WBConfCall 2015.11.05-Agenda and Minutes

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  • WS252 models deadline
  • SObA phenotype graph re-worked using cytoscape.js
  • Generating lists of transcription factor target genes


  • SObA (Summary of Ontology-based Annotation) graph for phenotype: examples
daf-3 <>
daf-2 <>

Re-worked from an earlier version which was based on Graphviz. It is to be made into a widget on Gene pages, immediately below the Phenotypes widget, providing a summarized view of a gene's annotated phenotypes in an ontology-aware manner.


  • 5 model changes
  • Paul will use GitHub to commit edits to the models.wrm
  • Molecule model (Karen)
  • Expression pattern model change, to accommodate RNA-seq data (Daniela)
  • Housekeeping: Last reviewed for ?CDS, ?Transcript (Gary W)
  • Housekeeping: Add UNIQUE to Gene tag in ?Transcript, to enforce 1 ?Gene per ?Transcript
  • Pathogen tag in #Phenotype_info (Karen & Chris)
  • Models freeze by next Friday, 13th Nov

WS252 build

  • Upload end of first week of December (4th)
  • WS252 build: due at end of first week in January (8th)
  • Release schedule updated

TF binding sites

  • We would like to be able to determine a list of potential target genes for transcription factors
  • Todd will load "TF binding site" sequence features to WormMine
  • It is not clear if we can perform this query with Intermine
  • We may be able to download a list of sequence feature chromosomal coordinates from WormMine and then upload those as a list to BioMart (ParaSite BioMart?) returning a list of genes within range of those coordinates