Hand-curated HPO terms below the organ-system top level that still name a bucket rather than a finding. Used by `just check-coarse-phenotypes`, which requires any phenotype bound to one of these to declare a `coarse_binding_basis`.
The second tier of coarse phenotype terms: HPO terms below the 23 organ-system roots (PhenotypeCategoryEnum) that still name a body system, a whole organ, or a gross body region rather than a clinical finding. The guard treats this set and PhenotypeCategoryEnum's meanings as one list.
THIS IS A HAND-CURATED LIST AND MUST NEVER BECOME A RULE. The tier is not uniform, and a depth, subsumption or naming-pattern rule over it would be wrong in both directions. HPO names 360 distinct "Abnormal*" terms used in this knowledge base, and the most-used ones are the ones a pattern would most confidently mis-flag.
Inclusion rule: the term names (a) a body system, (b) a whole organ, or (c) a gross body region, and asserts nothing about what is wrong with it. The morphology/physiology split terms directly under such a root are included with it, since they divide the bucket without narrowing it.
Deliberately EXCLUDED, with the reason, because each doubles as an established clinical finding at exactly that grain:
- HP:0001627 Abnormal heart morphology (149 uses) carries "Congenital
heart defect" as an EXACT synonym and is the correct binding for a paper
that reports CHD without naming a lesion.
- HP:0001999 Abnormal facial shape (177) is dysmorphic facies, a real
summary finding in dysmorphology.
- HP:0012443 Abnormal brain morphology (26) and HP:0002500 Abnormal
cerebral white matter morphology (48) are what a radiologist reports off
an MRI.
- HP:0012332 Abnormal autonomic nervous system physiology (30) is
dysautonomia.
- HP:0000164 Abnormality of the dentition (36) is "dental anomalies", a
reported syndromic feature.
Left out as genuinely undecided rather than judged: HP:0000504 Abnormality of vision, HP:0000925 Abnormality of the vertebral column, HP:0002926 Abnormality of thyroid physiology, HP:0002270 Abnormality of the autonomic nervous system. Each is arguably a bucket and arguably a finding; a wrong entry here costs a curator a false positive, so they wait for someone with an argument.
Adding a value is a schema pull request with that argument attached. Each value's `description` must be the term's exact canonical HPO label, so `just validate-terms-schema` verifies the whole list against the ontology.