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Enum: CoarseBindingBasisEnum

Why a descriptor is deliberately bound to a coarse, organ-system-level ontology term rather than a specific finding. Required by just check-coarse-phenotypes on any phenotype bound to one of the top-level HPO organ-system terms (the PhenotypeCategoryEnum meanings, the direct children of HP:0000118), which name a facet bucket rather than a clinical finding. The point is NOT to reward narrow terms -- manufacturing a specificity the source does not support is a worse defect than a coarse binding. The point is that a coarse binding should say which of these situations it is in, so the unexplained one (the curator who stopped early) is distinguishable from the three legitimate ones.

URI: dismech:enum/CoarseBindingBasisEnum

Permissible Values

Value Meaning Description Additional Info
VARIABLE_SPECTRUM None Involvement of this system is real and recurrent, but its form varies between... Title: Variable spectrum
SOURCE_UNSPECIFIED None The cited source characterizes the finding no further ("ocular involvement", ... Title: Source unspecified
NO_HPO_TERM None The claim is more specific than any available ontology term, and the coarse p... Title: No suitable ontology term
PATHOGRAPH_HUB None The node is a deliberately unqualified convergence point in the causal graph:... Title: Pathograph hub

Slots

Name Description
coarse_binding_basis Why this descriptor is deliberately bound to a coarse, organ-system-level ter...

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/monarch-initiative/dismech

LinkML Source

name: CoarseBindingBasisEnum
description: Why a descriptor is deliberately bound to a coarse, organ-system-level
  ontology term rather than a specific finding. Required by `just check-coarse-phenotypes`
  on any phenotype bound to one of the top-level HPO organ-system terms (the PhenotypeCategoryEnum
  meanings, the direct children of HP:0000118), which name a facet bucket rather than
  a clinical finding. The point is NOT to reward narrow terms -- manufacturing a specificity
  the source does not support is a worse defect than a coarse binding. The point is
  that a coarse binding should say which of these situations it is in, so the unexplained
  one (the curator who stopped early) is distinguishable from the three legitimate
  ones.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
permissible_values:
  VARIABLE_SPECTRUM:
    text: VARIABLE_SPECTRUM
    description: Involvement of this system is real and recurrent, but its form varies
      between patients with no characteristic finding to bind -- pleiotropy and variable
      expressivity, where enumerating every case would be arbitrary. The node's content
      is the organ-system involvement itself, typically with an aggregate frequency
      the source measured at that level. Like SOURCE_UNSPECIFIED this is a bare declaration
      with no companion slot. If the specific findings ARE known and evidenced, they
      are ordinary `phenotypes` entries with their own terms and evidence -- curate
      them that way rather than listing them inside this binding.
    title: Variable spectrum
  SOURCE_UNSPECIFIED:
    text: SOURCE_UNSPECIFIED
    description: The cited source characterizes the finding no further ("ocular involvement",
      "congenital heart defect" with no named lesion), so a narrower term would assert
      something the evidence does not. The evidence snippet is the proof, so this
      value needs no companion slot.
    title: Source unspecified
  NO_HPO_TERM:
    text: NO_HPO_TERM
    description: The claim is more specific than any available ontology term, and
      the coarse parent is the best honest anchor. `preferred_term` carries the specificity
      the ontology lacks and must differ from the bound label; record any term request
      in `term_gap`.
    title: No suitable ontology term
  PATHOGRAPH_HUB:
    text: PATHOGRAPH_HUB
    description: 'The node is a deliberately unqualified convergence point in the
      causal graph: a mechanism disrupts a system, and the system-level disruption
      is where several specific findings converge. It is defined by its INCOMING edges
      -- at least one causal edge in the same entry must target it. It takes no `frequency`,
      and the reason is narrower than "no clinical claim": a hub does assert that
      the system is involved, and carries evidence for that assertion like any other
      phenotype. What it cannot carry is a rate, because an unqualified system-level
      node names no finding whose occurrence could be counted -- the frequency belongs
      to each specific finding beside it. Do NOT connect it to the specific findings
      with `sequelae`, which is a causal edge: a coloboma is not caused by an eye
      abnormality, it is one. Those findings are ordinary `phenotypes` entries in
      their own right. Distinct from a pathophysiology node such as "disrupted eye
      development", which binds GO and asserts a process; a hub binds HP and asserts
      a system-level outcome. The two may sit in sequence.'
    title: Pathograph hub