# VOICE_PEDIATRIC — Phase 3 / Phase 4 reconciliation

- **Run label:** `2026-08-07_claude-opus-5-claudecode-generic-v3_rep2`
- **Arm:** BASELINE (input documents only)
- **Runtime / provider / model:** Claude Code / Anthropic / `claude-opus-5`
- **Reasoning effort:** `high` (observed value of `$CLAUDE_EFFORT`)
- **Mode:** four-phase project agent, generic prompt
- **Prompt:** `src/download/prompts/d4d_generic_arm_prompt.md`
- **Declared input bundle:** `data/preprocessed/concatenated/VOICE_PEDIATRIC_preprocessed.txt`
- **Manifest:** `data/preprocessed/source_manifest.yaml`
- **Full record:** `data/d4d_concatenated/claudecode_agent/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d.yaml`
- **Core record:** `data/d4d_concatenated/claudecode_agent_core/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d_core.yaml`

## Referent

`Dataset` admits one referent. The referent chosen is the **Bridge2AI-Voice Pediatric Dataset,
version 1.1.0, published on PhysioNet on 1 May 2026 under DOI `10.13026/h995-bt35`** — the
featurized, credentialed-access release containing derived audio features for 23,533 recordings
from 300 participants aged 2 to 18.

This choice is held consistently across both records: `id`, `doi`, `title`, `version`, `issued`,
`page` and `publisher` all identify that release, and every populated slot describes it rather
than the Bridge2AI-Voice programme as a whole.

Two candidate alternatives were rejected:

- **The Bridge2AI-Voice programme.** The bundle's IRB protocol and NIH RePORTER record describe a
  four-year, multi-institution data-generation project targeting 30,000 participants across five
  disease categories. That is the programme under which the pediatric cohort was collected, not a
  published dataset; the bundle's only versioned, DOI-bearing pediatric artefact is the PhysioNet
  release. Programme-level facts were used only where the evidence attaches them to this release
  (funding, governance instruments, retention terms, access model), and each is attributed in
  place.
- **The raw pediatric audio collection on Synapse (`syn73617068`).** This is a distinct
  distribution behind a separate controlled-access process. It is represented as a relationship
  (`related_datasets`, `derives_from`) and in `raw_sources`, not as the referent.

## Relationship to the adult VOICE dataset

The adult Bridge2AI-Voice dataset is documented in the same source corpus and is a **separate
PhysioNet project covering a distinct cohort**, generated concurrently by another agent from its
own bundle. It was represented here in exactly three ways, all evidence-bound:

1. `related_datasets[0]`: `target_dataset: https://physionet.org/content/b2ai-voice/`,
   `relationship_type: references`. `references` was chosen over any version or part-of
   relationship because the only dataset-level assertion in the bundle is the pediatric PhysioNet
   page's note that "the Bridge2AI-Voice Adult Dataset is also available on PhysioNet". The
   description states explicitly that the adult dataset is *not* a version, parent or superset of
   this dataset.
2. The top-level `description` closes by noting that this is a separate PhysioNet project from the
   adult dataset, which covers a distinct cohort under its own release series.
3. Top-level `source_caveats` records that the project documentation's healthsheet is scoped to the
   adult releases and that its answers were deliberately **not** carried into this record.

No adult-scoped figure was imported. In particular the adult healthsheet's 833 instances, 12-month
collection window, five recording sites, iPad/Avid AE-36 hardware, clinician diagnostic labeling,
ICD-10 label guidelines, Health Data Nexus hosting, semi-annual update cadence, Bridge2AI Summer
School use, and $40/$80 participant compensation appear nowhere in either record as pediatric
facts. Compensation is the clearest case: the protocol states compensation "will be provided to
the adult population only", so `participant_compensation` records the protocol clause and a
caveat, and asserts **no** compensation status for the pediatric cohort.

`related_datasets` is a full-only slot; the core schema has no counterpart, so the relationship
survives in core only through the shared `description` and `source_caveats`.

## Phase 3 — source and provenance audit

### Provenance boundary

- Factual inputs were the declared bundle and `data/preprocessed/source_manifest.yaml` only.
  Structure was derived at runtime from `Dataset` in `data_sheets_schema_all.yaml` and
  `CoreDataset` in `data_sheets_schema_core_all.yaml` via LinkML `SchemaView`, including induced
  slot ranges, cardinality, inlining, identifier status, and enum permissible values.
- No prior D4D record was read, opened, grepped or consulted, from any arm, label or date. Nothing
  under `data/d4d_concatenated/` was read except this run's own two outputs, and no
  `*_crate_d4d.yaml` or `*_crate_mapped_d4d.yaml` under `data/ro-crate_packages/` was touched. No
  `VOICE*` glob was used at any point; every path was named in full.
- `data/preprocessed/concatenated/VOICE_preprocessed.txt` (the adult bundle) was not read.
- No evaluation report, test fixture, schema `d4d:docExample` value, or model memory supplied any
  dataset fact.

### Source disagreements represented rather than resolved silently

| Topic | Disagreement | Treatment |
|---|---|---|
| Funding identifier | Pediatric release acknowledges `3OT2OD032720-01S1`; NIH RePORTER record in the bundle is `3OT2OD032720-01S3` (application 11376382); documentation footer shows a garbled `Award #3Tf-OTOD03272001S2` | All three positions recorded: two distinct `Grant` objects plus the shared core project number `OT2OD032720`; the garbled string is described in `source_caveats` and deliberately **not** transcribed as a grant number |
| Ethics review | Protocol revision V2 says the pediatric cohort was brought "under single IRB"; the same protocol says Canadian sites (MSH, SickKids, UofT) do not follow the single IRB and obtain separate REB approval; PhysioNet attributes approval to the SickKids REB | Two `EthicalReview` objects, one per position, plus a `source_caveats` on the second |
| HIPAA status | DTUA: data is PII under OMB M-07-16 and "not covered under HIPAA"; documentation: HIPAA de-identification rules applied = "Yes" | `hipaa_compliant` left **unset**; both statements recorded in `regulatory_restrictions.regulatory_restrictions` and `is_deidentified.deidentification_details`, with the conflict named in top-level `source_caveats` |
| Version currency | Documentation says "The pediatric dataset v1.0 is now available" while also announcing v1.1.0 on the same page | PhysioNet v1.1.0 record treated as authoritative; the discrepancy noted in `source_caveats` |
| DOI | `DOI (version 1.1.0)` = `10.13026/h995-bt35`; `DOI (latest version)` = `10.13026/mf9s-5r03`, although 1.1.0 is the newest version listed | Both recorded (`doi` and `version_access.latest_version_doi`) with a caveat on `version_access` |
| Personal names | "Jennifer Siu" (PhysioNet) vs "Jennifer Sui, MD" (documentation); "Donald Bolser" vs "Don Bolser" | PhysioNet author-list spelling used as the `name`; the variant recorded in the creator's `description` and in top-level `source_caveats` |
| Confidentiality | PhysioNet: release is "low risk"; DTUA: the Data is Personally Identifiable Information under a Certificate of Confidentiality | `confidential_elements_present: false` for the featurized release, with the DTUA characterisation and its narrower scope in that object's `source_caveats` |

### Omissions the evidence required

The following slots were left empty because the bundle supports no pediatric-scoped value:
`labeling_strategies` (no diagnostic labeling described for the pediatric cohort — the labeling
answers in the documentation are adult-scoped), `existing_uses`, `use_repository`, `other_tasks`,
`future_use_impacts`, `errata`, `imputation_protocols`, `annotation_analyses`,
`machine_annotation_tools`, `collection_timeframes` (no collection window is stated anywhere in
the bundle for this cohort), `splits`, `subsets`, `is_tabular`, `conforms_to`, `compression`,
`total_file_count`, `total_size_bytes`, `download_url`, `status`, `dialect` (core).
`raw_data_sources` was deliberately not populated because `raw_sources` carries the same content
in the richer shape with `access_url`; duplicating it would restate a value.

Ontology-term slots with `uriorcurie` ranges (`Instance.data_topic`, `Instance.data_substrate`,
`VariableMetadata.unit`) were left unset: the bundle supplies no `B2AI_TOPIC` / `B2AI_SUBSTRATE`
terms and inventing CURIEs would be fabrication.

### Shape and slot-filling corrections made in Phase 3

All corrections were applied to the **full** record first and then propagated to core.

1. `creators[12].name` — restored the accent: `Jean-Christophe Belisle-Pipon` →
   `Jean-Christophe Bélisle-Pipon`, matching the PhysioNet author list; the same fix applied inside
   `citation`.
2. `creators[16].name` — `Don Bolser` → `Donald Bolser` (PhysioNet author list), with the
   documentation's variant recorded in `description`.
3. `instances[0].missing_information` — removed. The `MissingInfo` object described missing
   *recording features* but was attached to the *participant* instance, and it restated
   `missing_data_documentation`.
4. `instances[1].sampling_strategies` — removed. A `SamplingStrategy` object was being used to
   carry per-file feature coverage counts, which is a shape mismatch; the same fact is already in
   `anomalies` and `missing_data_documentation`.
5. `updates.update_details` — evidence commentary ("the bundle contains no stated update cadence")
   moved out of the narrative slot into `updates.source_caveats`, per the rule that evidence
   commentary belongs in `source_caveats`.
6. `version_access.version_details` — DOI restatement removed and replaced with a
   `version_access.source_caveats` entry, so the slot no longer repeats `doi` and
   `latest_version_doi`.
7. `retention_limit` — `retention_details` was restating `retention_period` almost verbatim; both
   were rewritten so the period slot carries the periods and the details slot carries the
   surrounding provisions only.
8. `regulatory_restrictions.description` — the DACO email was removed from the prose because it is
   the value of the sibling `governance_committee_contact` slot.
9. `distribution_formats[0].format` — a full sentence in a `format` slot was replaced with the
   format tokens `Apache Parquet, TSV, JSON`; the explanatory prose moved to `description`.
10. `existing_uses: []` — an empty list was removed in favour of omission.
11. `Person`-ranged slots (`Creator.principal_investigator`,
    `ExportControlRegulatoryRestrictions.governance_committee_contact`) are **not** inlined in this
    schema and take an identifier reference, not an object. Inline `Person` objects were replaced
    with `mailto:` URI references built from addresses that appear verbatim in the bundle
    (`mailto:yaelbensoussan@usf.edu`, `mailto:DACO@b2ai-voice.org`), and the descriptive content
    moved into the parent object's `description`.
12. `issued` — reformatted to RFC3339 (`2026-05-01T00:00:00Z`); a naive ISO timestamp failed
    `date-time` validation.

### Constructed identifiers, disclosed

`FileCollection` and `File` require identifiers. The bundle's file listing is restricted
("This is a restricted-access resource"), so folder and file URLs were **constructed** from the
documented project URL `https://physionet.org/content/b2ai-voice-pediatric/1.1.0/` plus the folder
names (`features`, `phenotype`, `metadata`) and file names given verbatim in the PhysioNet data
description. This construction is disclosed in top-level `source_caveats` and again in
`file_collections[0].source_caveats`. No byte count, checksum, `md5` or `sha256` was invented; all
are absent from both records because none appears in the bundle.

Apache Parquet is not a member of `FormatEnum` and has no member of `MediaTypeEnum`, so `format`
and `media_type` were omitted on the nine parquet files and the format is stated in `description`
instead. The TSV files carry `format: TSV` and `media_type: text/tab-separated-values`.

### Re-validation after Phase 3 corrections

```bash
poetry run linkml-validate -s src/data_sheets_schema/schema/data_sheets_schema_all.yaml -C Dataset \
  data/d4d_concatenated/claudecode_agent/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d.yaml
poetry run linkml-term-validator validate-data \
  data/d4d_concatenated/claudecode_agent/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d.yaml \
  --schema src/data_sheets_schema/schema/data_sheets_schema_all.yaml --target-class Dataset
poetry run linkml-validate -s src/data_sheets_schema/schema/data_sheets_schema_core_all.yaml -C CoreDataset \
  data/d4d_concatenated/claudecode_agent_core/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d_core.yaml
poetry run linkml-term-validator validate-data \
  data/d4d_concatenated/claudecode_agent_core/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d_core.yaml \
  --schema src/data_sheets_schema/schema/data_sheets_schema_core_all.yaml --target-class CoreDataset
```

All four returned clean: `No issues found` for both schema validations and
`✅ Validation passed` for both term validations.

## Phase 4 — strict full/core reconciliation

### Schema-derived shared slots

Derived at runtime with `SchemaView` over `Dataset` and `CoreDataset`, comparing induced range,
multivalued, required, min/max cardinality and `inlined_as_list`:

- **78 schema-identical shared slots** — must be present in both or absent from both, with deeply
  identical parsed YAML.
- **1 projected slot** — `resources` (`Dataset` in full, `CoreDataset` in core). It is unpopulated
  in both records, so the projection is trivially equal with zero coverage on each side.
- **11 full-only slots populated:** `citation`, `collection_consents`, `consent_revocations`,
  `direct_collection`, `file_collections`, `participant_compensation`, `participant_privacy`,
  `related_datasets`, `relationships`, `third_party_sharing`, `variables`.
- **1 core-only slot populated:** `distributions`. `dialect` is unpopulated.

Populated root slots: **64 in full, 54 in core** (53 shared identity slots plus `distributions`).

### Synchronization and independent check

Phase 3 made the full record canonical, so one synchronization was performed, followed by an
independent run with no `--sync-core`:

```bash
poetry run python -m data_sheets_schema.d4d_pair_consistency \
  --full data/d4d_concatenated/claudecode_agent/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d.yaml \
  --core data/d4d_concatenated/claudecode_agent_core/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d_core.yaml \
  --sync-core

poetry run python -m data_sheets_schema.d4d_pair_consistency \
  --full data/d4d_concatenated/claudecode_agent/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d.yaml \
  --core data/d4d_concatenated/claudecode_agent_core/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d_core.yaml
```

Result of the independent check:

```
PASS: 78 schema-identical slots; projected slots=['resources']
WARNING [semantic-review-required] $.file_collections <-> $.distributions: Phase 4 must
semantically review related distribution content; deterministic matches=1,
unmatched core distributions=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
```

The pre-synchronization run reported seven `shared-slot-content` errors, all of them Phase 3
corrections that had not yet been propagated from full to core (items 1, 3, 5, 6, 7, 8 and 9
above). Synchronization propagated the canonical full values; no core value was preferred over a
full value, and no shared narrative was condensed, paraphrased, reordered or omitted in core.

### Semantic review of the related distribution content

The validator's warning marks related content for review; it is not evidence that review occurred.
The review was performed by comparing every field the two representations share. Full carries 3
`FileCollection` objects containing 12 `File` objects (15 identified nodes); core carries 13
`CoreDistribution` objects.

- **Coverage.** Every core distribution id exists in full (0 core-only ids). 13 of the 15 full ids
  are present in core. The two absent ids are the `features` and `phenotype` **collection**
  nodes — grouping containers with no distribution semantics. `CoreDistribution` is a flat
  distribution unit with no collection-membership slot, so the grouping is correctly a full-only
  structure rather than a dropped fact. All 12 file-level nodes are present on both sides, and the
  `metadata` node appears on both because it is documented only at folder granularity.
- **Field-by-field.** `name`, `path`, `description`, `format`, `media_type`, `compression`,
  `bytes`, `md5`, `sha256` and `hash` were compared for every id present on both sides. One
  conflict was found and fixed: the `metadata` node's `description` had been paraphrased in core
  ("Folder of metadata information…" vs "Metadata information…"). Core was rewritten to the full
  record's exact wording. **Zero conflicts remain.**
- **Scope agreement.** Both representations describe the same release (v1.1.0) at the same
  granularity; no historical release is mixed in. Recording counts stated per file
  (`n=23533` for the four torchaudio features and the PPGs, `n=23532` for the four SPARC features)
  are identical in both and are consistent with `instances[1].counts: 23533` and with the
  `anomalies` entry that records the one-recording difference.
- **Counts and dialect.** `total_file_count`, `total_size_bytes`, `is_tabular` and `compression`
  are unset in both records, and core's `dialect` is unset, so there is nothing to contradict. No
  count was asserted, because the bundle documents 11 data files plus "a data dictionary file" per
  data file without stating a total.
- **Top-level identity against distributions and version history.** `id`, `doi`, `version`,
  `issued`, `page`, `license` and `license_and_use_terms` all describe v1.1.0; every distribution
  path sits under the v1.1.0 project URL; `distribution_dates.release_dates` and
  `version_access.versions_available` agree on 1.0.0 = 17 December 2025 and 1.1.0 = 1 May 2026;
  `related_datasets[2]` (`is_new_version_of`, v1.0.0) is consistent with both. The historical
  v1.0.0 release is distinguished from the current release throughout rather than treated as a
  contradiction.
- **Access facts.** `license`, `license_and_use_terms.license_terms`,
  `regulatory_restrictions.confidentiality_level: restricted`, `distribution_formats[0].description`
  and `third_party_sharing.description` all state the same access model (credentialed user +
  signed DUA for the featurized release; controlled access via DACO for raw audio) without
  conflict.

### Outcome

**No unresolved contradiction remains within either record or between the two.** Every
schema-identical shared slot has identical presence and deeply identical parsed content; the one
projected slot is empty on both sides; the one related-content mapping was reviewed field by field
and its single divergence was corrected.

### Files changed in Phase 4

- `…/claudecode_agent_core/2026-08-07_claude-opus-5-claudecode-generic-v3_rep2/VOICE_PEDIATRIC_d4d_core.yaml`
  — synchronized shared slots from the Phase 3-audited full record; `metadata` distribution
  description aligned to the full record's exact wording; `# Phase 4 reconciliation: completed`
  added to the header.
- The full record was not modified in Phase 4; all its changes were made in Phase 3.

### Final results

| Check | Result |
|---|---|
| `linkml-validate` full (`Dataset`) | No issues found |
| `linkml-term-validator` full | Validation passed |
| `linkml-validate` core (`CoreDataset`) | No issues found |
| `linkml-term-validator` core | Validation passed |
| `d4d_pair_consistency` (no sync) | PASS — 78 schema-identical slots, 1 projected slot |
| Semantic review of `file_collections` ↔ `distributions` | Completed; 1 divergence found and corrected; 0 remaining |
| Populated root slots | full 64, core 54 |
| Line counts (informational only, not a quality gate) | full 1190, core 811 |
