kaiiam / demo Goto Github PK

xref EnvironmentOntology/envo#1006 (comment), trying @laurenechan's robot template (Sheet 1).

For the new ENVO-Robot-template-and-merge-workflow documentation the only obviously missing step is the ability to add annotation properties onto annotation properties, for example

James noted that it is possible and to see the following section form the robot template docs:

>A (axiom annotations): ROBOT can also annotate logical and annotation axioms. The axiom annotation will be on the axiom created on the cell to the left of the >A* template string. The > symbol can be used in front of any valid annotation character (>A, >AT, >AL, >AI)

In EnvironmentOntology/envo#1028 we were attempting a robot merge workflow to complie a robot module via template and then merge it into the envo-edit.owl. I was attempting to do this in EnvironmentOntology/envo#1043, but unfortunately the robot merge workflow seemed to shuffle the lines around hence the extremely large diff in the envo-edit.owl file, even though in protege it looks as expected. @pbuttigieg I Will experiment around with these issues in a branch here.

Attempting to see if I can use Robot methods including filter to make a simple BCODMO-SM

I'll be needing to implement some ROBOT templates for various projects so I'll be testing it out here.

Working toward a fully templated solution for UO, I'll follow @jamesaoverton's suggestion:

[Try using] robot export to generate one or more templates. I think the immediate goal should be a full conversion, so that robot diff shows that the current OWL and the new version from templates are exactly the same. That should reassure people. Then we can start cleaning and reorganizing.

xref Southern-Cross-Plant-Science/cdno#4

From @ddooley we have:

'plant part' and 'derives from' some Taxon is the minimal information required for describing the sample substance

"apple subClassOf 'pome fruit' and derives from some "Malus pumila'"

I'm reading this to be the owl equivalence axiom:

'PO term'
 and ('derives from' some 'NCBITaxon term')

@ddooley also mentions

All this suggests that the natural home for these sample substances will be under FoodOn's "part of organism" > "plant structure" branch (a PO term), e.g. 'apple' will be under 'pome fruit'.

Stating that this module should be under the FOODON:part of plant, in which case to assert this we would need to go with something like the second axiom I'd proposed:

'part of plant'
 and ('composed primarily of' some 
    ('PO term'
     and ('derives from' some 'NCBITaxon term')))

In EnvironmentOntology/envo#1028 we were attempting a robot merge workflow to compile a robot module via a robot template and then merge it into the envo-edit.owl. I was attempting to do this in EnvironmentOntology/envo#1043, but unfortunately the robot merge workflow seemed to shuffle the lines around hence the extremely large diff in the envo-edit.owl file, even though in protege it looks as expected. Chris informed me to look at the format, which were different, envo-edit.owl being in owl functional syntax, and the robot default .owl being xml-rdf.