Difference between revisions of "2016 Advisory Board Meeting"

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= Logistics =
 
= Logistics =
 +
*Caltech Map: [[Media:Caltech Map SAB 2016.pdf]]
 +
*Instructions for connecting to Network: [[Media:Wireless Instructions.pdf]]
  
 
== Attending ==
 
== Attending ==
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** Paul Kersey, Matt Berriman, Kevin Howe, Bruce Bolt, Jane Lomax, Michael Paulini, Paul Davis, Gary Williams
 
** Paul Kersey, Matt Berriman, Kevin Howe, Bruce Bolt, Jane Lomax, Michael Paulini, Paul Davis, Gary Williams
 
* OICR
 
* OICR
** Lincoln Stein, Todd Harris, Sibyl Gao, Adam Wright, Paulo Nuin
+
** Lincoln Stein, Todd Harris, Sibyl Gao, Adam Wright
  
 
== Travel ==
 
== Travel ==
Line 23: Line 25:
  
 
* [http://lab.stajich.org/home/people/jason-stajich Jason Stajich]
 
* [http://lab.stajich.org/home/people/jason-stajich Jason Stajich]
* [http://cherrylab.stanford.edu Mike Cherry]
+
* [http://cherrylab.stanford.edu Mike Cherry]--not present
 
* [http://irp.nih.gov/pi/brian-oliver Brian Oliver]
 
* [http://irp.nih.gov/pi/brian-oliver Brian Oliver]
 
* [http://hobertlab.org/ Oliver Hobert]
 
* [http://hobertlab.org/ Oliver Hobert]
 
* [http://www.neuro.uoregon.edu/westerf/lab.html Monte Westerfield]
 
* [http://www.neuro.uoregon.edu/westerf/lab.html Monte Westerfield]
* Robin Gasser (possible)
+
* [http://www.umassmed.edu/aroianlab Raffi Aroian]
 
+
* [http://villeneuve.stanford.edu/index.html Anne Villeneuve]
 +
* [http://biology.ucsd.edu/research/faculty/adchisholm  Andrew Chisholm], [http://blog.wormbase.org/2015/12/18/call-for-nominations-for-a-worm-board WormBoard]
  
 
= Discussion topics  =
 
= Discussion topics  =
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* '''Curation'''
 
* '''Curation'''
 
** How can we work with other MODs on curation strategy?
 
** How can we work with other MODs on curation strategy?
 +
** Are our priorities for curation appropriate?
 +
** How can we best make use of LEGO annotation?
  
 
* '''Genomics'''
 
* '''Genomics'''
** How should we prioritise species for curation effort?
+
** C. elegans
** Would a community curation system for gene models be useful for nematodes?
+
*** Should we update the reference genome with data from Li et al?
** Integration between WormBase and WB ParaSite - to what extent is this required?
+
*** What is the status of the initiative to select  (and sequence) a new reference strain?
 
+
*** Should we curate gene models in key strain genomes (e.g. Hawaiian)?
 +
*** A graph genome for C. elegans?
 +
*** Is curation/processing/display of all RNASeq data sets for C. elegans valuable? Sustainable?
 +
** Other species
 +
*** What criteria should be used to assess whether a genome is elevated to "core" status?
 +
*** Is special treatment of C. briggsae, C. remanei, C. brenneri and C. japonica still justified in light of the Caenorhabditis genome project?
 +
*** Would a community curation system for gene models be successful for nematodes?
 +
*** Where to focus curation effort for other nematodes?
 +
*** Integration between WormBase and WB ParaSite - to what extent is this required?
 +
 
* '''User interface'''
 
* '''User interface'''
 
** How best to measure the utility of WormBase (and similar resources)?
 
** How best to measure the utility of WormBase (and similar resources)?
Line 52: Line 66:
 
** Is the amount of effort we invest in maintaining/extending wormMine typical for other *Mine deployments?
 
** Is the amount of effort we invest in maintaining/extending wormMine typical for other *Mine deployments?
 
** Is use of non-open-source software for core data management an acceptable risk?
 
** Is use of non-open-source software for core data management an acceptable risk?
 
  
 
== Specific topics for project meeting / working groups ==
 
== Specific topics for project meeting / working groups ==
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** Specific plans for the next 6-12 months
 
** Specific plans for the next 6-12 months
 
** extending use to non-Caenorhabiditis sp
 
** extending use to non-Caenorhabiditis sp
 +
* '''WormBase and human disease'''
 +
** Linking C. elegans alelles to human pathogenic variants, or variants of unknown significance
 +
** What about a disease portal? Could be as simple as having a separate tab, this serves to increase visibility
 +
**Increasing number of papers on therapeutics for disease (drugs, small molecules, herbals)
 +
**Increasing number of papers on disease exacerbating metals and compounds (falls into two broad areas-disease and toxicity)
 
* '''How to better integrate WormBase services (i.e. WB and WBPS)'''
 
* '''How to better integrate WormBase services (i.e. WB and WBPS)'''
 
** Integrated search - what do we need to do to make this work?
 
** Integrated search - what do we need to do to make this work?
Line 71: Line 89:
 
* '''Texpresso for parasitic worms'''
 
* '''Texpresso for parasitic worms'''
 
** Discussions already started on this
 
** Discussions already started on this
*'''Gene summaries-legacy manual descriptions, the automatic gene descriptions, and community contributions to either of the former'''
+
*'''Gene summaries, one too many: legacy manual descriptions, the automatic gene descriptions, and community contributions'''
**How do we reconcile the different descriptions
+
**A plan to phase out the un-maintainable manual descriptions: Start with the oldest (by last_updated date) descriptions  
**Which ones do we choose to show on the website?  Showing all of them will be messy, and probably will confuse the users more than they will help
+
** Currently community contributions could be to a manual description, to an automated one or could be entirely new
**When do we pull the plug on the manual descriptions? Is it worth initiating a project to merge the manual and automatic descriptions
+
**With the automated descriptions being amenable to updates and the addition of new data (as and when they get curated in WB), should we even solicit community contributions?
(The above topic is most likely suited for a break-out group, but all suggestions and ideas welcome!)
+
**How do we merge the community contributions and the automated descriptions? Should we display them as one or separate them?
  
 
= Agenda (preliminary) =
 
= Agenda (preliminary) =
 +
 +
Google drive with useful docs in https://drive.google.com/drive/u/0/folders/0BwFG0nRdT4ZGVjM1REpNT0Q5YXM
  
 
== Wed 3rd Feb ==
 
== Wed 3rd Feb ==
  
* 1400 : Project meeting (part one)
+
* 1400 : Project meeting (part one). Morgan Library ([http://www.caltech.edu/map/william-g-kerckhoff-laboratories-of-the-biological-sciences Kerckhoff] 2nd fl)
  
 
== Thu 4th Feb ==
 
== Thu 4th Feb ==
 
+
'''[http://www.caltech.edu/map/w-m-keck-center Keck Conference Center] (Building 127, Room 155, Head towards the Broad cafe, past the gene pool)'''
 +
* 0900-0915 - Arrivals and discussion
 
* 0915-0930 - Introduction - Paul Sternberg
 
* 0915-0930 - Introduction - Paul Sternberg
 
* 0930 : Literature curation
 
* 0930 : Literature curation
** 0930-0935 - Overview - status and priorities - Chris
+
** 0930-0935 - Overview - status and priorities - Chris Grove
** 0935-0945 - Automation - doing more with less (Automated gene summaries) - Ranjana
+
** 0935-0945 - Automated identification of data - Karen Yook
** 0945-0955 - Community curation - overview, status, tracking - Mary Ann & Chris
+
** 0945-0955 - Automated writing of gene summaries - Ranjana Kishore
** 0955-1005 - Micropublications - an incentive for community participation - Daniela
+
** 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris
** 1005-1015 - LEGO - Kimberly
+
** 1005-1015 - Micropublications - an incentive for community participation - Daniela Raciti
** 1015-1045 - Discussion (+ specific questions for SAB)
+
** 1015-1025 - LEGO - Kimberly Van Auken
 +
** 1025-1045 - Discussion (+ specific questions for SAB)
  
 
* 1045 - 1100 : BREAK
 
* 1045 - 1100 : BREAK
  
 
* 1100 : Genomics
 
* 1100 : Genomics
** 1100-1120 - Integration and curation of hundreds of nematode genomes - Kevin
+
** 1100-1120 - Overview - genomics at WormBase - Kevin
** 1120-1140 - Curation and analysis of all C. elegans RNASeq gene expression data - Gary
+
** 1120-1140 - Curation and analysis of all RNASeq gene expression data - Gary
 
** 1140-1200 - WormBase and parasitic worms - Jane
 
** 1140-1200 - WormBase and parasitic worms - Jane
 
** 1200-1230 - Discussion (+ specific questions for SAB)
 
** 1200-1230 - Discussion (+ specific questions for SAB)
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* 1330 : User interface
 
* 1330 : User interface
** 1330-1350 - WormBase web-site - usage, outreach etc - Todd
+
** 1330-1345 - Website - architecture, structure, usage, outreach - Todd
** 1350-1400 - JBrowse - A new genome browser for WormBase  
+
** 1345-1350 - JBrowse - A new genome browser for WormBase - Todd
** 1400-1410 - Visualisation of Ontology annotations (incl WOBr, SObA etc) - Raymond
+
** 1350-1400 - Focus on new website features - Sibyl
** 1410-1425 - WormMine - Paulo
+
** 1400-1410 - Visualisation of Ontology annotations (incl [http://www.wormbase.org/tools/ontology_browser WOBr], [http://www.wormbase.org/species/c_elegans/gene/WBGene00000898#-bc-10 SObA]) - Raymond
 +
** 1410-1425 - WormMine - Todd
 
** 1425-1500 - Discussion (+ specific questions for SAB)
 
** 1425-1500 - Discussion (+ specific questions for SAB)
  
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* 1515: Infrastructure and interoperability
 
* 1515: Infrastructure and interoperability
** 1515-1530 - Overview of current data management strategy and vision for future - Todd / Kevin
+
** 1515-1530 - Overview of current data management strategy and vision for future - Kevin
 
** 1530-1545 - Database migration - status and roadmap - Adam
 
** 1530-1545 - Database migration - status and roadmap - Adam
 
** 1545-1600 - The InterMOD project and cross-MOD interoperability - Todd
 
** 1545-1600 - The InterMOD project and cross-MOD interoperability - Todd
Line 127: Line 150:
  
 
== Fri 5th Feb ==
 
== Fri 5th Feb ==
 
+
'''[http://www.caltech.edu/map/robert-a-millikan-memorial-library Millikan Library] Board room'''
 
* 0800-0900 : Advisors breakfast
 
* 0800-0900 : Advisors breakfast
 
* 0900-1130 : Advisors report back to whole group
 
* 0900-1130 : Advisors report back to whole group
 
* 1400-whenever : Project meeting (part two)
 
* 1400-whenever : Project meeting (part two)

Latest revision as of 13:27, 4 February 2016

The 2016 edition of the WormBase Scientific Advisory Board meeting will take place at Caltech on 4/5 Feb 2016.

Logistics

Attending

  • Hinxton
    • Paul Kersey, Matt Berriman, Kevin Howe, Bruce Bolt, Jane Lomax, Michael Paulini, Paul Davis, Gary Williams
  • OICR
    • Lincoln Stein, Todd Harris, Sibyl Gao, Adam Wright

Travel

  • Hinxton
    • Will fly out on the 2nd of Feb, and return on Sun 7th Feb (cheap flights)
  • OICR
    • Arrive 3rd Feb, depart 6th Feb
  • Remote workers
    • Mary Ann - arrive 2nd Feb (evening), leave 7th Feb (evening)

Advisors

Discussion topics

Organisation of SAB talks

Agenda for the SAB itself will be organised into 4 main sections. Each section will have a short overview/scene-setting talk, followed by selected specfic talks. Each section will end with a time-tabled open discussion, which we should use to discuss strategy in that area, and put any specfic questions we have to the advisory board. Please add suggested questions/discussion topics for each section below.

  • Curation
    • How can we work with other MODs on curation strategy?
    • Are our priorities for curation appropriate?
    • How can we best make use of LEGO annotation?
  • Genomics
    • C. elegans
      • Should we update the reference genome with data from Li et al?
      • What is the status of the initiative to select (and sequence) a new reference strain?
      • Should we curate gene models in key strain genomes (e.g. Hawaiian)?
      • A graph genome for C. elegans?
      • Is curation/processing/display of all RNASeq data sets for C. elegans valuable? Sustainable?
    • Other species
      • What criteria should be used to assess whether a genome is elevated to "core" status?
      • Is special treatment of C. briggsae, C. remanei, C. brenneri and C. japonica still justified in light of the Caenorhabditis genome project?
      • Would a community curation system for gene models be successful for nematodes?
      • Where to focus curation effort for other nematodes?
      • Integration between WormBase and WB ParaSite - to what extent is this required?
  • User interface
    • How best to measure the utility of WormBase (and similar resources)?
    • What new tools / views should we have (e.g. enrichment tool, RNASeq querying)
  • Infrastructure and interoperability
    • How important is it that our infrastructure solution is reusable by other MODs (or genomics data management projects)
    • Is the amount of effort we invest in maintaining/extending wormMine typical for other *Mine deployments?
    • Is use of non-open-source software for core data management an acceptable risk?

Specific topics for project meeting / working groups

  • Cross-site communication
    • Unification of documentation and code; what are our standards for documentation? For code?
  • Database migration
    • Specific plans for the next 6-12 months
    • extending use to non-Caenorhabiditis sp
  • WormBase and human disease
    • Linking C. elegans alelles to human pathogenic variants, or variants of unknown significance
    • What about a disease portal? Could be as simple as having a separate tab, this serves to increase visibility
    • Increasing number of papers on therapeutics for disease (drugs, small molecules, herbals)
    • Increasing number of papers on disease exacerbating metals and compounds (falls into two broad areas-disease and toxicity)
  • How to better integrate WormBase services (i.e. WB and WBPS)
    • Integrated search - what do we need to do to make this work?
    • Cross-site tools
      • Enrichment tool
      • Data mining
        • ParaSite has provision to replace BioMart with a system that supports "biologist friendly" queries, e.g. using set operation (a la EuPathDB, PomBase)
        • Is this on the InterMine road map?
        • If not, can we develop something that can be used in both WB and WBPS that complements (rather than competes with) WormMine?
  • Texpresso for parasitic worms
    • Discussions already started on this
  • Gene summaries, one too many: legacy manual descriptions, the automatic gene descriptions, and community contributions
    • A plan to phase out the un-maintainable manual descriptions: Start with the oldest (by last_updated date) descriptions
    • Currently community contributions could be to a manual description, to an automated one or could be entirely new
    • With the automated descriptions being amenable to updates and the addition of new data (as and when they get curated in WB), should we even solicit community contributions?
    • How do we merge the community contributions and the automated descriptions? Should we display them as one or separate them?

Agenda (preliminary)

Google drive with useful docs in https://drive.google.com/drive/u/0/folders/0BwFG0nRdT4ZGVjM1REpNT0Q5YXM

Wed 3rd Feb

  • 1400 : Project meeting (part one). Morgan Library (Kerckhoff 2nd fl)

Thu 4th Feb

Keck Conference Center (Building 127, Room 155, Head towards the Broad cafe, past the gene pool)

  • 0900-0915 - Arrivals and discussion
  • 0915-0930 - Introduction - Paul Sternberg
  • 0930 : Literature curation
    • 0930-0935 - Overview - status and priorities - Chris Grove
    • 0935-0945 - Automated identification of data - Karen Yook
    • 0945-0955 - Automated writing of gene summaries - Ranjana Kishore
    • 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris
    • 1005-1015 - Micropublications - an incentive for community participation - Daniela Raciti
    • 1015-1025 - LEGO - Kimberly Van Auken
    • 1025-1045 - Discussion (+ specific questions for SAB)
  • 1045 - 1100 : BREAK
  • 1100 : Genomics
    • 1100-1120 - Overview - genomics at WormBase - Kevin
    • 1120-1140 - Curation and analysis of all RNASeq gene expression data - Gary
    • 1140-1200 - WormBase and parasitic worms - Jane
    • 1200-1230 - Discussion (+ specific questions for SAB)
  • 1230-1330 : LUNCH
  • 1330 : User interface
    • 1330-1345 - Website - architecture, structure, usage, outreach - Todd
    • 1345-1350 - JBrowse - A new genome browser for WormBase - Todd
    • 1350-1400 - Focus on new website features - Sibyl
    • 1400-1410 - Visualisation of Ontology annotations (incl WOBr, SObA) - Raymond
    • 1410-1425 - WormMine - Todd
    • 1425-1500 - Discussion (+ specific questions for SAB)
  • 1500-1515 : BREAK
  • 1515: Infrastructure and interoperability
    • 1515-1530 - Overview of current data management strategy and vision for future - Kevin
    • 1530-1545 - Database migration - status and roadmap - Adam
    • 1545-1600 - The InterMOD project and cross-MOD interoperability - Todd
    • 1600-1630 - Discussion (+ specific questions for SAB)

1630-1645 : BREAK

  • 1645-1800: General discussion
    • Threat to NIH funding and alternative funding strategies
    • Working more closely with other MODs
    • How to make WormBase more useful/appealing to biomedical scientists

Fri 5th Feb

Millikan Library Board room

  • 0800-0900 : Advisors breakfast
  • 0900-1130 : Advisors report back to whole group
  • 1400-whenever : Project meeting (part two)