2015 International Worm Meeting

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
  • Using personal communications

• 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

• Job posting
  • a couple of 'PI to be' asked if we had a specific Job portal where they could recruit grad students/postdocs
  • Micheal P sent the link to the forum: http://forums.wormbase.org/index.php?board=1.0

• Steinernema gene names
  • Marissa from Ali Mortazavi's lab asked if we could apply C. elegans gene names to Steinernema genes when there is one-to-one orthology

• RNAseq display
  • Julie Ahringer suggested to change the RNAseq data display, elevating the Hillier dataset by displaying it at the top of the expression widget in a graphical way

• PI lists
  • Sophie Jarriault would like lists of PI listed by e.g. based in Europe

• Outreach suggestions
• You Tube tutorials
• FAQs
• Regular WBG article to have Top Tips, Top Help Desk questions