Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Phenotype assay model proposal (Chris) === | === Phenotype assay model proposal (Chris) === | ||
* Trying to create a model that can accommodate complex genotypes and make querying phenotype experimental data easier | * Trying to create a model that can accommodate complex genotypes and make querying phenotype experimental data easier | ||
− | * Want to co-opt | + | * Want to co-opt an existing, unused model ?Phenotype_assay to encapsulate details of an experiment |
+ | * Proposal is to pull several tags from ?RNAi and #Phenotype_info into the ?Phenotype_assay class | ||
+ | * Remaining tags in ?RNAi could be used to hold RNAi mapping information | ||
+ | * Remaining rags in #Phenotype_info can be used to describe the nature of an allele in the context of a phenotype, or nature of phenotype (Ease of scoring) | ||
+ | * Maybe should keep penetrance, quality and EQ annotations in #Phenotype_info so as to provide detail for each phenotype when multiple phenotypes are used | ||
+ | * It is currently difficult to recreate a phenotype annotation made by a curator using the OA, as so much experimental detail is captured exclusively in the hash |
Revision as of 20:29, 8 September 2016
Contents
Previous Years
2016 Meetings
September 1, 2016
Working group discussions
- More clear about issues surrounding orthology sets
- ZFIN has protein curation that may be becoming a bit out of date
Single-cell RNA profiling
- We've been curating some data, but not clear how to display the data
- Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
- Genes that are detected at convincing levels (present call) in cell/tissue
- Should we display expression data that we do not (or cannot) update differently from other data
- Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
- Could capture quantitative assessments; transcripts per million, etc.
- Should we provide an analysis of raw data to users to perform their own comparative analyses
- Bob Goldstein's group prepared software tools in their paper; could we make use of them?
- Big question: how do we handle divergent (expression) data?
- David (Angeles) working on an expression data analysis pipeline
- Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
- There's difficulty in reconciling small and large datasets (or different data types)
- Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
- In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage
September 8, 2016
TransgeneOme import (Daniela)
- adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data.
- for the records- documentation on the import here: http://wiki.wormbase.org/index.php/TransgeneOme_import
- Daniela and Juancarlos worked on parsing large JSON import
- Data is dynamic: people can add images and annotations; will be updated every WormBase release
- Do we want to import the person that created the annotation via the TransgeneOme project?
- Maybe, but should be free text instead of a modeled tag for WBPersons (Raymond)
- It is likely sufficient to point WB users to the TransgeneOme annotation, without explicitly referencing the contributor
Phenotype assay model proposal (Chris)
- Trying to create a model that can accommodate complex genotypes and make querying phenotype experimental data easier
- Want to co-opt an existing, unused model ?Phenotype_assay to encapsulate details of an experiment
- Proposal is to pull several tags from ?RNAi and #Phenotype_info into the ?Phenotype_assay class
- Remaining tags in ?RNAi could be used to hold RNAi mapping information
- Remaining rags in #Phenotype_info can be used to describe the nature of an allele in the context of a phenotype, or nature of phenotype (Ease of scoring)
- Maybe should keep penetrance, quality and EQ annotations in #Phenotype_info so as to provide detail for each phenotype when multiple phenotypes are used
- It is currently difficult to recreate a phenotype annotation made by a curator using the OA, as so much experimental detail is captured exclusively in the hash