Declare what constitutes an activity unit

[vanaukenk]

For the Noctua form (and presumably for other reasons), it would be helpful to declare in the specs what constitutes an 'activity unit'.

Could we replace <MolecularFunction> below with <ActivityUnit> ?

<MolecularFunction> @<TypedMolecularFunction> AND { enabled_by: @<MolecularEntity> {0,1}; part_of: @<BiologicalProcess> {0,1}; occurs_in: @<CellularComponent> {0,1}; has_output: @<MolecularEntity> ; has_input: @<MolecularEntity> ; provides_direct_input_for: @<MolecularFunction> {0,1}; adding the following seems to break both the js and java shex implementations for: http://noctua-dev.berkeleybop.org/download/gomodel:R-HSA-156582/owl directly_positively_regulates: @<MolecularFunction> *; } // rdfs:comment "A molecular function"

[goodb]

@vanaukenk The naming so far has followed the pattern of using the root ontology class that the instances that would fit the shape would have as their 'category'. e.g. this shape is meant to define all the potential contextual attributes of any instance of a molecular function. Note that these are not required for it to validate - e.g. it could simply be a node typed with MF and it would pass as long as it didn't have any other properties hanging off of it.

What do you think of adding a different shape that requires the attributes to be filled in? e.g. an instance does not match the ActivityUnit shape unless it has an enabler, is part of a bp, etc.

[vanaukenk]

What do you think of adding a different shape that requires the attributes to be filled in? e.g. an instance does not match the ActivityUnit shape unless it has an enabler, is part of a bp, etc.

That's an interesting idea. I'd like to talk more with @tmushayahama about this one since it had implications for how he was presenting annotations in the table view of the Noctua form.

[pgaudet]

@goodb Can you explain what exactly is a shape?

Are these 'stanzas' shapes ?

<MolecularFunction> @<TypedMolecularFunction> AND { enabled_by: @<MolecularEntity> {0,1}; part_of: @<BiologicalProcess> {0,1}; occurs_in: @<CellularComponent> {0,1}; has_output: @<MolecularEntity> ; has_input: @<MolecularEntity> ; provides_direct_input_for: @<MolecularFunction> {0,1}; adding the following seems to break both the js and java shex implementations for: http://noctua-dev.berkeleybop.org/download/gomodel:R-HSA-156582/owl directly_positively_regulates: @<MolecularFunction> *; } // rdfs:comment "A molecular function"

Thanks, Pascale

[goodb]

@pgaudet yes a "shape" as I have been using the word here corresponds to blocks like the one you mention there for MolecularFunction. I would call that the MolecularFunction shape and the whole file with all of them as the schema.

Shapes are very much akin to class definitions in an ontology.

If you have time, there is good documentation here: https://book.validatingrdf.com/bookHtml010.html

[cmungall]

What actually is an activity unit?

[pgaudet]

Thanks @goodb Reading https://book.validatingrdf.com/bookHtml010.html, it seems like the 'go-cam-shapes.shex' document is a ShExC document. Section 4.2 in that document indicates that shapes can be names using ':name' (I am not sure I am looking at the right thing, because the format you have in the 'go-cam-shapes.shex' document is different (ie they dont use the '<>' characters).

But assuming this is the same format (since it's also '.shex'), then we could name that shape as follows:

':Molecular entity'

@ AND { bl:category [GoMolecularFunction:] ; enabled_by: @ {0,1}; etc Giving names would make it much easier to refer to objects. Pascale

[pgaudet]

@cmungall

What actually is an activity unit?

In fact we had defined it in the previous version of the GO-CAM spec google doc, but this have been overwritten. I think it's really important that we define stuff. I started a glossary for go-shapes: https://docs.google.com/document/d/14pw6L0YccENKpvQG1rGFLY73zfGp7dk5ZsK8D7saIJA/edit

(we can have this elsewhere; right now it's at least useful for me!).

Thanks, Pascale

[cmungall]

Maybe start a new issue for this? shexc allows all the standard URI shortening approaches

On Fri, Jul 12, 2019 at 6:13 AM pgaudet notifications@github.com wrote:

Thanks @goodb https://github.com/goodb Reading https://book.validatingrdf.com/bookHtml010.html, it seems like the 'go-cam-shapes.shex' document is a ShExC document. Section 4.2 in that document indicates that shapes can be names using ':name' (I am not sure I am looking at the right thing, because the format you have in the 'go-cam-shapes.shex' document is different (ie they dont use the '<>' characters).

But assuming this is the same format (since it's also '.shex'), then we could have

':Molecular entity' @ AND { bl:category [GoMolecularFunction:] ; enabled_by: @ {0,1}; etc

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[cmungall]

Still don't understand: if it is the smallest unit (what is a unit?) of a GO-Cam 'centered around' a MA, how is that different from an MA?

Sorry to be pedantic good to be precise

I suspect the intent for an AU to be an actual grouping of units, i.e what was previously termed an annoton, but I could be wrong

On Fri, Jul 12, 2019 at 6:15 AM pgaudet notifications@github.com wrote:

@cmungall https://github.com/cmungall

What actually is an activity unit?

In fact we had defined it in the previous version of the GO-CAM spec google doc, but this have been overwritten. I think it's really important that we define stuff. I started a glossary for go-shapes: https://docs.google.com/document/d/14pw6L0YccENKpvQG1rGFLY73zfGp7dk5ZsK8D7saIJA/edit

(we can have this elsewhere; right now it's at least useful for me!).

Thanks, Pascale

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[pgaudet]

I think @thomaspd uses a Molecular Activity as Molecular Function, at least in papers. I think we should run this by him.

[cmungall]

Yes, I think the only concept we need here is MolecularActivity

On Fri, Jul 12, 2019 at 11:30 AM pgaudet notifications@github.com wrote:

I think @thomaspd https://github.com/thomaspd uses a Molecular Activity as Molecular Function, at least in papers. I think we should run this by him.

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[cmungall]

Shall we close this?

[pgaudet]

Let's discuss this on today's call.

We need to be clear that the Activity Unit is not the same as a Molecular Function. In our Noctua documentation, a MF is often described as a Molecular Activity.

[pgaudet]

I just read #48 If we do that, then I think we need to keep 'Activity Unit'.

[vanaukenk]

I think we can close this.