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 == | ||
Line 9: | Line 11: | ||
** 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 | + | ** 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] | ||
* [http://www.umassmed.edu/aroianlab Raffi Aroian] | * [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 = | ||
Line 38: | Line 41: | ||
* '''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''' | ||
− | ** | + | ** C. elegans |
− | ** Would a community curation system for gene models be | + | *** 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 == | ||
Line 63: | Line 76: | ||
* '''WormBase and human disease''' | * '''WormBase and human disease''' | ||
** Linking C. elegans alelles to human pathogenic variants, or variants of unknown significance | ** 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 73: | Line 89: | ||
* '''Texpresso for parasitic worms''' | * '''Texpresso for parasitic worms''' | ||
** Discussions already started on this | ** Discussions already started on this | ||
− | *'''Gene summaries | + | *'''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) = | = 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 | + | ** 0935-0945 - Automated identification of data - Karen Yook |
− | ** 0945-0955 | + | ** 0945-0955 - Automated writing of gene summaries - Ranjana Kishore |
** 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris | ** 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris | ||
− | ** 1005-1015 - Micropublications - an incentive for community participation - Daniela | + | ** 1005-1015 - Micropublications - an incentive for community participation - Daniela Raciti |
− | ** 1015-1025 - LEGO - Kimberly | + | ** 1015-1025 - LEGO - Kimberly Van Auken |
** 1025-1045 - Discussion (+ specific questions for SAB) | ** 1025-1045 - Discussion (+ specific questions for SAB) | ||
Line 100: | Line 119: | ||
* 1100 : Genomics | * 1100 : Genomics | ||
− | ** 1100-1120 - Overview - | + | ** 1100-1120 - Overview - genomics at WormBase - Kevin |
− | ** 1120-1140 - Curation and analysis of all | + | ** 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) | ||
Line 108: | Line 127: | ||
* 1330 : User interface | * 1330 : User interface | ||
− | ** 1330- | + | ** 1330-1345 - Website - architecture, structure, usage, outreach - Todd |
− | ** 1350 | + | ** 1345-1350 - JBrowse - A new genome browser for WormBase - Todd |
− | ** 1400-1410 - Visualisation of Ontology annotations (incl WOBr, SObA | + | ** 1350-1400 - Focus on new website features - Sibyl |
− | ** 1410-1425 - WormMine - | + | ** 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) | ||
Line 117: | Line 137: | ||
* 1515: Infrastructure and interoperability | * 1515: Infrastructure and interoperability | ||
− | ** 1515-1530 - Overview of current data management strategy and vision for future - | + | ** 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 130: | 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.
Contents
Logistics
- Caltech Map: Media:Caltech Map SAB 2016.pdf
- Instructions for connecting to Network: Media:Wireless Instructions.pdf
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
- Jason Stajich
- Mike Cherry--not present
- Brian Oliver
- Oliver Hobert
- Monte Westerfield
- Raffi Aroian
- Anne Villeneuve
- Andrew Chisholm, WormBoard
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?
- C. elegans
- 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)