Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Raymond has added a link to the tool on the Tools page | * Raymond has added a link to the tool on the Tools page | ||
* Raymond will submit a ticket to put on the main Tools dropdown | * Raymond will submit a ticket to put on the main Tools dropdown | ||
+ | |||
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+ | == September 22, 2016 == | ||
+ | |||
+ | === GOC meeting at USC, November 4-6, Noctua Workshop November 7 === | ||
+ | *Next GO Consortium meeting is in early November at USC | ||
+ | *The consortium meeting will run from Friday, 11/4 - Sunday, 11/6 | ||
+ | *Noctua/LEGO workshop will be on Monday, 11/7 | ||
+ | *[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Logistics Meeting Logistics Page] | ||
+ | **We will need to add all WB curators to the attendees table | ||
+ | *[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda Meeting Agenda - in progress] |
Revision as of 16:57, 22 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- ZFIN has protein curation that may be becoming a bit out of date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
September 15, 2016
Strain curation with disease
- People create transgenic strains for modeling human disease
- We currently only curate strains in CGC (where we get our strain list)
- Other strains have been added via direct communication with Mary Ann
- Ranjana would like to capture strains affecting human disease from the literature
- Many strains not available in WormBase
- Is it worth curating these other strains? Yes; one concern that we would be diluting the quality of existing strains
- Big concern is whether or not the strain(s) are available
- (Raymond) Two aspects of strain curation: 1) strains that are available (e.g. from CGC) 2) carrier of genotype to use for other curation (like disease)
- (Raymond) We could just capture genotype as free text
- Would be best to curate the strains, regardless of availability
- Ranjana will send some example papers/strains to Mary Ann and they will discuss
- We could create links from strains in WB to the CGC (or state that people should write directly to the source lab; might be problematic).
WormBase header changes
- Miyuki has been working on new WormBase header; requests feedback
- Available on staging
Tissue enrichment analysis
- Tool is live and ready to use
- Raymond has added a link to the tool on the Tools page
- Raymond will submit a ticket to put on the main Tools dropdown
September 22, 2016
GOC meeting at USC, November 4-6, Noctua Workshop November 7
- Next GO Consortium meeting is in early November at USC
- The consortium meeting will run from Friday, 11/4 - Sunday, 11/6
- Noctua/LEGO workshop will be on Monday, 11/7
- Meeting Logistics Page
- We will need to add all WB curators to the attendees table
- Meeting Agenda - in progress