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Include clade type in phyloreference definition #6

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gaurav opened this issue Feb 8, 2019 · 2 comments · Fixed by #61
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Include clade type in phyloreference definition #6

gaurav opened this issue Feb 8, 2019 · 2 comments · Fixed by #61
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programming only No discussion necessary; just pure programming needed

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@gaurav
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gaurav commented Feb 8, 2019

Each phyloref definition should include a clade type. To start with, we could include all the clade types currently supported by PhyloRegnum, which includes "apomorphy-based_standard", "apomorphy-modified_crown_clade", "crown-based_total_clade", "minimum-clade_standard", "maximum-crown-clade", "maximum-total-clade", "maximum-clade_standard" and "minimum-crown-clade" (I'll get a full list from Nico when I implement this). This information could then be incorporated into generated ontologies to distinguish between crown-clades and total-clades (phyloref/phyloref-ontology#33).
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gaurav commented Jul 15, 2019

Decision: let's make this a verbatim text field for now.

@gaurav gaurav added the programming only No discussion necessary; just pure programming needed label Aug 8, 2019
@gaurav gaurav mentioned this issue Jan 26, 2021
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gaurav commented Feb 9, 2021

After discussing this on the Phyloref call on January 27, 2021, we decided to have a phylorefType field that has one of the following values:

  • phyloref:PhyloreferenceUsingMinimumClade for minimum-clade phylorefs.
  • phyloref:PhyloreferenceUsingMaximumClade for maximum-clade phylorefs.
  • phyloref:PhyloreferenceUsingApomorphy for apomorphy-based phylorefs.

These values would then be added to the list of superclasses for the phyloreference, so that a minimum-class phyloreference would be a subclass of phyloref:PhyloreferenceUsingMinimumClade. I've implemented this in PR #61.

gaurav added a commit that referenced this issue Feb 12, 2021
@gaurav
Merge pull request #61 from phyloref/add-phyloref-type
9817433 
This PR adds a phyloreference type (`phylorefType`) to phyloreferences as defined in #6. The value of phylorefType must be one of the following classes from the Phyloref ontology:
- `phyloref:PhyloreferenceUsingMinimumClade` for minimum-clade phylorefs.
- `phyloref:PhyloreferenceUsingMaximumClade` for maximum-clade phylorefs.
- `phyloref:PhyloreferenceUsingApomorphy` for apomorphy-based phylorefs.

Separately, we calculate the phyloreference type while we are generating the logical expression (based on the internal and external specifiers), and make the phyloreference a subclass of that class. If the provided phylorefType differs from the computed phyloref type, we will throw an error and refuse to create this phyloreference.

Closes #6.
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Add phyloref type to phyloreferences phyloref/phyx.js
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