Create class hierarchy diagram

[ahwagner]

From #533:

Please add a figure showing the class hierarchy to illustrate inheritance. This would be especially helpful for an abstract class like Location, which is listed as a datatype for several attributes but is not included in the documentation so it is difficult to know which child classes are valid for a given attribute.

[larrybabb]

Here's the class diagram.

[larrybabb]

@ahwagner and others.... I'd love any feedback in terms of making the diagram easier to understand. I do think we may need different versions or representations of the class diagram, including more detailed versions focused on individual classes. But for now we are trying to get the basic view down to a single page to give users a sense of the scope and breadth and organization of VRS.

[ahwagner]

This looks good to me. FWIW, I think this is exactly the level of detail needed for this diagram, which covers a lot of ground.

[Mrinal-Thomas-Epic]

This is a great one page overview! I think the only thing that might be helpful to add is a "uses" type relationship (e.g., Allele uses SequenceLocation and SequenceExpression)

[rrfreimuth]

Thanks, @larrybabb ! I think this is great. The "inheritance view" is important and aids understanding.

A single diagram cannot show everything. I agree that another diagram that illustrates more of a structural domain perspective (detail within the classes and relevant relations/compositions) would also be helpful at some point.

[ahwagner]

@larrybabb one update to request: Ga4ghIdentifiableObject is in VRS, not gks.core. We should either move it up to core (I would prefer this), or revise this figure to match the spec. Otherwise I think this looks good.

[larrybabb]

[korikuzma]

@larrybabb how do you decide on when to include ABC? For example, Variation is included, but MolecularVariation, SystemicVariation, and Location are not.

[korikuzma]

@larrybabb LiteralSequenceExpression vrs is black, but should be blue

[korikuzma]

@larrybabb CisPhaseBlock --> CisPhasedBlock

[larrybabb]

@larrybabb how do you decide on when to include ABC? For example, Variation is included, but MolecularVariation, SystemicVariation, and Location are not.

@korikuzma Alex and I decided that only Classes that are strictly organizational do not go in the class hierarchy diagram. Since MolecularVariation and SystemicVariation are more about grouping types of Variation we did not include them in the more technical inheritance class diagram. Does that make sense? (please discuss with Alex as well)

[korikuzma]

@larrybabb how do you decide on when to include ABC? For example, Variation is included, but MolecularVariation, SystemicVariation, and Location are not.

@korikuzma Alex and I decided that only Classes that are strictly organizational do not go in the class hierarchy diagram. Since MolecularVariation and SystemicVariation are more about grouping types of Variation we did not include them in the more technical inheritance class diagram. Does that make sense? (please discuss with Alex as well)

@larrybabb that makes sense. But what about Location, it seems similar to Variation?