Signaling Workshop February 2010
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Please suggest agenda items, relevant papers and other information relating to signaling GO terms that you would like discussed at this workshop.
Participants
GO Annotators | Remote Participants | GO Editors | GO Developers | Signaling Experts |
---|---|---|---|---|
Dr Ruth Lovering (BHF-UCL) Dr Varsha Khodiyar (BHF-UCL) Dr Sandra Orchard (Intact) Dr Peter D'Eustachio (Reactome) Dr Rachael Huntley(GOA) Dr Val Wood (PombeBase) Dr Susan Tweedie (FlyBase) |
Dr Alex Diehl (MGI/UB Medical School; GO curator/GO editor) |
Dr Rebecca Foulger (GO Editorial) Dr Midori Harris (GO Editorial; TBC) Dr Paola Roncaglia (GO Editorial from March 2011) |
Chris Mungall (Berkeley) (Thursday only) |
Dr Andrea Townsend-Nicholson (UCL) Dr Andrew Winter (University Edinburgh) Dr Andrew Chatr-aryamontri (University Edinburgh) |
Where and When
Date: Wednesday 16th February and Thursday 17th February, 2011.
Where: EMBL-EBI.
Wednesday: A2-33
Thursday: Courtyard room
- Travel instructions to the EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD [2]
- Please let EBI reception know you have arrived, and Rebecca will come and meet you.
Accommodation
The following participants have rooms reserved on site for the nights of Tuesday 15th and Wednesday 16th February:
- Dr Andrew Winter
- Dr Andrew Chatr-aryamontri
- Dr Andrea Townsend-Nicholson
- Dr Ruth Lovering
The following participants have rooms reserved on site for the nights of Wednesday 16th February:
- Dr Varsha Khodiyar
The following participants have rooms reserved on site for the nights of Monday 14th, Tuesday 15th, Wednesday 16th and Thursday 17th February.
- Dr Paola Roncaglia
All other participants are local or have arranged their own accommodation. Please let Rebecca know if this changes.
Dinners
- For participants arriving on the Tuesday, and for anyone else who would like to join us, a meal will be arranged on Tuesday 15th February at the Hinxton Red Lion.
- A workshop meal will be arranged for Wednesday 16th February at the John Barleycorn in Duxford.
- Lunches on the Wednesday and Thursday will be at the on-site Murrays restaurant. Lunch vouchers will be provided for all participants.
- Tea and Coffee will be provided in the meeting rooms
Programme
Wednesday 16th February
9:15am | Tea and Coffee | |
9:30am | Welcome and introduction | Rebecca |
9:35am | Introduction to GO | Rebecca |
9:50am | ||
11am | Coffee break | |
11:45am | ||
12:30pm | Lunch @ on-site campus restaurant | |
2pm | ||
3:00 pm | Coffee break | |
5pm | Close |
Thursday 17th February
9:15am | Tea and Coffee | |
9:30am | Recap of decisions made on Day 1. | Rebecca |
10am | Chris will present work he's doing making automatic links between Reactome and GO signaling terms | Chris Mungall |
10:30am | Work through the insulin receptor signaling pathway to create a curation manual for annotators | |
11am | Coffee break | |
12:30pm | Lunch @ on-site campus restaurant | |
3:00 pm | Close |
Relevant papers and other resources
Biochemistry of Signal Tranduction and Regulation. Gerhard Krauss. ISBN:3-527-29241-1
Cell Signaliing. John T. Hancock. ISBN:0199264678
The Biochemistry of Cell Signalling. Ernst J. M. Helmreich. ISBN: 0198508204
Signal Transduction. Gompert et al. ISBN: 9787030182173. (recommended by Andrea: provides a history on signal transduction)
Topics
- How the signaling node should be split
- cellular vs tissue vs organismal?
- pathway vs process?
- Defining and placing:
- signal transduction
- signal transmission
- signaling pathway
- Defining initiation of signal transduction:
- Currently used to annotate both ligands and receptors- is this correct?
- Which of its children do we want to keep?
- Defining 'creation of a signal':
- Where does the process start... transcription/translation or later?
- Receptor processing:
- Should receptor processing terms go under 'signaling' to be siblings with the 'creation of a signal' term?
- OR should receptor processing terms go under 'regulation of signaling'?
- Connecting the networks
- How to connect the cell surface receptors with the intracellular 'modules' they signal through
- Dealing with ligand-receptor signaling that is not 1:1
- What is a signal transducer?
- receptors?
- ligands?
- downstream kinases?
- RECEPTORS
- Should ligand-gated ion channels be given receptor parents?
- Should receptors be divided into 'transport receptors' that deliver nutrients into the cell, and 'signaling receptors' that transduce a signal.
- Should the RECEPTOR terms be kept in FUNCTION, or PROCESS terms created to replace them?
- signal reception (synonym: receptor)
- primary signal transduction (synonym: receptor)
- receptor-mediated endocytosis
- How should receptor-mediated endocytosis be linked to signaling?
- Is the first step in RME (receptor binding to nutrient/ligand) signal transduction?
- Where do RME receptors (eg LDLR, transferrin receptor) fit in?
- CELL CYCLE CHECKPOINTS (Val)
- How do the checkpoints fit with the signal transduction terms.
- Val has been in contact with Paul Russell about checkpoints: He said: the term DNA damage checkpoint would represent the gene products involved in signalling only.
- Connecting the signaling terms and response terms
SourceForge Signaling Items
receptors and HAS_PART: http://sourceforge.net/tracker/?func=detail&aid=3103037&group_id=36855&atid=440764
receptor signaling proteins: http://sourceforge.net/tracker/?func=detail&aid=3101487&group_id=36855&atid=440764
purigenic receptors: http://sourceforge.net/tracker/?func=detail&aid=3088079&group_id=36855&atid=440764
MAPKKK cascade: http://sourceforge.net/tracker/?func=detail&aid=3085150&group_id=36855&atid=440764
Calcium-mediated signaling; http://sourceforge.net/tracker/?func=detail&aid=3077377&group_id=36855&atid=440764
morphogen: http://sourceforge.net/tracker/?func=detail&aid=3026415&group_id=36855&atid=440764
norrin signaling (example of non 1:1 receptor:ligand signaling) : http://sourceforge.net/tracker/?func=detail&aid=3041964&group_id=36855&atid=440764
hormone and hormone receptor signaling: http://sourceforge.net/tracker/?func=detail&aid=2974691&group_id=36855&atid=440764
Connecting up receptors and intracellular modules:
wnt signaling via hippo cascade: http://sourceforge.net/tracker/?func=detail&aid=3032564&group_id=36855&atid=440764
wnt signaling via JNK cascade: http://sourceforge.net/tracker/?func=detail&aid=3023417&group_id=36855&atid=440764
PI3K/AKT signaling: http://sourceforge.net/tracker/?func=detail&aid=3008502&group_id=36855&atid=440764
Minutes
Notes
Definition Adjustments:
Obsoleted Terms:
Moved Terms:
New Terms: