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

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(Created page with "= Agenda = * WS252 models deadline = Minutes =")
 
 
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= Agenda =
 
= Agenda =
 
* WS252 models deadline
 
* WS252 models deadline
 +
* SObA phenotype graph re-worked using cytoscape.js
 +
* Generating lists of transcription factor target genes
  
 
= Minutes =
 
= 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 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

Latest revision as of 18:47, 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 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