Align with GO CAM google doc spec and paper

[cmungall]

https://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit

[cmungall]

• [ ] MolecularFunction -> MolecularActivity

[vanaukenk]

Leaving this ticket open for now, as I'm sure there's more documentation to do.

That said, it'd be good to know if we want a Google doc to be the permanent home for this, or do we want to have all of this ultimately reside on the GOC wiki.

[goodb]

Pretty clear to me that you don't want the gdoc to be a final home. That one hasn't been edited in more than a year and is unlikely to match what is now live in the schema. I think there needs to be a way to have legible documentation generated automatically from the schema itself which is the ultimate source of truth here.

[lpalbou]

Do you have any recommendation of where to look to generate a schema from the Shex ? I suppose we could also ask on the Shex gitter / forum. They may be working on something as it seems a pretty generic use case for them

On Nov 2, 2020, at 2:46 PM, goodb notifications@github.com wrote:

 Pretty clear to me that you don't want the gdoc to be a final home. That one hasn't been edited in more than a year and is unlikely to match what is now live in the schema. I think there needs to be a way to have legible documentation generated automatically from the schema itself which is the ultimate source of truth here.

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[goodb]

Not specifically no. That would be a good forum to engage with for this issue. I think it would be pretty easy to write code that could generate a web page or wiki page from a schema. With appropriate inline comments in the schema elements, that would serve the purpose.

[ericprud]

Here's an example of some HTML built from some ShExJ: DDI_4-DR0.2 ConceptSystem . The "⇩"s represent EXTENDS clicking them copies the extended shape inline. It uses an experimental namespace (undocumneted) to capture UML annotations and uses https://github.com/commonmark/commonmark.js as a datatype to know to interpret it as markdown.

It's conveniently cut-and-paste-able for email and issues, e.g.:

ConceptSystem   ⇩AnnotatedIdentifiable  
│       Whether the collection is a bag or a set: a bag is a collection with duplicates allowed, a set is a collection without duplicates.
├▻type  CollectionType  ?
│       If members are ordered set to true, if unordered set to false.
├▭isOrdered xsd:boolean ?
│       A structure containing specific relationships between members of the collection.
├▻isStructuredBy    ⇩Identifiable   *
│   │       Provides information on reflexivity, transitivity, and symmetry of relationship using a descriptive term from an ennumeration list. Use if all relations within this relation structure are of the same specification.
│   ├▻hasRelationSpecification  RelationSpecification   
│   │       Restricted to ConceptRelation. ConceptRelations making up the relation structure.
│   └▻hasMemberRelation     *
│         │     Restricts source object to Concept for relationshp
│         ├▻source  Concept 
│         │     Restricts target object to Concept for relationshp
│         └▻target  Concept 
│       The conceptual basis for the collection of members.
└▻definingConcept   Concept *

but the HTML is unpleasant if the annotations are long (see platformType in InstanceVariable) because I never figured out a CSS-only way to create indented vertical lines. I think FHIR does this with bootstrap but the markup is hilariously complex.

If anyone can guide me on the markup, I can update the tool.