WBConfCall 2015.11.05-Agenda and Minutes

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