Annotation Conf. Call 2018-06-12: Difference between revisions
Jump to navigation
Jump to search
(→GPCR) |
|||
(23 intermediate revisions by 2 users not shown) | |||
Line 10: | Line 10: | ||
**4th Tuesday: GO-CAM Working Group | **4th Tuesday: GO-CAM Working Group | ||
**5th Tuesday: ad hoc, as needed | **5th Tuesday: ad hoc, as needed | ||
*One Zoom URL for all - https://stanford.zoom.us/j/976175422 | |||
== Annotation Reviews == | == Annotation Reviews == | ||
=== Signaling Projects === | === Signaling Projects === | ||
==== Canonical Wnt Signaling ==== | ==== Canonical Wnt Signaling ==== | ||
*[https://github.com/geneontology/go-annotation/issues/1967 Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway'] | |||
**Outstanding reviews: BHF-UCL, MGI, PARL, UniProt, Zfin | |||
*[https://github.com/geneontology/go-annotation/issues/1966 Review annotations wrt GO:0060070 'canonical Wnt signaling pathway'] | |||
**Outstanding reviews: ARUK-UCL, BHF-UCL, DFLAT, MGI, ParkinsonsUK-UCL, UniProt, WB, Zfin | |||
**Annotation questions: | |||
***Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway | |||
****Therefore, it's difficult to say definitively which Wnts are part of which types of Wnt signaling pathways; the experiments and context should be the guiding information | |||
***Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling | |||
****Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway | |||
***Upstream components | |||
****Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better | |||
== Annotation File Pipelines == | == Annotation File Pipelines == | ||
Line 33: | Line 36: | ||
= Minutes = | = Minutes = | ||
On call: | On call: George, Giulia, Harold, Kimberly, Li, Michele, Midori, Penelope, Rob, Ruth, Sabrina, Sandy, Stacia, Suzi A., Suzi L., Tanya, Val | ||
== GO Annotation Meetings == | |||
*Will switch to new schedule above, effective immediately. | |||
*Will use https://stanford.zoom.us/j/976175422 for all calls | |||
*email will be sent to go-consortium list to alert everyone to the new schedule | |||
== Annotation Reviews == | |||
=== Signaling Projects === | |||
==== Canonical Wnt Signaling ==== | |||
*Please continue to review canonical Wnt signaling annotations in the spreadsheets and mark the action you've taken | |||
*Only annotations that potentially need review were included in the spreadsheets | |||
*If there are any questions about whether or not a gene product, particularly a Wnt ligand, is part of or regulating Wnt signaling, feel free to post information about that in the relevant github ticket for discussion | |||
== Annotation File Pipelines == | |||
*Groups can now post a Source URL in their datasets.yaml file to have annotation files, and gpi files, retrieved by GO Central as part of the new release pipeline | |||
*Monthly releases of GO data will be versioned and archived for end-users; will correspond to data that is displayed in AmiGO for that month | |||
*Daily snapshot releases are also available for consortium groups to consume the latest ontology files, or get timely feedback on annotation QA/QC | |||
**Note that we are still discussing what files groups should display on their respective websites, but leaning towards the versioned, monthly releases | |||
*Groups should start checking the reports files on snapshot.geneontology.org | |||
**There are multiple reports, but we are hoping to consolidate these into fewer files with one main report in HTML | |||
**Things that need to be addressed in reports: | |||
***URLs for annotation rules don't resolve to an accessible webpage - gives an Access denied page on geneontology.org (Harold will put in a ticket for this) | |||
*Note that information on annotation rules can be found on geneontology/go-site/metadata: https://github.com/geneontology/go-site/tree/master/metadata/rules | |||
*Issues that need to be reported wrt the annotation file pipelines should be added to the tracker at: https://github.com/geneontology/pipeline/issues | |||
*We need to confirm whether the various gp2 . files are still needed | |||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Latest revision as of 11:12, 3 July 2018
Meeting URL
GO Annotation Meetings
- Still will be Tuesdays at 8am PDT
- Proposed meeting schedule:
- 1st Tuesday: Alliance Gene Function
- 2nd Tuesday: GO Consortium
- 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
- 4th Tuesday: GO-CAM Working Group
- 5th Tuesday: ad hoc, as needed
- One Zoom URL for all - https://stanford.zoom.us/j/976175422
Annotation Reviews
Signaling Projects
Canonical Wnt Signaling
- Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway'
- Outstanding reviews: BHF-UCL, MGI, PARL, UniProt, Zfin
- Review annotations wrt GO:0060070 'canonical Wnt signaling pathway'
- Outstanding reviews: ARUK-UCL, BHF-UCL, DFLAT, MGI, ParkinsonsUK-UCL, UniProt, WB, Zfin
- Annotation questions:
- Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway
- Therefore, it's difficult to say definitively which Wnts are part of which types of Wnt signaling pathways; the experiments and context should be the guiding information
- Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling
- Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway
- Upstream components
- Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better
- Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway
Annotation File Pipelines
- Annotation files can now be deposited on a publicly accessible site (SVN submission is no longer needed)
- The source URL for annotation (and gpi) files should be entered in the Source tag of each group's datasets.yaml file
- Reports are available on a daily basis: http://snapshot.geneontology.org/reports/index.html
- QA//QC checks - Eric and Pascale are still working on implementing all of these
- Documentation: http://wiki.geneontology.org/index.php/Release_Pipeline
Minutes
On call: George, Giulia, Harold, Kimberly, Li, Michele, Midori, Penelope, Rob, Ruth, Sabrina, Sandy, Stacia, Suzi A., Suzi L., Tanya, Val
GO Annotation Meetings
- Will switch to new schedule above, effective immediately.
- Will use https://stanford.zoom.us/j/976175422 for all calls
- email will be sent to go-consortium list to alert everyone to the new schedule
Annotation Reviews
Signaling Projects
Canonical Wnt Signaling
- Please continue to review canonical Wnt signaling annotations in the spreadsheets and mark the action you've taken
- Only annotations that potentially need review were included in the spreadsheets
- If there are any questions about whether or not a gene product, particularly a Wnt ligand, is part of or regulating Wnt signaling, feel free to post information about that in the relevant github ticket for discussion
Annotation File Pipelines
- Groups can now post a Source URL in their datasets.yaml file to have annotation files, and gpi files, retrieved by GO Central as part of the new release pipeline
- Monthly releases of GO data will be versioned and archived for end-users; will correspond to data that is displayed in AmiGO for that month
- Daily snapshot releases are also available for consortium groups to consume the latest ontology files, or get timely feedback on annotation QA/QC
- Note that we are still discussing what files groups should display on their respective websites, but leaning towards the versioned, monthly releases
- Groups should start checking the reports files on snapshot.geneontology.org
- There are multiple reports, but we are hoping to consolidate these into fewer files with one main report in HTML
- Things that need to be addressed in reports:
- URLs for annotation rules don't resolve to an accessible webpage - gives an Access denied page on geneontology.org (Harold will put in a ticket for this)
- Note that information on annotation rules can be found on geneontology/go-site/metadata: https://github.com/geneontology/go-site/tree/master/metadata/rules
- Issues that need to be reported wrt the annotation file pipelines should be added to the tracker at: https://github.com/geneontology/pipeline/issues
- We need to confirm whether the various gp2 . files are still needed