WormBase-Caltech Weekly Calls

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January 4, 2018

WS264 Upload

  • Citace upload to Wen, Tuesday January 16th, by 10am PST
  • Upload to Hinxton on Jan 19th

Strain data import to AGR for disease

  • Will begin to consider pulling in strains into AGR
  • Will need to think about how genotypes are built and stored at other MODs
  • We should encourage authors to include strain IDs
  • Diseases are annotated to genes, alleles, and strains within WB

Curating phenotypes and diseases to strains or genotypes

  • Should we generate a ?Genotype class to capture genotypes without a known strain name? Or to capture relevant/relative genotypes thought to be responsible for a phenotype or disease?
  • We could create un-named strain objects, that use a new unique identifier as a primary identifier and represent the entire genotype of a strain used
    • Introduction of a new ?Strain class attribute of a unique serial identifier (like WBStrain00001) would be very costly to implement; would need to consider how crucial this is before implementing
    • We can, instead, use new strain (public) names like "WBPaper00012345_Strain1", etc. instead of creating new unique ID attribute for un-named strains
  • When curating phenotypes to strains, we will want to specify what is the relevant/relative genotype that is causative/correlated with the disease or phenotype observation
    • Would be best if the specification of the relevant genotype used controlled vocabularies (when possible) and free text (when needed); would need to work out the logistics/mechanics of such curation
    • Transgene-phenotype curation currently specifies causative gene, but would be more complicated for strains
  • Alternatively, we could create the ?Genotype class to represent the abstract "relative"/"relevant" genotype thought to be responsible for the phenotype or disease, and annotate directly to that ?Genotype object
  • ?Strain approach:
    • Use strain if named (but important to know if the control strain is not simply N2)
      • If control strain is simply N2, causative genotype (and respective components) can be inferred from strain genotype
      • If control strain is not N2, causative genotype and components would need to be specified at the moment of phenotype/disease curation (by mechanism to be worked out)
    • If no strain name provided, create "un-named" strain that contains the entire genotype provided by authors
      • Control strain issues above would still need to be addressed
  • ?Genotype approach:
    • ?Genotype class could represent individual instances of relevant/relative genotypes that are suggested to be causative for a disease or phenotype
    • ?Genotype objects would be created with formal construction, with DB associations to each component object (e.g. alleles, transgenes, etc.) as well as free text descriptions (for components with no corresponding DB object)
    • Such ?Genotype objects could be used repeatedly throughout a paper when applicable, but would likely not be used in any other papers (we would likely accumulate redundant objects in the DB)
  • We may want to consider strains with same public name that have diverged
    • Apply new strain names with prefixes/suffixes? Create new strain objects? Keep original?
  • Need to determine how each AGR member DB curates phenotypes or diseases to genotypes: is each "genotype" a relative or absolute genotype?

January 11, 2018

IWM swag

  • Eppendorf tube openers with WormBase logo?

Update on AFP Form

  • Idea is to move from author flagging to author validation of text mining and data submission wherever possible
  • Goal is to flag all data types in a paper and either curate at WB or share with a group that does curate that data
  • SVM flags and author flags can/will be used as filters in TPC
  • Provide examples of what we want for each type of data to help avoid confusion
  • Recognize entities automatically and show list to author
    • Species, strains, genes, alleles, transgenes, etc.
    • Ask to verify or add unrecognized
    • Could show known/existing objects with checkboxes
    • Possibly include unrecognized pattern matching objects? Ask author to verify if these are real?
    • For strains:
      • Show recorded genotype for verification; maybe ask to update/modify if needed?
    • For transgenes:
      • When author submits new transgene, send them to a transgene form, or send them an email asking for details?
      • Form could be for both strain and transgene
  • Mapping data: still ask for? Maybe for balancers, but no one is reporting that. Could still ask if there's interest
  • Maybe provide option for author to save their progress and return to the form later
  • Phenotypes
    • Ask for allele, RNAi and overexpression phenotypes with links to Phenotype form
    • Also ask for drug/chemical and environmental perturbations (call treatment?); store as free text for now, accommodate with new data model when available
  • Gene site- and time-of-action, mosaic
    • Appears to be confusion from authors about mosaics. Should we keep this?
    • Will keep gene site-of-action and time-of-action; leave unchecked (no SVM, yet) but allow users to indicate
  • Cell and anatomy data
    • Cell function ("Cell ablation (laser/genetic) data, optogenetics")
    • Ultrastructural analysis
  • Interaction data
    • Genetic interactions
    • Physical interactions
    • Functional complementation
  • Comparative genomics
  • Gene expression & regulation

January 18, 2018

WormBase Tutorials

  • May be good to get (possibly anonymous) written questions or suggestions after presenting
  • Wen will have Skype call with Yishi Jin
  • Micropublications
    • how do we peer-review single experiment? No supporting information to corroborate a larger story
    • Is the greater benefit of peer-review that the whole story is assessed by reviewers
    • Do MPs help or hurt reproducibility?
    • Larger papers may have lots of poor experiments that don't get much attention but still pass peer review
    • Dedicated peer review on single experiment may be more rigorous
    • What are the criteria/minimal requirements to micropublish?
  • Concise descriptions
    • SimpleMine has multiple descriptions output; people asked about the different types
    • Yishi Jin suggested that we remind users to update manually written descriptions
    • Showing last-updated date is important
    • Automated descriptions relies on primary data; will rely on forms and community submissions
    • Microreviews? Would want to guide authors what data we want; provide a template?
  • Public/community education issues
    • Users shouldn't assume that WormBase is comprehensively up to date
  • Wen will also present at MidWest meeting (Ann Arbor, MI) in April and Boulder, Colorado in May
    • Will assess topic interest ahead of time

New Cytoscape display for interactions

  • Sibyl developed a new Cytoscape display for interactions, now live with WS262 release
  • Simplified colors and subtypes
  • Redraw button to clean up the graph based on what you want to see
  • Play around and let Sibyl and/or Chris know about issues

January 25, 2018

UCSF visit report