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| | [[Category:Signaling]] |
| Return to [[Main_Page|GOC Main Page]] | | Return to [[Main_Page|GOC Main Page]] |
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| Return to Signaling Main Page [[http://wiki.geneontology.org/index.php/Signaling]] | | Return to Signaling Main Page [[http://wiki.geneontology.org/index.php/Signaling]] |
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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.
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| ----
| | PLEASE SEE THE REVISED PAGE AT: |
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| | | http://gocwiki.geneontology.org/index.php/Signaling_Workshop_February_2011 |
| == Participants ==
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| {| class="wikitable" border="1"
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| ! GO Annotators
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| ! Remote Participants
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| ! GO Editors
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| ! GO Developers
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| ! Signaling Experts
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| | Dr Ruth Lovering (BHF-UCL)<br/>Dr Varsha Khodiyar (BHF-UCL)<br/>Dr Sandra Orchard (Intact)<br/>Dr Peter D'Eustachio (Reactome) <br/>Dr Rachael Huntley(GOA) <br/>Dr Val Wood (PombeBase)<br/>Dr Susan Tweedie (FlyBase)
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| | Dr Alex Diehl<br/> (MGI/UB Medical School; <br/> GO curator/GO editor)
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| | Dr Rebecca Foulger (GO Editorial)<br/>Dr Midori Harris (GO Editorial; TBC)<br/>Dr Paola Roncaglia (GO Editorial from March 2011)
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| | Chris Mungall (Berkeley)<br/> (Thursday only)
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| | Dr Andrea Townsend-Nicholson (UCL)<br/>Dr Andrew Winter (University Edinburgh)<br/>Dr Andrew Chatr-aryamontri (University Edinburgh)
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| |}
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| == Where and When ==
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| Date: Wednesday 16th February and Thursday 17th February, 2011.
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| Where: EMBL-EBI.
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| Wednesday: A2-33
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| Thursday: Courtyard room
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| * Travel instructions to the EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD [http://www.ebi.ac.uk/Information/Travel/travel.html]
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| * Please let EBI reception know you have arrived, and Rebecca will come and meet you.
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| == Accommodation ==
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| The following participants have rooms reserved on site for the nights of Tuesday 15th and Wednesday 16th February:
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| *Dr Andrew Winter
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| *Dr Andrew Chatr-aryamontri
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| *Dr Andrea Townsend-Nicholson
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| *Dr Ruth Lovering
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| The following participants have rooms reserved on site for the nights of Wednesday 16th February:
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| *Dr Varsha Khodiyar
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| The following participants have rooms reserved on site for the nights of Monday 14th, Tuesday 15th, Wednesday 16th and Thursday 17th February.
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| *Dr Paola Roncaglia
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| All other participants are local or have arranged their own accommodation. Please let Rebecca know if this changes.
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| == Dinners ==
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| *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.
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| The Red Lion Menu's are available:
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| *A workshop meal will be arranged for Wednesday 16th February at the John Barleycorn in Duxford.
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| *Lunches on the Wednesday and Thursday will be at the on-site Murrays restaurant. Lunch vouchers will be provided for all participants.
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| *Tea and Coffee will be provided in the meeting rooms
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| == FUNDING ==
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| The GO signaling workshop is jointly funded by GO (75%) and UCL-BHF (25%).
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| The EBI Industry Programme, lead by Dominic Clark, is kindly funding the lunches and the workshop dinner on the Wednesday evening.
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| == Programme ==
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| Wednesday 16th February
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| {| border="1" cellpadding="2" width=1000px
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| |-valign="top"
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| |width="5%"|'''9:15am'''
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| |width="90%"|Tea and Coffee
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| |width="5%"|
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| |-valign="top"
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| |'''9:30am'''
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| | Welcome and introduction
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| |Rebecca
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| |-valign="top"
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| |'''9:35am'''
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| |[http://gocwiki.geneontology.org/images/7/70/Signalworkshopintro.pdf Introduction] to GO
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| |Rebecca
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| |-valign="top"
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| |'''9:50am'''
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| |-valign="top"
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| |-valign="top"
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| |'''11am'''
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| |Coffee break
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| |-valign="top"
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| |'''11:45am'''
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| |-valign="top"
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| |'''12:30pm'''
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| |Lunch @ on-site campus restaurant
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| |-valign="top"
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| |'''2pm'''
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| |-valign="top"
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| |'''3:00 pm'''
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| |Coffee break
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| |-valign="top"
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| |'''5pm'''
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| |Close
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| |}
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| Thursday 17th February
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| {| border="1" cellpadding="2" width=1000px
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| |-valign="top"
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| |width="5%"|'''9:15am'''
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| |width="90%"|Tea and Coffee
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| |width="5%"|
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| |-valign="top"
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| |'''9:30am'''
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| | Recap of decisions made on Day 1.
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| |Sandra
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| |-valign="top"
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| |'''10am'''
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| |Chris will present work he's doing making automatic links between Reactome and GO signaling terms
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| |Chris Mungall
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| |-valign="top"
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| |'''10:30am'''
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| | Work through the insulin receptor signaling pathway to create a curation manual for annotators
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| |-valign="top"
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| |-valign="top"
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| |'''11am'''
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| |Coffee break
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| |-valign="top"
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| |-valign="top"
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| |'''12:30pm'''
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| |Lunch @ on-site campus restaurant
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| |-valign="top"
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| |-valign="top"
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| |'''3:00 pm'''
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| |Close
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| |}
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| == Relevant papers and other resources ==
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| Biochemistry of Signal Tranduction and Regulation. Gerhard Krauss. ISBN:3-527-29241-1
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| Cell Signaliing. John T. Hancock. ISBN:0199264678
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| The Biochemistry of Cell Signalling. Ernst J. M. Helmreich. ISBN: 0198508204
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| Signal Transduction. Gompert et al. ISBN: 9787030182173. (recommended by Andrea: provides a history on signal transduction)
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| == Topics ==
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| A presentation on all the signaling topics is [http://gocwiki.geneontology.org/images/c/c0/Signalworkshop_problems.pdf here]
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| *<font color="blue">How the signaling node should be split</font color>
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| **cellular vs tissue vs organismal?
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| **pathway vs process?
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| *<font color="purple">Defining and placing:</font color>
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| **signal transduction
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| **signal transmission
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| **signaling pathway
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| *<font color="orange">Defining initiation of signal transduction:</font color>
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| ***Currently used to annotate both ligands and receptors- is this correct?
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| ***Which of its children do we want to keep?
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| *<font color="teal">Defining 'creation of a signal':</font color>
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| **Where does the process start... transcription/translation or later?
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| *<font color="grey">Receptor processing:</font color>
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| **Should receptor processing terms go under 'signaling' to be siblings with the 'creation of a signal' term?
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| **OR should receptor processing terms go under 'regulation of signaling'?
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| *<font color="green">Connecting the networks</font color>
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| **How to connect the cell surface receptors with the intracellular 'modules' they signal through
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| *<font color="red">Dealing with ligand-receptor signaling that is not 1:1</font color>
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| *<font color="magenta">What is a signal transducer?</font color>
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| **receptors?
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| **ligands?
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| **downstream kinases?
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| *<font color="blue">RECEPTORS</font color>
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| **Should ligand-gated ion channels be given receptor parents?
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| **Should receptors be divided into 'transport receptors' that deliver nutrients into the cell, and 'signaling receptors' that transduce a signal.
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| **Should the RECEPTOR terms be kept in FUNCTION, or PROCESS terms created to replace them?
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| ***signal reception (synonym: receptor)
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| ***primary signal transduction (synonym: receptor)
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| *<font color="orange">receptor-mediated endocytosis</font color>
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| **How should receptor-mediated endocytosis be linked to signaling?
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| **Is the first step in RME (receptor binding to nutrient/ligand) signal transduction?
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| **Where do RME receptors (eg LDLR, transferrin receptor) fit in?
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| *<font color="navy">CELL CYCLE CHECKPOINTS (Val)</font color>
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| **How do the checkpoints fit with the signal transduction terms.
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| **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.
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| *<font color="violet">Connecting the signaling terms and response terms</font color>
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| == SourceForge Signaling Items ==
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| receptors and HAS_PART: http://sourceforge.net/tracker/?func=detail&aid=3103037&group_id=36855&atid=440764
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| receptor signaling proteins: http://sourceforge.net/tracker/?func=detail&aid=3101487&group_id=36855&atid=440764
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| purigenic receptors: http://sourceforge.net/tracker/?func=detail&aid=3088079&group_id=36855&atid=440764
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| MAPKKK cascade: http://sourceforge.net/tracker/?func=detail&aid=3085150&group_id=36855&atid=440764
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| Calcium-mediated signaling; http://sourceforge.net/tracker/?func=detail&aid=3077377&group_id=36855&atid=440764
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| morphogen: http://sourceforge.net/tracker/?func=detail&aid=3026415&group_id=36855&atid=440764
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| norrin signaling (example of non 1:1 receptor:ligand signaling) : http://sourceforge.net/tracker/?func=detail&aid=3041964&group_id=36855&atid=440764
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| hormone and hormone receptor signaling: http://sourceforge.net/tracker/?func=detail&aid=2974691&group_id=36855&atid=440764
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| Connecting up receptors and intracellular modules:
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| wnt signaling via hippo cascade: http://sourceforge.net/tracker/?func=detail&aid=3032564&group_id=36855&atid=440764
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| wnt signaling via JNK cascade: http://sourceforge.net/tracker/?func=detail&aid=3023417&group_id=36855&atid=440764
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| PI3K/AKT signaling: http://sourceforge.net/tracker/?func=detail&aid=3008502&group_id=36855&atid=440764
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| == Minutes ==
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| == Notes ==
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| Definition Adjustments:
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| Obsoleted Terms:
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| Moved Terms:
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| New Terms:
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