2015 International Worm Meeting

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20th International C. elegans Meeting, UCLA, June 24-28, 2015

Questions and Feature/Functionality Requests, by Topic

  • WormMine:
    • Network (Cytoscape) export from WormMine (probably more relevant when interactions are imported, but could theoretically be used for many datatypes)
    • Quick-share of WormMine results (a button to share a table immediately)
  • JBrowse:
    • Searching JBrowse with consensus sequences (I think that was the question/request)
  • WOBr (WormBase Ontology Browser):
    • Searching for a set of genes that are only known to be expressed in a particular cell or tissue (exclusive expression)
  • Gene Ontology annotations and enrichment:
    • Ontology term enrichment aside from just Gene Ontology terms, e.g. phenotype terms
    • Gene Ontology annotations made to specific transcripts (not just genes; this is a GO consortium issue also)
  • Concise descriptions:
    • Using Worm Breeder's Gazette (& meeting abstracts) for automated concise descriptions
  • Micropublications:
    • Will µPublications be indexed by PubMed?
    • Will µPublication preclude inclusion in later publication?
  • Allele-Phenotype Form:
    • In context of Allele-Phenotype form, making phenotypes searchable by checking genes involved in similar biological processes/functions (suggested by Harald Hutter)
    • So far we've received one, accidental, flagging of a paper for allele-phenotype data; one submission by Paul
  • Phenotypes display:
  • Grouping phenotypes in Phenotypes widget by type/branch of the ontology (suggested by Harald Hutter)
    • Would be great if we could have ontology-based annotations displayed/searchable as a minimal ontology, only displaying terms (children) of the ontology that are directly relevant to the annotation)
    • Could be directed-acyclic graph (DAG) or simple text tree
  • Million Mutation alleles
    • Julie Ahringer and several others requested separating the Million Mutation alleles and all other alleles into separate tables in the Genetics widget display for a given gene
  • UniProt ID conversion
    • There were several requests to convert a list of UniProt IDs (results of Mass-Spec analysis) to WB gene IDs for subsequent analysis