Deprecate UPHENO:0001002, rename UPHENO:0001001 (#1009)

.gitignore

@@ -323,4 +323,5 @@ src/ontology/reports/xrefs.tsv
 src/ontology/imports/*.json
 /src/metadata
 src/mappings/*.owl
+.claude/
 .claude/settings.local.json

docs/pipeline.md

@@ -84,6 +84,39 @@ Pattern names like `abnormalAnatomicalEntity.yaml` define:
 
 The pipeline matches these patterns against species phenotype ontologies to find which terms match which patterns, then uses the matches to build the uPheno intermediate layer.
 
+### DOSDP TSV filler data
+
+Filler data lives in `src/patterns/data/default/` (hand-curated) and `src/patterns/data/automatic/` (generated).
+
+Each TSV has a `defined_class` column (the IRI) plus columns for each pattern variable. dosdp-tools supports special override columns to set per-row annotations on the defined class:
+
+| Column | Effect |
+|--------|--------|
+| `defined_class_name` | Override the pattern-generated label |
+| `defined_class_definition` | Override the pattern-generated definition |
+| `defined_class_comment` | Add rdfs:comment |
+| `defined_class_exact_synonym` | Add exact synonym |
+| `defined_class_narrow_synonym` | Add narrow synonym |
+| `defined_class_broad_synonym` | Add broad synonym |
+| `defined_class_related_synonym` | Add related synonym |
+| `defined_class_namespace` | Set OBO namespace |
+
+These are defined in the DOSDP spec (`PrintfAnnotationOBO.overrides` in dosdp-tools source).
+
+### Source of truth for OWL components
+
+All OWL files in `src/ontology/components/` are **generated** — never edit them directly. Sources of truth:
+
+| Component | Source |
+|-----------|--------|
+| `upheno-top.owl` | `src/templates/phenotype-top-level.tsv` (ROBOT template) |
+| `upheno-manual-curation.owl` | `src/templates/upheno-ssspo-groupings-no-eq.tsv` + `phenotypes-without-patterns.tsv` |
+| `upheno-alignments.owl` | `src/templates/upheno-ssspo-alignments-no-eq.tsv` + `phenotype-alignments.tsv` + `root-alignments.tsv` |
+| `upheno-species-neutral.owl` | DOSDP pipeline output (`upheno_layer.owl`) |
+| `upheno-mappings.owl` | SSSOM mapping files in `src/mappings/` |
+| `upheno-bridge.owl` | SPARQL construct over species-independent mappings |
+| `upheno-deprecated.owl` | `src/templates/obsolete.tsv` |
+
 ## Pipeline Phases (from `upheno.Makefile`)
 
 1. **`prepare_patterns_for_matching`**: Copies patterns from `dosdp-dev/` to `curation/patterns-for-matching/`

src/patterns/data/default/phenotype.tsv

@@ -1,2 +1,2 @@
-defined_class	defined_class_name	bearer
-http://purl.obolibrary.org/obo/UPHENO_0001001	phenotype	owl:Thing
+defined_class	defined_class_name	bearer	defined_class_definition
+http://purl.obolibrary.org/obo/UPHENO_0001001	phenotypic feature	owl:Thing	An observable characteristic of an organism expressed as a deviation, alteration, or qualified state relative to a reference condition, resulting from genetic, environmental, or gene-environment influences. 

src/patterns/data/default/phenotype_modified.tsv

@@ -1,2 +1,2 @@
 defined_class	defined_class_name	bearer	modifier
-http://purl.obolibrary.org/obo/UPHENO_0001002	phenotypic effect	owl:Thing	PATO:0000460
+

src/scripts/upheno_build.py

@@ -397,12 +397,12 @@ def generate_warning_for_group(group, map_labels, df_cross_species, df_species_i
         parents = {
             p
             for pid in non_upheno_ids
-            for p in map_superclasses.get(pid, ["UPHENO:0001002"])
+            for p in map_superclasses.get(pid, ["UPHENO:0001001"])
             if p and isinstance(p, str) and p.startswith("UPHENO:")
         }
 
         if not parents:
-            parents.add("UPHENO:0001002")
+            parents.add("UPHENO:0001001")
 
         if len(upheno_ids) == 0:
             upheno_label = generate_upheno_label(group, map_labels)

src/templates/obsolete.tsv

@@ -17552,3 +17552,4 @@ http://purl.obolibrary.org/obo/UPHENO_0088423		true	http://purl.obolibrary.org/o
 http://purl.obolibrary.org/obo/UPHENO_0088424		true	http://purl.obolibrary.org/obo/CHEBI_16410-http://purl.obolibrary.org/obo/BFO_0000004-abnormallyIncreasedLevelOfChemicalEntityInLocation.tsv		
 http://purl.obolibrary.org/obo/UPHENO_0016048		true	http://purl.obolibrary.org/obo/GO_0000785-http://purl.obolibrary.org/obo/ZFA_0009177-abnormalMorphologyOfAnatomicalEntityInLocation.tsv		
 http://purl.obolibrary.org/obo/UPHENO_0056750		true	http://purl.obolibrary.org/obo/GO_0000785-http://purl.obolibrary.org/obo/ZFA_0009111-abnormallyIncreasedNumberOfAnatomicalEntityInLocation.tsv		
+http://purl.obolibrary.org/obo/UPHENO_0001002	phenotypic effect	true	Deprecated in favor of UPHENO:0001001	http://purl.obolibrary.org/obo/UPHENO_0001001	https://github.com/obophenotype/upheno/issues/1009

src/templates/phenotype-top-level.tsv

@@ -32,7 +32,6 @@ UPHENO:3000004	renal/urinary system phenotype	UPHENO:0001001	phenotype	http://pu
 UPHENO:3000006	taste/olfaction phenotype	UPHENO:0001001	phenotype	http://purl.obolibrary.org/obo/upheno#top_level
 UPHENO:3000007	vision/eye phenotype	UPHENO:0001001	phenotype	http://purl.obolibrary.org/obo/upheno#top_level
 UPHENO:0050177	renal system phenotype	UPHENO:3000004	renal/urinary system phenotype	
-UPHENO:0001002	phenotypic effect	UPHENO:0001001	phenotype	
 UPHENO:0078688	abnormal sensory perception of taste	UPHENO:3000006	taste/olfaction phenotype	
 UPHENO:0078689	abnormal sensory perception of smell	UPHENO:3000006	taste/olfaction phenotype	
 UPHENO:0087427	renal system morphology phenotype	UPHENO:3000004	renal/urinary system phenotype