SkyeAv · SkyeAv · Aug 24, 2026 · Aug 24, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,11 @@
 
 All notable changes to this project are documented in this file.
 
+## Unreleased
+
+### Breaking Changes
+- **Retrieval-source entries now use `resource_id` as their sole identifier.** Generated edges no longer duplicate each nested `sources` entry's provenance identifier into `sources[].id`; readers should use `sources[].resource_id`. Tablassert's validator supplies the inherited `id` only to its in-memory compatibility copy while the pinned Biolink model still requires it.
+
 ## 13.0.0 - 2026-08-24
 
 ### Breaking Changes

diff --git a/docs/configuration/table.md b/docs/configuration/table.md
@@ -451,7 +451,7 @@ Override fields:
 | `knowledge_level` | String | No | Override-specific KL value. Defaults to `statistical_association`. |
 | `agent_type` | String | No | Override-specific AT value. Defaults to `data_analysis_pipeline`. |
 
-Tablassert emits the graph-level infores (or `infores:<graph-name>` when unset) as the primary entry of the Biolink `sources` list on each edge, `{resource_id: "infores:multiomics-kg", resource_role: "primary_knowledge_source", upstream_resource_ids: [...], source_record_urls: [...]}`, with one additional `supporting_data_source` entry per upstream. When `override.upstream_source_record_urls` is set, the primary entry emits no `source_record_urls` and each mapped supporting entry carries its own instead. No flat `primary_knowledge_source` scalar is emitted: current translator-ingests practice carries retrieval provenance only in `sources`, and the Biolink `RetrievalSource` class is where `resource_id` / `upstream_resource_ids` / `source_record_urls` are defined. (Each entry also mirrors `resource_id` into `id` because the generated Biolink classes still require it; that mirror disappears once biolink-model [#1706](https://github.com/biolink/biolink-model/issues/1706) lands.) The override cannot set a per-section primary source; manual infores CURIEs belong in `upstream_resource_ids`. Older flat `resource_id` / `primary_knowledge_source` output has been removed so generated KGX matches the Biolink edge contract.
+Tablassert emits the graph-level infores (or `infores:<graph-name>` when unset) as the primary entry of the Biolink `sources` list on each edge, `{resource_id: "infores:multiomics-kg", resource_role: "primary_knowledge_source", upstream_resource_ids: [...], source_record_urls: [...]}`, with one additional `supporting_data_source` entry per upstream. When `override.upstream_source_record_urls` is set, the primary entry emits no `source_record_urls` and each mapped supporting entry carries its own instead. No flat `primary_knowledge_source` scalar is emitted: current translator-ingests practice carries retrieval provenance only in `sources`, and the Biolink `RetrievalSource` class is where `resource_id` / `upstream_resource_ids` / `source_record_urls` are defined. Each retrieval-source entry uses `resource_id` as its sole identifier. The override cannot set a per-section primary source; manual infores CURIEs belong in `upstream_resource_ids`. Older flat `resource_id` / `primary_knowledge_source` output has been removed so generated KGX matches the Biolink edge contract.
 
 ### Annotations
 

diff --git a/src/tablassert/biolink.py b/src/tablassert/biolink.py
@@ -643,6 +643,40 @@ def is_multivalued(cls: type[Any], field: str) -> bool:
     return any(get_origin(arg) is list for arg in get_args(annotation))
 
 
+@cache
+def _retrieval_source_id_required() -> bool:
+    """Whether the installed model still requires the inherited source ``id`` field."""
+    retrieval_source: Any = getattr(_bm, "RetrievalSource", None)
+    id_field: Any = getattr(retrieval_source, "model_fields", {}).get("id")
+    return id_field is not None and id_field.is_required()
+
+
+def _validation_record(record: dict[str, Any], *, edge: bool) -> dict[str, Any]:
+    """Add only in-memory compatibility aliases needed by the installed Biolink model.
+
+    ``RetrievalSource`` in the currently pinned model still requires the inherited
+    ``Entity.id`` even though ``resource_id`` is the canonical provenance identifier
+    emitted by Tablassert. The alias is used solely for Pydantic validation; it never
+    changes the decoded KGX record or the files written by the pipeline.
+    """
+    if not edge:
+        return record
+    if not _retrieval_source_id_required():
+        return record
+    sources: Any = record.get("sources")
+    if not isinstance(sources, list):
+        return record
+    normalized: list[Any] = []
+    changed: bool = False
+    for source in sources:
+        if isinstance(source, dict) and "id" not in source and "resource_id" in source:
+            normalized.append({**source, "id": source["resource_id"]})
+            changed = True
+        else:
+            normalized.append(source)
+    return {**record, "sources": normalized} if changed else record
+
+
 def validate_record(record: dict[str, Any], *, edge: bool) -> list[str]:
     """Validate one KGX record against the Biolink class named by its ``category``.
 
@@ -659,7 +693,7 @@ def validate_record(record: dict[str, Any], *, edge: bool) -> list[str]:
     category: str = categories[0] if isinstance(categories, list) and categories else str(categories or "")
     cls: type[Any] = association_class(category) if edge else node_class(category)
     try:
-        cls(**record)
+        cls(**_validation_record(record, edge=edge))
     except ValidationError as error:
         return [f"{'.'.join(str(part) for part in item['loc']) or '?'}: {item['type']}" for item in error.errors()]
     return []

diff --git a/src/tablassert/lib.py b/src/tablassert/lib.py
@@ -354,16 +354,12 @@ def value(lf: pl.LazyFrame, col: str, x: object) -> pl.LazyFrame:
 def _retrieval_source(resource_id: str, resource_role: str, upstream: list[str] | None = None, urls: list[str] | None = None) -> pl.Expr:
     """Build one ``RetrievalSource`` struct expression.
 
-    Every entry declares the same five fields so that :func:`retrieval_sources` can
+    Every entry declares the same four fields so that :func:`retrieval_sources` can
     ``concat_list`` them into a single ``list[struct]`` column; absent list fields are
     typed nulls, which the Rust null-stripper removes from the emitted JSON.
     """
     empty: pl.Expr = pl.lit(None, dtype=pl.List(pl.String))
     return pl.struct(
-        # `id` duplicates `resource_id`, but RetrievalSource inherits `id` from
-        # `entity` and the generated Pydantic classes require it, so omitting it
-        # fails KGX validation. Stays until biolink-model #1706/#1731 land.
-        pl.lit(resource_id).alias("id"),
         pl.lit(resource_id).alias("resource_id"),
         pl.lit(resource_role).alias("resource_role"),
         (pl.concat_list([pl.lit(x) for x in upstream]) if upstream else empty).alias("upstream_resource_ids"),

diff --git a/tests/test_biolink.py b/tests/test_biolink.py
@@ -453,6 +453,29 @@ def test_validate_kgx_never_passes_a_missing_file(tmp_path: Path) -> None:
     assert report["edges"]["missing"] is True
 
 
+def test_validate_kgx_accepts_resource_id_only_retrieval_sources(tmp_path: Path) -> None:
+    """Validation aliases ``resource_id`` to the pinned model's inherited ``id`` in memory only."""
+    nodes: Path = tmp_path / "n.ndjson"
+    edges: Path = tmp_path / "e.ndjson"
+    nodes.write_text(json.dumps({"id": "HGNC:11998", "name": "TP53", "category": ["biolink:Gene"]}) + "\n")
+    edge: dict[str, Any] = {
+        "id": "e1",
+        "subject": "HGNC:11998",
+        "predicate": "biolink:associated_with",
+        "object": "MONDO:0008903",
+        "category": ["biolink:Association"],
+        "knowledge_level": "statistical_association",
+        "agent_type": "data_analysis_pipeline",
+        "sources": [{"resource_id": "infores:test", "resource_role": "primary_knowledge_source"}],
+    }
+    edges.write_text(json.dumps(edge) + "\n")
+
+    report: dict[str, Any] = validate_kgx(nodes, edges)
+    assert "id" not in json.loads(edges.read_text())["sources"][0]
+    assert report["edges"]["valid"] == 1
+    assert report["ok"] is True
+
+
 def test_validate_kgx_separates_pending_extras_from_real_failures(tmp_path: Path) -> None:
     """``valid_excluding_pending`` forgives a deliberate extra; ``valid`` stays strict."""
     nodes: Path = tmp_path / "n.ndjson"

diff --git a/tests/test_cover_lib.py b/tests/test_cover_lib.py
@@ -205,14 +205,7 @@ def test_compile_graph_unlinks_stale_tmp_outputs(monkeypatch: Any, tmp_path: Pat
             "agent_type": ["manual_agent"],
             "primary_knowledge_source": ["infores:un-kg"],
             "sources": [
-                [
-                    {
-                        "id": "infores:un-kg",
-                        "resource_id": "infores:un-kg",
-                        "resource_role": "primary_knowledge_source",
-                        "source_record_urls": ["https://example.org/un.tsv"],
-                    }
-                ]
+                [{"resource_id": "infores:un-kg", "resource_role": "primary_knowledge_source", "source_record_urls": ["https://example.org/un.tsv"]}]
             ],
         }
     ).write_parquet(sub)

diff --git a/tests/test_lib.py b/tests/test_lib.py
@@ -577,10 +577,7 @@ def test_tcode_collect_nests_upstream_resource_ids_in_sources(fixtures_path: Pat
     primary: dict[str, Any] = next(s for s in sources if s["resource_role"] == "primary_knowledge_source")
     assert primary["upstream_resource_ids"] == ["infores:pubmed-central"]
     assert {s["resource_id"] for s in sources if s["resource_role"] == "supporting_data_source"} == {"infores:pubmed-central"}
-    # `id` mirrors `resource_id`: RetrievalSource inherits a required `id` from
-    # `entity` in the generated Biolink classes, so it stays until biolink-model
-    # #1706/#1731 land.
-    assert all(s["id"] == s["resource_id"] for s in sources)
+    assert all("id" not in s for s in sources)
 
 
 def test_normalize_category_list_with_biolink_prefix() -> None:
@@ -740,7 +737,7 @@ def test_tcode_collect_nests_source_record_urls_in_sources(fixtures_path: Path)
     assert "source_record_urls" not in result.columns
     primary: dict[str, Any] = next(s for s in result["sources"].to_list()[0] if s["resource_role"] == "primary_knowledge_source")
     assert primary["source_record_urls"] == ["https://example.com/test.tsv"]
-    assert primary["id"] == primary["resource_id"]
+    assert "id" not in primary
 
 
 def test_tcode_collect_upstream_source_record_urls_rehome_urls(fixtures_path: Path) -> None:
@@ -1195,13 +1192,12 @@ def test_compile_graph_emits_ndjson(monkeypatch: Any, tmp_path: Path, rig_factor
     monkeypatch.chdir(tmp_path)
     sub: Path = tmp_path / "sub.parquet"
     primary: dict[str, Any] = {
-        "id": "infores:smoke",
         "resource_id": "infores:smoke",
         "resource_role": "primary_knowledge_source",
         "upstream_resource_ids": ["infores:pubmed-central"],
         "source_record_urls": ["https://pmc.ncbi.nlm.nih.gov/bin/table1.xlsx"],
     }
-    supporting: dict[str, Any] = {"id": "infores:pubmed-central", "resource_id": "infores:pubmed-central", "resource_role": "supporting_data_source"}
+    supporting: dict[str, Any] = {"resource_id": "infores:pubmed-central", "resource_role": "supporting_data_source"}
     pl.DataFrame(
         {
             "subject": ["A", "B"],
@@ -1316,7 +1312,6 @@ def spy_open(
             "sources": [
                 [
                     {
-                        "id": "infores:utf8-kg",
                         "resource_id": "infores:utf8-kg",
                         "resource_role": "primary_knowledge_source",
                         "source_record_urls": ["https://example.org/utf8.tsv"],
@@ -1361,7 +1356,6 @@ def write_sub(p: Path, subj: str, obj: str) -> None:
                 "sources": [
                     [
                         {
-                            "id": "infores:cb-kg",
                             "resource_id": "infores:cb-kg",
                             "resource_role": "primary_knowledge_source",
                             "source_record_urls": ["https://example.org/cb.tsv"],
@@ -1422,7 +1416,6 @@ def test_compile_graph_keeps_qualifiers_and_publications_on_edges(monkeypatch: A
             "sources": [
                 [
                     {
-                        "id": "infores:qual-kg",
                         "resource_id": "infores:qual-kg",
                         "resource_role": "primary_knowledge_source",
                         "source_record_urls": ["https://example.org/qual.tsv"],
@@ -2531,7 +2524,6 @@ def test_compile_graph_folds_unknown_annotations_into_supporting_text(monkeypatc
             "sources": [
                 [
                     {
-                        "id": "infores:fold-kg",
                         "resource_id": "infores:fold-kg",
                         "resource_role": "primary_knowledge_source",
                         "source_record_urls": ["https://example.org/fold.tsv"],
@@ -2582,7 +2574,6 @@ def test_compile_graph_passes_approval_ids_through_verbatim(monkeypatch: Any, tm
             "sources": [
                 [
                     {
-                        "id": "infores:approval-kg",
                         "resource_id": "infores:approval-kg",
                         "resource_role": "primary_knowledge_source",
                         "source_record_urls": ["https://example.org/approval.tsv"],
@@ -2940,9 +2931,8 @@ def test_build_pipeline_e2e_smoke_with_monkeypatched_fullmap(monkeypatch: Any, t
     primary_source: dict[str, Any] = next(x for x in edge_rows[0]["sources"] if x["resource_role"] == "primary_knowledge_source")
     assert primary_source["resource_id"] == "infores:pipeline-kg"
     assert primary_source["upstream_resource_ids"] == ["infores:pubmed-central"]
-    # `id` mirrors `resource_id` (required by the generated Biolink classes), and
-    # no flat scalar duplicates the primary source.
-    assert primary_source["id"] == primary_source["resource_id"]
+    # Source provenance uses `resource_id` without a duplicate Biolink `id`.
+    assert "id" not in primary_source
     assert "primary_knowledge_source" not in edge_rows[0]
     assert {row["id"] for row in node_rows} == {"HGNC:1100", "HGNC:11998"}
     assert rig["name"] == "PIPELINE_KG v0.1.0 Resource Ingest Guide"

diff --git a/tests/test_rig.py b/tests/test_rig.py
@@ -22,7 +22,7 @@
 
 
 def _source_entry(primary: str, url: str, upstream: list[str] | None = None) -> list[dict[str, Any]]:
-    entry: dict[str, Any] = {"id": primary, "resource_id": primary, "resource_role": "primary_knowledge_source", "source_record_urls": [url]}
+    entry: dict[str, Any] = {"resource_id": primary, "resource_role": "primary_knowledge_source", "source_record_urls": [url]}
     if upstream:
         entry["upstream_resource_ids"] = upstream
     return [entry]
@@ -85,14 +85,13 @@ def test_rig_edge_type_info_separates_roles_properties_qualifiers_and_files(tmp_
                 "MONDO:1",
                 sources=[
                     {
-                        "id": "infores:test-kg",
                         "resource_id": "infores:test-kg",
                         "resource_role": "primary_knowledge_source",
                         "upstream_resource_ids": ["infores:pubmed-central"],
                         "source_record_urls": ["https://pmc.ncbi.nlm.nih.gov/bin/table1.xlsx"],
                     },
-                    {"id": "infores:pubmed-central", "resource_id": "infores:pubmed-central", "resource_role": "supporting_data_source"},
-                    {"id": "infores:aggregator", "resource_id": "infores:aggregator", "resource_role": "aggregator_knowledge_source"},
+                    {"resource_id": "infores:pubmed-central", "resource_role": "supporting_data_source"},
+                    {"resource_id": "infores:aggregator", "resource_role": "aggregator_knowledge_source"},
                 ],
                 p_value=0.01,
                 publications=["PMID:1"],