WBConfCall 2015.10.01-Agenda and Minutes

From WormBaseWiki
Jump to navigationJump to search


Summary of Ontology-based Annotations (SObA)

  • Caltech (Raymond, Juancarlos, Chris) worked on new phenotype summary view
  • Had a round of feedback and review
  • Caltech would like to get the new view up and running for the website
  • May need to work out Javascript issues (collisions) between main site and auxiliary scripts & dependencies
  • Best to use existing libraries, JQuery; will probably only use simple custom-written Javascript
  • Code generated at Caltech will be documented and archived on GitHub
  • Can consider Cytoscape JS

SAB 2016

  • February 4th-5th, 2016, Thursday & Friday
  • Who are advisors; any suggestions send to Paul
  • What feedback do we want from SAB this year?
  • What new tools or features should we be working on? What do other sites have that we don't?
  • We should bring data/feedback on community curation form usage
  • Would be good to have an assessment/comparison of what all the MODs have and how they perform

Legacy site usage

  • Bill Mohler asking about neuron images (from White thesis, Mind of a Worm/Worm Atlas)
    • neurons colored red in images on legacy
  • Raymond will work with Daniela to get anatomy-associated images displayed on the website
  • Need to find the images
  • These cartoons are a nice complement to Virtual Worm images


  • Build starts next week
  • People should write entries for release notes and send to Hinxton

Gene association files (GAFs)

  • GAFs currently need to be processed for downstream use/analysis in the WormBase Ontology Browser, etc.
  • Raymond requesting the generation of separately formatted GAFs for different downstream applications
  • One issue is qualitative vs. quantitative data (e.g. qualitative expression pattern annotations vs quantitative RNA-Seq analyses)
  • Would be good to have distinct views of expression data, based on confidence and/or method
  • This has implications for comparative analysis of species available in ParaSite

Help Desk question about papers with cell lineage data

  • We don't have papers specifically flagged for cell lineage data - however, authors are asked to flag mosaic data, ablation data, and cell function data. The AFP (and CFP) "cellfunc", "siteaction", "mosaic", and "ablationdata" datatypes are called "blastomere", "exprmosaic", "geneticmosaic", "laserablation" in the Curation Status form, there has been data flagged by authors for these datatypes ( http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi)
  • It is on Raymond's to do list; not a trivial problem