2015 LEGO Jamboree Logistics: Difference between revisions
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[[Category:Consortium | [[Category: GO Consortium Meetings]] | ||
== Dates == | == Dates == | ||
* December 8-10, 2015 | * December 8-10, 2015 | ||
Line 11: | Line 11: | ||
== Participants == | == Participants == | ||
'''First Name Last Name | email''' | |||
* Giulia Antonazzo | ga362@gen.cam.ac.uk | |||
* Lionel Breuza | lionel.breuza@isb-sib.ch | |||
* Alan Bridge | alan.bridge@isb-sib.ch | |||
* Aurore Britan | Aurore.Britan@isb-sib.ch | |||
* Seth Carbon |sjcarbon@lbl.gov | |||
* Isabelle Cusin | Isabelle.Cusin@isb-sib.ch | |||
* Stacia Engel |stacia@stanford.edu | |||
* Marc Feuermann |marc.feuermann@isb-sib.ch | |||
* Pascale Gaudet |pascale.gaudet@sib-sib.ch | |||
* David Hill |david.hill@jax.org | |||
* Valérie Hinard |Valerie.Hinard@isb-sib.ch | |||
* Ruth Lovering |r.lovering@ucl.ac.uk | |||
* Huaiyu Mi |huaiyumi@usc.edu | |||
* Chris Mungall |cjmungall@lbl.gov | |||
* Anne Niknejad |Anne.Niknejad@unil.ch | |||
* Sylvain Poux |sylvain.poux@isb-sib.ch | |||
* Paul Thomas |pdthomas@med.usc.edu | |||
* Kimberly Van Auken |vanauken@caltech.edu | |||
* Valerie Wood |vw253@cam.ac.uk | |||
==Hotels== | ==Hotels== | ||
Line 19: | Line 38: | ||
===Tuesday, December 8th=== | ===Tuesday, December 8th=== | ||
BlueJeans: https://bluejeans.com/921716595 | |||
====Schedule==== | ====Schedule==== | ||
*10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris | *10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris | ||
**For a more general audience | **For a more general audience | ||
* | *11:30am Workshop Begins: More specific introduction to LEGO for curators | ||
*Lunch | *Lunch | ||
*1:30pm? Hands-on with Noctua | *1:30pm? Hands-on with Noctua | ||
**Creating simple annatons in Noctua | **Demo: Creating simple annatons in Noctua (David) | ||
*** A simple enzyme paper ''Pfkl''-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280 | *** A simple enzyme paper ''Pfkl''-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280 | ||
*** A regulation paper ''Pfkl''-- http://www.ncbi.nlm.nih.gov/pubmed/6446714 | **** Main figure to annotate: Figure 1 (open circles) | ||
*** A regulation paper ''Pfkl''-- http://www.ncbi.nlm.nih.gov/pubmed/6446714 also see http://www.ncbi.nlm.nih.gov/books/NBK22395/ | |||
**** Main figure to annotate: Figure 4 | |||
====Discussion and Action Items==== | ====Discussion and Action Items==== | ||
===Wednesday, December 9th=== | ===Wednesday, December 9th=== | ||
BlueJeans: https://bluejeans.com/421981965 | |||
====Schedule==== | ====Schedule==== | ||
*Continuing on with annotation examples and suggested papers from participants: | *Continuing on with annotation examples and suggested papers from participants: | ||
=====November Annotation Consistency Exercise===== | |||
*Annotating causal relationships and downstream effects | *Annotating causal relationships and downstream effects | ||
**TAIR annotation consistency exercise: [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.] | **TAIR annotation consistency exercise: [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.] | ||
*Annotations involving specific isoforms | **[http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2015-11-24 November Annotation Consistency Exercise] | ||
**WormBase: [http://www.ncbi.nlm.nih.gov/pubmed/25148942 MIG-10 (Lamellipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans.] | =====MGI===== | ||
*Role of SWI/SNF complex during retinogenesis | |||
**MGI: [http://dev.biologists.org/content/142/23/4092 Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma] '''Open Access''' | |||
*Autophagy and cellular differentiation | |||
**MGI and Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/17476689 PIM-2 is an independent regulator of chondrocyte survival and autophagy in the epiphyseal growth plate.] | |||
=====PomBase===== | |||
*This paper shows that the Msd1/wdr8 complex is transported to the SPB by dynein, and then subsequently involved in microtubule attachment to the SPB | |||
**PomBase: [http://www.ncbi.nlm.nih.gov/pubmed/25987607 The Msd1-Wdr8-Pkl1 complex anchors microtubule minus ends to fission yeast spindle pole bodies] '''Open Access''' | |||
*Localized cell polarization and GTPase cycle - to be discussed possibly at a later time | |||
**PomBase: [http://www.ncbi.nlm.nih.gov/pubmed/24554432 The Tea4-PP1 landmark promotes local growth by dual Cdc42 GEF recruitment and GAP exclusion.] '''Open Access''' | |||
=====Swiss-Prot===== | |||
*Regulation of cell proliferation, ubiquitin ligase activity, protein stabilization and localization | |||
**Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of HDM2.] '''Open Access''' | |||
*Signaling pathways and their outputs | |||
**Swiss-Prot:[http://www.ncbi.nlm.nih.gov/pubmed/26527061 cAMP/PKA enhances interleukin-1β-induced interleukin-6 synthesis through STAT3 in glial cells] | |||
*Apoptotic cell clearance pathway | |||
**Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/23596312 Bruton's tyrosine kinase is required for apoptotic cell uptake via regulating the phosphorylation and localization of calreticulin] '''Open Access''' | |||
=====UCL===== | |||
*miRNA-mediated regulation of transcription factor activity and transcription of enzyme responsible for H2S production and subsequent cell differentation | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/21659522 Specificity protein-1 as a critical regulator of human cystathionine gamma-lyase in smooth muscle cells.] '''Open Access''' | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/22034194 MicroRNA-21 represses human cystathionine gamma-lyase expression by targeting at specificity protein-1 in smooth muscle cells.] | |||
*Mix of species in paper | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/25088257 Ubiquitin-specific protease 19 regulates the stability of the E3 ubiquitin ligase MARCH6.] | |||
*Useful example of when the substrate is a non-protein (for the ribonuclease activity). | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/21317875 Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response.] '''Open Access''' | |||
*Looks like a relatively simple annotation model | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/11163209 ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs.] '''Open Access''' | |||
*More complicated view of ER stress and UPR | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/20160352 Wolfram syndrome 1 gene negatively regulates ER stress signaling in rodent and human cells.] '''Open Access''' | |||
*Regulation of transcription factor activity via protein stabilization, localization - direct or indirect regulation? | |||
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/17015834 DJ-1, a cancer- and Parkinson's disease-associated protein, stabilizes the antioxidant transcriptional master regulator Nrf2.] '''Open Access''' | |||
=====WormBase===== | |||
*Annotations involving specific isoforms and feedforward circuits; also anatomical and life stage annotation context | |||
**WormBase: [http://www.ncbi.nlm.nih.gov/pubmed/25148942 MIG-10 (Lamellipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans.] '''Open Access''' | |||
====Discussion and Action Items==== | ====Discussion and Action Items==== | ||
===Thursday, December 10th=== | ===Thursday, December 10th=== | ||
BlueJeans: https://bluejeans.com/161891171 | |||
====Schedule==== | ====Schedule==== | ||
*Future plans and thoughts | *Future plans and thoughts | ||
**Seeding models | **Seeding models | ||
**Plans for going forward | **Plans for going forward | ||
***Dedicated LEGO curation conference calls? | |||
====Discussion and Action Items==== | ====Discussion and Action Items==== | ||
==Remote Attendees== | ==Remote Attendees== | ||
Doug Howe - ZFIN - sorry I can't be there in person! If you are able to webcast any portions, I'd be happy to drink lots of coffee on my end. | |||
Sabrina Toro - ZFIN | |||
==Group photo== | ==Group photo== | ||
[[Image: LEGO_jamboree_2015_group_photo.JPG |1200px]] |
Latest revision as of 11:53, 12 April 2019
Dates
- December 8-10, 2015
- Start 9am December 8
- End at noon December 10, optionally continue through 4pm or so.
Venue
Geneva, Switzerland
Campus Biotech
Participants
First Name Last Name | email
- Giulia Antonazzo | ga362@gen.cam.ac.uk
- Lionel Breuza | lionel.breuza@isb-sib.ch
- Alan Bridge | alan.bridge@isb-sib.ch
- Aurore Britan | Aurore.Britan@isb-sib.ch
- Seth Carbon |sjcarbon@lbl.gov
- Isabelle Cusin | Isabelle.Cusin@isb-sib.ch
- Stacia Engel |stacia@stanford.edu
- Marc Feuermann |marc.feuermann@isb-sib.ch
- Pascale Gaudet |pascale.gaudet@sib-sib.ch
- David Hill |david.hill@jax.org
- Valérie Hinard |Valerie.Hinard@isb-sib.ch
- Ruth Lovering |r.lovering@ucl.ac.uk
- Huaiyu Mi |huaiyumi@usc.edu
- Chris Mungall |cjmungall@lbl.gov
- Anne Niknejad |Anne.Niknejad@unil.ch
- Sylvain Poux |sylvain.poux@isb-sib.ch
- Paul Thomas |pdthomas@med.usc.edu
- Kimberly Van Auken |vanauken@caltech.edu
- Valerie Wood |vw253@cam.ac.uk
Hotels
Agenda
Tuesday, December 8th
BlueJeans: https://bluejeans.com/921716595
Schedule
- 10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris
- For a more general audience
- 11:30am Workshop Begins: More specific introduction to LEGO for curators
- Lunch
- 1:30pm? Hands-on with Noctua
- Demo: Creating simple annatons in Noctua (David)
- A simple enzyme paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
- Main figure to annotate: Figure 1 (open circles)
- A regulation paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/6446714 also see http://www.ncbi.nlm.nih.gov/books/NBK22395/
- Main figure to annotate: Figure 4
- A simple enzyme paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
- Demo: Creating simple annatons in Noctua (David)
Discussion and Action Items
Wednesday, December 9th
BlueJeans: https://bluejeans.com/421981965
Schedule
- Continuing on with annotation examples and suggested papers from participants:
November Annotation Consistency Exercise
- Annotating causal relationships and downstream effects
- TAIR annotation consistency exercise: The MYB36 transcription factor orchestrates Casparian strip formation.
- November Annotation Consistency Exercise
MGI
- Role of SWI/SNF complex during retinogenesis
- Autophagy and cellular differentiation
PomBase
- This paper shows that the Msd1/wdr8 complex is transported to the SPB by dynein, and then subsequently involved in microtubule attachment to the SPB
- Localized cell polarization and GTPase cycle - to be discussed possibly at a later time
Swiss-Prot
- Regulation of cell proliferation, ubiquitin ligase activity, protein stabilization and localization
- Swiss-Prot: A novel ARF-binding protein (LZAP) alters ARF regulation of HDM2. Open Access
- Signaling pathways and their outputs
- Apoptotic cell clearance pathway
UCL
- miRNA-mediated regulation of transcription factor activity and transcription of enzyme responsible for H2S production and subsequent cell differentation
- Mix of species in paper
- Useful example of when the substrate is a non-protein (for the ribonuclease activity).
- Looks like a relatively simple annotation model
- More complicated view of ER stress and UPR
- Regulation of transcription factor activity via protein stabilization, localization - direct or indirect regulation?
WormBase
- Annotations involving specific isoforms and feedforward circuits; also anatomical and life stage annotation context
Discussion and Action Items
Thursday, December 10th
BlueJeans: https://bluejeans.com/161891171
Schedule
- Future plans and thoughts
- Seeding models
- Plans for going forward
- Dedicated LEGO curation conference calls?
Discussion and Action Items
Remote Attendees
Doug Howe - ZFIN - sorry I can't be there in person! If you are able to webcast any portions, I'd be happy to drink lots of coffee on my end. Sabrina Toro - ZFIN