Signalling Workshop Agenda: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
mNo edit summary |
||
(23 intermediate revisions by 6 users not shown) | |||
Line 1: | Line 1: | ||
= Signaling Workshop Agenda = | |||
== Chairs == | |||
*Ruth (UCL) will chair the morning session; Kimberly (WB) will chair the afternoon session | *Ruth (UCL) will chair the morning session; Kimberly (WB) will chair the afternoon session | ||
== Meeting Schedule == | |||
{| {{Prettytable}} class='sortable' | {| {{Prettytable}} class='sortable' | ||
Line 28: | Line 29: | ||
| 11:30am - 12:30pm | | 11:30am - 12:30pm | ||
| MAPK Signaling - David H. (MGI) and Sabrina (ZFIN) | | MAPK Signaling - David H. (MGI) and Sabrina (ZFIN) | ||
| | | Ruth (UCL) | ||
|- | |- | ||
| 12:30pm - 1:30pm | | 12:30pm - 1:30pm | ||
Line 36: | Line 37: | ||
| 1:30pm - 2:30pm | | 1:30pm - 2:30pm | ||
| GPCR Signaling - Pascale (SIB) and Petra (dictyBase) | | GPCR Signaling - Pascale (SIB) and Petra (dictyBase) | ||
| | | | ||
|- | |- | ||
| 2:30pm - 3:00pm | | 2:30pm - 3:00pm | ||
| JAK/STAT Signaling - Giulia (FB) and Ruth (UCL) | | JAK/STAT Signaling - Giulia (FB) and Ruth (UCL) | ||
| | | Pascale (SIB) | ||
|- | |- | ||
| 3:00pm - 3:30pm | | 3:00pm - 3:30pm | ||
| Ca2+ Signaling involved in Mammalian Fertilization - Penelope (UniProt) | | Ca2+ Signaling involved in Mammalian Fertilization - Penelope (UniProt) | ||
| | | Sabrina (ZFIN) | ||
|- | |- | ||
| 3:30pm - 4:00pm | | 3:30pm - 4:00pm | ||
Line 56: | Line 57: | ||
|} | |} | ||
== General Outline for Presentations == | |||
*Since the different signaling topics are at various stages of analysis, not all groups will be expected to report on each aspect listed below. | |||
*However, we'd like to have an overall similar structure to the presentations, so please follow this outline as much as you can. | |||
*Also, the proposed changes to annotations and the ontology will likely go hand-in-hand, so feel free to combine these areas as needed to make the most effective presentation. | |||
**Summary of analysis | |||
**Proposed changes to annotations | |||
**Proposed changes to ontology | |||
**Outstanding issues | |||
**GO-CAM model (please include model URL) | |||
*Possible discussion topics for the end of the day | |||
**Did this approach to topic-focused curation/analysis work? | |||
**Did it improve the annotations? | |||
**Did it improve the ontology? | |||
**Do we have suitable GO-CAM models? | |||
**How will the ontology design patterns and MF refactoring help with modeling signaling pathways? | |||
**Overall - things that worked; things that didn’t work | |||
**Suggestions for improvements to this process and analysis tools that might help make the process more efficient | |||
**What are the plans going forward? | |||
== Analysis == | |||
*[https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGQmlCYm5VRHNMNW8 Signaling Project folder on GO's Google Drive] | |||
*[https://github.com/geneontology/go-annotation/projects/4 Signaling Projects page on GitHub's geneontology/go-annotation] | |||
== Minutes == | |||
*[https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit?usp=sharing Signaling Workshop Minutes] | |||
== Proposed topics for discussion (suggested prior to meeting; please see table above for actual topics and schedule) == | == Proposed topics for discussion (suggested prior to meeting; please see table above for actual topics and schedule) == | ||
Line 72: | Line 98: | ||
| [http://www.cellsignallingbiology.org/csb/002/002.pdf cell signaling pathways | | [http://www.cellsignallingbiology.org/csb/002/002.pdf cell signaling pathways | ||
| useful overview of lots of different types of pathways | | useful overview of lots of different types of pathways | ||
| | | | ||
|- | |- | ||
Line 105: | Line 125: | ||
|} | |} | ||
==Other databases with signalling | == Other databases with signalling pathway s== | ||
* [http://reactome.org/ Reactome] | * [http://reactome.org/PathwayBrowser/#/R-HSA-162582 Reactome] | ||
* [http://signor.uniroma2.it SIGNOR] [https://www.ncbi.nlm.nih.gov/pubmed/26467481 SIGNOR paper] | * [http://signor.uniroma2.it SIGNOR] [https://www.ncbi.nlm.nih.gov/pubmed/26467481 SIGNOR paper] | ||
==Additional Notes== | ==Additional Notes== | ||
[http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop Back to Signalling Workshop Logistics Page] | |||
Line 116: | Line 137: | ||
[[Category: GO Consortium Meetings]] | [[Category: GO Consortium Meetings]] | ||
[[Category: | [[Category: Workshops]] |
Latest revision as of 10:02, 9 April 2019
Signaling Workshop Agenda
Chairs
- Ruth (UCL) will chair the morning session; Kimberly (WB) will chair the afternoon session
Meeting Schedule
Time | Item | Minutes |
---|---|---|
9:00am - 9:15am | Opening Remarks - Ruth (UCl) | Val (PomBase) |
9:20am - 9:45am | Summary of Approach to Analysis and Project Organization - David H. (MGI) and Kimberly (WB) | Val (PomBase) |
9:50am - 10:50am | Canonical Wnt Signaling - Helen (FB) and Kimberly (WB) | Val (PomBase) |
11:00am - 11:30am | BREAK | na |
11:30am - 12:30pm | MAPK Signaling - David H. (MGI) and Sabrina (ZFIN) | Ruth (UCL) |
12:30pm - 1:30pm | LUNCH | na |
1:30pm - 2:30pm | GPCR Signaling - Pascale (SIB) and Petra (dictyBase) | |
2:30pm - 3:00pm | JAK/STAT Signaling - Giulia (FB) and Ruth (UCL) | Pascale (SIB) |
3:00pm - 3:30pm | Ca2+ Signaling involved in Mammalian Fertilization - Penelope (UniProt) | Sabrina (ZFIN) |
3:30pm - 4:00pm | BREAK | na |
4:00pm - 5:00pm | Discussion |
General Outline for Presentations
- Since the different signaling topics are at various stages of analysis, not all groups will be expected to report on each aspect listed below.
- However, we'd like to have an overall similar structure to the presentations, so please follow this outline as much as you can.
- Also, the proposed changes to annotations and the ontology will likely go hand-in-hand, so feel free to combine these areas as needed to make the most effective presentation.
- Summary of analysis
- Proposed changes to annotations
- Proposed changes to ontology
- Outstanding issues
- GO-CAM model (please include model URL)
- Possible discussion topics for the end of the day
- Did this approach to topic-focused curation/analysis work?
- Did it improve the annotations?
- Did it improve the ontology?
- Do we have suitable GO-CAM models?
- How will the ontology design patterns and MF refactoring help with modeling signaling pathways?
- Overall - things that worked; things that didn’t work
- Suggestions for improvements to this process and analysis tools that might help make the process more efficient
- What are the plans going forward?
Analysis
- Signaling Project folder on GO's Google Drive
- Signaling Projects page on GitHub's geneontology/go-annotation
Minutes
Proposed topics for discussion (suggested prior to meeting; please see table above for actual topics and schedule)
Proposer (and group) | Signaling pathway | Reference | What this pathway offers | link to uploaded figures and noctua model |
---|---|---|---|---|
Judy (MGI) | General information | [http://www.cellsignallingbiology.org/csb/002/002.pdf cell signaling pathways | useful overview of lots of different types of pathways | |
Ruth (UCL) | Gastrin signaling | PMID:26205660 | Multiple intracellular signaling pathways converge to regulate transcription (see Fig 2) Fig2B nicely groups different 'parts' of the pathway. Also brings to discussion annotation of entities responsible for release of the ligand. | impossible to get this modelled in GO-CAM before October |
Ruth (UCL) | Apoptosis | Apoptosis working group | this has already been worked on in GO and guidelines established, need to consider aligning to these | Apoptosis curation manual |