Paul Pavlidis

> @ppavlidis you mentioned the need for a tabular output, this can fit in here with the new `AbstractBatchProcessingCLI` class. Ok I will probably look at that this week

I doubt this is a bug per se. I would handle it as a curator issue first (and it is a cancer data set) There can be corrupt CEL files,...

This doesn't affect ontologies as far as I know. Besides removing the tables, we also will need/want to remove foreign key references in other tables. I've done the code removal;...

BTW I forgot that we already have been making regular dumps of the data in /space/gemmaData/PhenocartaExport, so we should also save the most recent of those (I've deleted all the...

I'm not sure but CHIRO might be what we want https://github.com/obophenotype/chiro However: * Hasn't been updated in at least 3 years; last release was 8 years ago * Uses DO...

It looks like we could use CHEBI to do some additional inference we aren't via the has_role relations like: ``` ... ``` CHEBI_10362=β-Cryptoxanthin RO_0000087=has role CHEBI_22586=antioxidant

Sounds good, I forgot about the masked-preferred thing -- it is not exposed in the web interface and this probably a big cause of the confusion. You can test the...

Here is an example of something that is going wrong and which I find confusing - I don't know how to fix it. https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?shortName=GSE11135 This data set was long flagged...

By the way, as I mentioned I was worried that changing the QT class hierarchy will be complicated, so it seems easier if we just clarify the name/meaning of "masked...

gene_info is the file we use already and we parse the gene type already, but it is not used. It is held in the NCBIGeneInfo so adding this would be...