Difference between revisions of "WBConfCall 2015.11.05-Agenda and 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