Paul Pavlidis

Add "constitutively activating variant" as a subclass of "gain_of_function_variant"

2

**What is this request referring to?** Constitutively activating variant **What is the name you would like SO to give the term?** constitutively_activating_variant **What is the definition that you would like...

New term requests

1

label: BV2 synonyms: NICR63 cell xref: https://www.cellosaurus.org/CVCL_0182 subclass of immortal microglial cell line cell (http://purl.obolibrary.org/obo/CLO_0000098) label: LN228 synonyms LN 229; LN229; LNT-229 xref: https://www.cellosaurus.org/CVCL_0393 label: M249 xref: https://www.cellosaurus.org/CVCL_D755 Thanks.

incorrect batch information badges

5

The logic behind these has to be reviewed again, as there are still problems with the wrong badge being shown. It probably needs a more thorough revamp. Example: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?shortName=GSE74634 -...

quantitation type validation error

3

For an RNA-seq data set: [GSE228497](https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=27644) while running `rnaseqDataAdd` This triggers warnings, not an exception, thankfully. These data are not ratiometric and are definitely on a log2 scale, and looks...

Generating DEA archive files can fail for analyses with continuous factors

1

As flagged in https://github.com/PavlidisLab/GemmaCuration/issues/328 ExpressionDataFileServiceImpl.analysisResultSetWithContrastsToString:621 is the culprit

Heatmaps don't always show the experimental design information

2

Sometimes the heatmap fails to show the column heading information. I've seen this happen but it's not easily reproducible. It was working fine with [this experiment](https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=27066) but then the sample...

There are some operations like ExpressionExperimentService.addFactorValues (used to assign values to continuous factors) which create FactorValues, and generate thousands of ACL SELECT queries in the process FactorValues are SecuredChildren of...

ArrayDesignDao.numCompositeSequenceWithGenes doesn't return right results when dummy geneproducts are present

1

For the [human generic platform](https://gemma.msl.ubc.ca/arrays/showArrayDesign.html?id=735), this returns only ~1800, but ArrayDesignDao.numGenes returns the expected (larger) value ( ses the GENE2CS table), as does this query: `select count(distinct cs.ID) from COMPOSITE_SEQUENCE...