Difference between revisions of "WBConfCall 2015.11.05-Agenda and Minutes"

From WormBaseWiki
Jump to navigationJump to search
m
m
Line 11: Line 11:
 
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.
 
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.
  
= WS252 =  
+
== WS252 ==  
 
* 5 model changes
 
* 5 model changes
 
* Paul will use GitHub to commit edits to the models.wrm
 
* Paul will use GitHub to commit edits to the models.wrm
Line 21: Line 21:
 
* Models freeze by Friday 13th
 
* Models freeze by Friday 13th
  
= WS252 build =
+
== WS252 build ==
 
* Upload end of first week of December (4th)
 
* Upload end of first week of December (4th)
 
* WS252 build: due at end of first week in January (8th)
 
* WS252 build: due at end of first week in January (8th)
 
* Release schedule updated
 
* Release schedule updated
  
= TF binding sites =
+
== 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

Revision as of 17:11, 5 November 2015

Agenda

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

Minutes

  • SObA (Summary of Ontology-based Annotation) graph for phenotype: examples
daf-3 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000899>
daf-2 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00000898>

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.

WS252

  • 5 model changes
  • Paul will use GitHub to commit edits to the models.wrm
  • Molecule model (Karen)
  • Expression pattern, for managing RNA-seq data (Daniela)
  • Housekeeping: Last reviewed CDS,transcript (Gary W)
  • Housekeeping: Add UNIQUE tag to transcript to gene, 1 gene per CDS
  • Pathogen tag in #Phenotype_info
  • Models freeze by Friday 13th

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