a very fundamental question for GO - what information do we want to capture and why? | |||
**There are fundamental differences between the annotations that might result, say, from an HTP localization screen vs a well-studied gene for which we know exactly where and how it functions | |||
*Should we use different qualifiers for CC? | |||
*Should the GO supply different files with different qualifiers for our users? | |||
*In terms of Noctua, what should the behavior be for simply adding a conventional CC annotation? | |||
*ACTION ITEM: Draft different proposals for how to handle GO annotation statements going forward | |||
**Annotation of well-studied genes vs annotation of isolated observations and GO-CAM models vs conventional annotation | |||
**These proposals should be in place by the October GO meeting so we can discuss and make a decision | |||
**Stakeholders and considerations: | |||
***Developers | |||
****Tool development and maintenance | |||
*****Changes to existing UI | |||
****Impacts on data storage | |||
****Impacts on annotation file generation | |||
****Impacts on data display | |||
***Curators | |||
****Efficiency of annotation | |||
*****Capturing all data when reading a paper vs capturing only a defined subset of data | |||
****Consistency of annotation | |||
*****Adding more relations increases the number of decision points during curation which could lead to more inconsistency, and could, at least temporarily, reduce efficiency | |||
****Dealing with legacy annotation | |||
*****Individual groups could decide what is best for their annotation set | |||
****Need for clear curation guidelines | |||
***Users | |||
****Clarity in semantics of GO annotation | |||
*****Precision of results in building genes sets (eliminating false positive and false negatives) | |||
*****Informativeness of enrichment results and other summary analyses | |||
****Ease of use of GO data, i.e. would GO users effectively use different slices of GO annotation | |||
****Opportunities to use GO for different types of analyses | |||
****Communication and outreach if changes are made to current practice | |||
== Different annotation scenarios for Cellular Component == | |||
**DPY-19 mannosyltransferase | |||
***endoplasmic reticulum - functional | |||
**ENU-3.6 - novel | |||
***cytoplasm - functional?? (not known, but no compelling reason to think it's not) | |||
**DAF-16 Forkhead TF | |||
***cytoplasm - sequestered, not functional | |||
***nucleus - functional | |||
**WNT3a - receptor agonist activity | |||
***endoplasmic reticulum lumen - trafficking, not functional | |||
***extracellular exosome - functional | |||
**HIST2H2AC - this is actually manually annotated to root MF, but has IBA and IEA for DNA binding | |||
***nucleus - functional | |||
***extracellular exosome - functional?? (not known, but no compelling reason to think it is) | |||
**NRAS - GTPase | |||
***Golgi apparatus - functional and trafficking, depending on context | |||
***membrane - functional | |||
***extracellular exosome - functional?? (not known, no compelling reason for either functional or non-functional) | |||
[[Category:GO-CAM]] | |||
[[Category: |
Latest revision as of 05:43, 16 April 2019
Zoom URL
https://stanford.zoom.us/j/679970729
Agenda
github Trackers
- Clarification about which one(s) to use
- noctua - client and middleware code
- noctua-models - annotation (may be merged with go-annotation)
- minerva
Table Editor Workbench
- Chris and Seth will demo the new 'Simple annoton editor' workbench now available in Noctua
- The table editor allows curators to add, and edit, simple annotons in a table format
- Annotations entered in the table are automatically added to the Noctua graph editor
Annotation Provenance
- Review of how attribution is assigned for Noctua annotations
- de novo annotations
- imported annotations using function and component companions
Annotating with any UniProtID
- Use add individual functionality
Minutes
- On call: Chris, Harold, Karen, Kevin, Kimberly, Pascale, Paul T., Rob, Sabrina, Sage, Seth, Stacia, Suzi
New Noctua Features
- Curators can submit an issue to the github tracker from the Issues menu
- Model will be automatically referenced in the github ticket and the github ticket number will be listed in the models menu
- Simple annoton editor
- Curators are prompted to add an annoton, but can add distinct parts of the annoton, if needed
- Will be prompted to add evidence and a reference
- References are fairly neutral right now - can add PMIDs, GO_REFs - just need to have them be properly formatted (e.g., PMID:nnnnnnnn or GO_REF:nnnnnnnn)
- Save annoton button adds the annoton to the graphical view, but curators still need to add a title and save their models in the graph view
- ACTION: Curators need to test the editor and give feedback.
Modeling in Noctua
- We discussed what the current modeling statements in Noctua actually mean
- For example, the model currently requires that a molecular_function is associated with a cellular component
- Is it possible to make a different type of statement in Noctua, or GO in general?
- For example, a TF is observed in the cytoplasm, but it does not execute its MF there
- Curators should read Paul T.'s chapter about representation of function in the GO Handbook
- Can different localizations be annotated using different CC qualifiers?
- Counter-argument
- Shouldn't GO just be focused on capturing where activities occur?
- Adding more relations to CC could potentially generate another point for annotation inconsistency and noise
- One question: when would curators make an annotation to a CC and when not?
- If you don't know anything about a protein but its localization, curators would typically make that CC
- There is a distinction between saying a protein localizes to a CC and likely functions there vs a protein localizes to a CC and we don't know if it actually has a function there
- This is a very fundamental question for GO - what information do we want to capture and why?
- There are fundamental differences between the annotations that might result, say, from an HTP localization screen vs a well-studied gene for which we know exactly where and how it functions
- Should we use different qualifiers for CC?
- Should the GO supply different files with different qualifiers for our users?
- In terms of Noctua, what should the behavior be for simply adding a conventional CC annotation?
- ACTION ITEM: Draft different proposals for how to handle GO annotation statements going forward
- Annotation of well-studied genes vs annotation of isolated observations and GO-CAM models vs conventional annotation
- These proposals should be in place by the October GO meeting so we can discuss and make a decision
- Stakeholders and considerations:
- Developers
- Tool development and maintenance
- Changes to existing UI
- Impacts on data storage
- Impacts on annotation file generation
- Impacts on data display
- Tool development and maintenance
- Curators
- Efficiency of annotation
- Capturing all data when reading a paper vs capturing only a defined subset of data
- Consistency of annotation
- Adding more relations increases the number of decision points during curation which could lead to more inconsistency, and could, at least temporarily, reduce efficiency
- Dealing with legacy annotation
- Individual groups could decide what is best for their annotation set
- Need for clear curation guidelines
- Efficiency of annotation
- Users
- Clarity in semantics of GO annotation
- Precision of results in building genes sets (eliminating false positive and false negatives)
- Informativeness of enrichment results and other summary analyses
- Ease of use of GO data, i.e. would GO users effectively use different slices of GO annotation
- Opportunities to use GO for different types of analyses
- Communication and outreach if changes are made to current practice
- Clarity in semantics of GO annotation
- Developers
Different annotation scenarios for Cellular Component
- DPY-19 mannosyltransferase
- endoplasmic reticulum - functional
- ENU-3.6 - novel
- cytoplasm - functional?? (not known, but no compelling reason to think it's not)
- DAF-16 Forkhead TF
- cytoplasm - sequestered, not functional
- nucleus - functional
- WNT3a - receptor agonist activity
- endoplasmic reticulum lumen - trafficking, not functional
- extracellular exosome - functional
- HIST2H2AC - this is actually manually annotated to root MF, but has IBA and IEA for DNA binding
- nucleus - functional
- extracellular exosome - functional?? (not known, but no compelling reason to think it is)
- NRAS - GTPase
- Golgi apparatus - functional and trafficking, depending on context
- membrane - functional
- extracellular exosome - functional?? (not known, no compelling reason for either functional or non-functional)
- DPY-19 mannosyltransferase