Difference between revisions of "2015 International Worm Meeting"

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* '''Phenotypes display''':
 
* '''Phenotypes display''':
* Grouping phenotypes in Phenotypes widget by type/branch of the ontology (suggested by Harald Hutter)
+
** 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)
 
** 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
 
** Could be directed-acyclic graph (DAG) or simple text tree
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* '''Job posting'''
 
* '''Job posting'''
 
**a couple of 'PI to be' asked if we had a specific Job portal where they could recruit grad students/postdocs
 
**a couple of 'PI to be' asked if we had a specific Job portal where they could recruit grad students/postdocs
**an example for zfin is: https://wiki.zfin.org/display/jobs/Zebrafish-Related+Job+Announcements and xenbase: http://www.xenbase.org/community/jobSearch.do?method=search
+
** Micheal P sent the link to the forum: http://forums.wormbase.org/index.php?board=1.0
  
 
* '''Steinernema gene names'''
 
* '''Steinernema gene names'''
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* '''RNAseq display'''
 
* '''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
 
** 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

Latest revision as of 13:54, 8 July 2015

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
  • 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