Adding genes with alternate capitalizations to the same model

[Jeremy Sandler]

Hello,

I'm building a set of small GRN models comparing the same GRN and tissue in different organisms. I've come across a problem that BioTapestry will not let me add the same genes with different capitalizations to the same network. For example, in drosophila and zebrafish, genes are written uncapitalized "gene1, gene2", while in mouse, the same genes are capitalized "Gene1, Gene2". When I try to add both versions, I get the following error:

"Gene is Not New. Gene already exists in a parent model. You will be placing an existing gene."

Is there a way around this error? I would like to create side by side models of GRNs without having to build a new model for each species and switch back and forth for every change.

Thanks,

Jeremy Sandler

[William Longabaugh]

Jeremy:

BioTapestry does support name overrides at the second level "View from All Nuclei (VfA)", which is the model level where side-by-side comparisons are appropriate. Given the VfG model in the first attachment, the VfA submodel in the second attachment can be created using the Gene Property dialog (third attachment).

The enforcement of gene name uniqueness, including case, in the top-level VfG is crucial to conform to the BioTapestry model hierarchy. A gene can only exist once in the VfG, as that is the underpinning of how the model hierarchy is designed.

 

I would recommend using a single gene vocabulary when working the model, then switching names only as a final step as a cosmetic fix. You might even call the gene "Gene1/gene1" at the VfG level and then tailor it in both region instances in the VfA. This "name override" feature is very, very old, and there are likely hidden bugs when using it.

Thanks for your interest in Biotapestry.

Bill

 

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[Bill Longabaugh]

I should note that a combination name ("Gene1/gene1") at the VfG level makes the most sense if you are working with different names e.g. "Toll-2/18w"

Bill 

[Malcolm Cook]

Might it suit your purposes to relabel the genes as "<geneName>/<organism>"  yielding, e.g.,gene1/mouse gene2/mouse Gene1/danio Gene2/danio ?

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