design refinement of existing CatVrs recipes #64
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larrybabb
commented
Nov 5, 2024
larrybabb
commented
- embed *Properties into recipes
- refine DefiningContext to DefiningAllele & DefiningLocation
- redraft CategoricalCnv on recent design changes
* refine DefiningContext to DefiningAllele & DefiningLocation * redraft CategoricalCnv on recent design changes
| @@ -42,6 +42,14 @@ $defs: | |||
| ordered: false | |||
| items: | |||
| $ref: "#/$defs/Constraint" | |||
| mappings: | |||
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@larrybabb I'm think we should reevaluate whether it makes sense to keep mappings in CategoricalVariant.
| - $ref: "#/$defs/DefiningAlleleContext" | ||
| - $ref: "#/$defs/DefiningLocationContext" | ||
| - $ref: "#/$defs/CopyCountConstraint" | ||
| - $ref: "#/$defs/CopyChangeConstraint" |
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I know that the word constraint was dropped from the DefiningAlleleContext and DefiningLocationcontext, but should we be consistent and make the drop the word constraint from the others as well or is there a rationale for distinguishing between them?
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Also, have we discussed yet updating the CopyCountConstraint and CopyChangeConstraint into a single copy constraint along the lines of the most recent iteration of that constraint in the discussion here?
| ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a | ||
| human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` | ||
| refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` | ||
| refers to variants or locations that translate from the codon(s) represented by the defined concept. |
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These are now out of date. Need to update with descriptions appropriate to the nee;y enumerated relations. @ahwagner what is translates_through?
| inherits: Constraint | ||
| description: >- | ||
| The defining allele and its associated relationships that are congruent | ||
| with member variants. |
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Given recent thinking wrt hypothetical lower-order AdjacencyConstraint, which takes, eg, two vrs:Location arguments and the stipulates that they are now adjacent (potentially mediated by a linker sequence, etc), the gates are open to the idea that a single vrs object may satisfy be reused to satisfy the arguments of multiple states (which also means the logic is now non-linear, which I don't think is a problem, but I'll make a note in my brain to ponder later).
So, is there a reason to have the dichotomy of a DefiningLocationContext and DefiningAlleleContext instead of a DefiningLocationContext and a DefiningStateContext where the latter state context functions more akin to a sequence or functional entity (like a gene) completely divorced from a location in the genome, and therefore a system where a vrs:Allele would be sufficient to satisfy both the DefiningLocationContext and DefiningStateContext, but a vrs:Location would only satisfy the DefiningLocationContext?
Or put another way, in splitting out the DefiningContextConstraint, we now have one constraint that only handles location information, and another that... does the smae thing as the prior DefiningContextConstraint.
| description: >- | ||
| Defined relationships between members of the categorical variant and the defining context. | ||
| Defined relationships from which members relate to the defining context. | ||
| ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a |
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Ditto above, this needs to be updated in line with the new relations.
| ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a | ||
| human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` | ||
| refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` | ||
| refers to variants or locations that translate from the codon(s) represented by the defined concept. | ||
| matchCharacteristic: |
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I am excited to see what this gets us.
