Difficult to read metabolic models when all small molecules are displayed

[ValWood]

The metabolic pathways are very hard to consume when they display all of the small molecules.
It would be better if there was a toggle to "collapse small molecules" so that you could see only the entities.

e.g
http://noctua.geneontology.org/workbench/noctua-alliance-pathway-preview/?model_id=gomodel%3AYeastPathways_TCA-EUK-PWY

http://noctua.geneontology.org/workbench/noctua-alliance-pathway-preview/?model_id=gomodel%3A633b013300000306

[vanaukenk]

Also, we should filter out duplicates in the list on the right side of the model.

[vanaukenk]

I think display of metabolic models needs some more discussion to address:

1. Possible different view with or without the chemicals
2. If we don't display the chemicals, figure out a rule for displaying 'provides input for' in the gene-only display.
3. Removing duplicate small molecules from the right-hand list.
4. How to get these models to display on the Alliance pages, i.e. meet the minimal criteria for a 'causal' model.

@cmungall

[ValWood]

If we don't display the chemicals, what causal relations would/should exist between the genes?

provides input for (rather than has input/has output). In the instances where we do add the chemical we use both...

[vanaukenk]

provides input for (rather than has input/has output). In the instances where we do add the chemical we use both...

Yes, sorry, that was more of a rhetorical question - this is our only relation option, but we'd need to figure out the display when that relation is not explicit in the model.

[ValWood]

But you always need one or the other? Sometimes we add both (i.e in cases where we really want to include the chemical before they can be imputed)

[ValWood]

And the display works:

[ValWood]

Ok I get it now. If only the chemical connections are present you would need to infer the gene-gene relation...

[vanaukenk]

Ok I get it now. If only the chemical connections are present you would need to infer the gene-gene relation...

Exactly!