# AI_READI full/core reconciliation — 2026-07-28_claude-opus-5-deprimed_rep1

**Arm:** HEALTHSHEET-ONLY (single structured upstream source)
**Runtime / provider / model:** Claude Code / Anthropic / claude-opus-5[1m]
**Mode:** four-phase project agent, de-primed. Temperature 0.0.

**Declared factual input (only source of dataset facts):**
`data/preprocessed/concatenated/AI_READI_healthsheet_only.txt` (539 lines, 56,453 bytes;
14 sections, 84 questions, 81 answered)

**Structural authority:**
- Full: `src/data_sheets_schema/schema/data_sheets_schema_all.yaml`, class `Dataset`
- Core: `src/data_sheets_schema/schema/data_sheets_schema_core_all.yaml`, class `CoreDataset`

**Outputs:**
- Full: `data/d4d_concatenated/claudecode_agent_healthsheet/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d.yaml`
- Core: `data/d4d_concatenated/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d_core.yaml`
- Provenance: `data/d4d_concatenated/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_provenance.yaml` (`record_mode: live`)

---

## Phase 3 — Source and provenance audit

### 3.1 Provenance boundary

Factual inputs actually read during this run, in order:

1. `.claude/agents/d4d-provenance-guard.md` (policy)
2. `.claude/commands/d4d-full-core.md`, `.claude/commands/d4d-agent.md` (method)
3. `data/preprocessed/concatenated/AI_READI_healthsheet_only.txt` (the only factual source)
4. Both LinkML schemas, read through `SchemaView` rather than as raw YAML, to derive the
   induced slot inventory, ranges, cardinality, required status, inlining behavior, and enum
   permissible values for `Dataset`, `CoreDataset`, and every reachable nested class
5. The same-run Phase 1 full YAML, as the Phase 2 input

No prior full or core D4D record was read, grepped, or opened, from this arm or any other.
The only directory listing performed was `ls data/d4d_concatenated/claudecode_agent_healthsheet/`,
which returned directory names only and was used solely to confirm the new version label does not
collide with an existing one — no file contents entered context. No evaluation report, rubric
output, reconciliation report, test fixture, or `d4d:docExample` value was used as evidence.
The source manifest was deliberately not consulted; this arm declares its single bundle explicitly.

Structure was derived from the schemas only. No field name, nested-object shape, or value was
copied from a documentation example or from prior generated YAML.

### 3.2 Findings against the source bundle

Five findings. All were resolved from the declared bundle; none was resolved by preferring a value
because it already appeared in either generated record.

**F1 — Award identifier rendered two ways in the source (corrected).**
The bundle gives the award as `OT2ODO32644` (Motivation, funding question, line 97) and as
`OT2OD032644` (Collection, personnel question, line 416). The two strings differ: the first
substitutes a letter `O` for a zero and is one character short of the NIH `OT2` + institute code +
six digits pattern that the second follows, and both statements share the `OD` institute code.
The internally well-formed rendering `OT2OD032644` is recorded in `funders[0].grants[0].grant_number`,
and the grant `description` now states that the source renders the identifier in two forms and which
one was recorded. No external source was consulted to break the tie.

**F2 — Stale scope carried inside the source (corrected).**
The Composition section states the dataset "contains data from all participants who have been
enrolled during the first year of data collection for AI-READI" (line 117). This scope contradicts
the rest of the same document, which repeatedly scopes version 3 to data collected between
July 19, 2023 and May 1, 2025 — through the end of the *second* year — for 2280 participants
(Versioning, Composition, Collection). The narrower "first year" phrasing is a leftover from an
earlier version's answer. The record asserts complete enrollment over "the data collection period"
rather than reproducing the stale year scope, and `sampling_strategies[0].description` documents the
discrepancy and the resolution explicitly.

**F3 — Unsupported DUO permission codes (corrected).**
Phase 1 initially emitted `license_and_use_terms.data_use_permission:
[health_medical_biomedical_research, publication_required]`. Neither is supported. The bundle says
the license was tailored "to enable reuse ... for commercial or research purpose", which is broader
than the DUO health/medical/biomedical restriction, and says only that use "requires citation to the
resources specified in https://docs.aireadi.org", which is an attribution requirement, not the DUO
publication-required condition. The slot was removed from both records. The citation requirement is
retained as free text in `license_and_use_terms.license_terms` and `intended_uses[0].usage_notes`.

**F4 — Unsupported variable data type (corrected).**
`variables[0].data_type: float` was emitted for the logMAR visual acuity variable. The bundle
records that Snellen variables were dropped and only logMAR measurements remain, but states no
storage or value type. The `data_type` slot was removed; `variable_name`, `measurement_technique`,
and `quality_notes` remain, all directly source-backed.

**F5 — URI scheme normalized (corrected).**
The bundle writes the distribution platform as `http://fairhub.io/` (line 500). Phase 1 wrote
`https://fairhub.io/` in `page` and `publisher` while using `http://fairhub.io/` in
`distribution_formats[0].access_urls`. All three now use the source form, `http://fairhub.io/`,
so the three statements of the same fact agree within each file and between the two files.

### 3.3 Source tensions retained deliberately, with explicit scope

Two internal tensions in the bundle are genuine properties of the source and were preserved rather
than smoothed over:

- **Balance claims.** The Challenge section says "the pilot study is not balanced across these
  parameters", a statement scoped to the pilot phase, while the General Information section says
  enrollment is ongoing and "periodic updates to data releases may not have achieved balanced
  distribution across groups". Both are carried in `known_biases[0]`, each with its own scope
  intact, so a historical claim is not presented as a current one.
- **Demographic sub-populations.** The Demographic Information section answers "No" to whether the
  dataset identifies demographic sub-populations, while Composition states that the controlled-access
  tier contains race, ethnicity, sex, and 5-digit zip code. These are not contradictory once the
  access tier is accounted for: the released public tier does not identify sub-populations. The "No"
  answer is recorded in `subpopulations[0]` and the controlled-tier content in
  `sensitive_elements[1]` and `resources[1]`, keeping the tiers distinct.

### 3.4 Internal consistency checks (both files)

Repeated facts were checked for agreement wherever they appear:

| Fact | Occurrences checked | Result |
|---|---|---|
| 2280 participants (v3) | `description`, `instances[0].counts`, `subsets[*]`, `splits[0]`, `version_access.versions_available/version_details` | consistent |
| 204 (v1) / 1067 (v2) participants | `version_access` (two statements) | consistent, including the 863-additional arithmetic given in the source |
| Collection window 2023-07-19 → 2025-05-01 | `collection_timeframes[0].start_date/end_date/timeframe_details`, `description`, `version_access` | consistent |
| Version identity = 3 | `version`, `description`, `version_access`, `resources` scoping | consistent |
| DOI 10.60775/fairhub.3 | `id`, `doi`, `version_access.latest_version_doi`, `distribution_formats[0].access_urls` | consistent |
| License at 10.5281/zenodo.17555036 | `license`, `license_and_use_terms`, `ip_restrictions`, `regulatory_restrictions`, `discouraged_uses`, `prohibited_uses` | consistent |
| Release dates May 2024 / Nov 2024 / Nov 2025 | `distribution_dates`, `version_access` | consistent (the source's "released fall 2025" and "distributed in November 2025" are compatible and both retained) |
| IRB approval 2022-12-20, UW | `ethical_reviews[0]`, `human_subject_research.irb_approval` | consistent |
| Access tiering (public vs DUA) | `description`, `resources`, `sensitive_elements`, `regulatory_restrictions`, `license_and_use_terms`, `known_limitations[3]` | consistent |
| No labels provided | `instances[0].label/label_description`, `labeling_strategies[0]`, `tasks[0]` | consistent |
| Split 70/15/15 | `subsets[*]`, `splits[0]` | consistent; the source's two balancing-variable lists (age/sex/race-ethnicity/study group, and sex/race-ethnicity/diabetes status) are both quoted rather than merged |

No unsupported, stale, or mis-scoped assertion remains after F1–F5.

### 3.5 Phase 2 discoveries back-ported to full

None. Phase 2 found no core field that the full record left empty and no fact the full extraction
had missed. Every core-eligible fact already had a full-schema slot populated in Phase 1, and the
two core-only slots (`distributions`, `dialect`) have no support in this bundle — see 4.4. The
Phase 3 corrections F1–F5 were applied to the full record first, and the core record was then
regenerated from the corrected full record.

### 3.6 Coverage note

The bundle is a Healthsheet alone: no publications, documentation, license text, or IRB protocol.
Consequently the record carries no file-level facts (no file counts, sizes, formats, checksums, or
paths), no named individuals, no ORCIDs, no organizational identifiers beyond the three site names,
and no ontology-term annotations for data topic or substrate. Those slots are absent rather than
filled, which is the correct outcome for this arm; the source's own three unanswered questions
(de-identification measures, de-identification preprocessing, erratum) are likewise represented by
absence, or, where the source's silence is itself informative, by an explicit statement that the
source left the question unanswered (`preprocessing_strategies[1]`, `is_deidentified`,
`participant_privacy[0].reidentification_risk`).

---

## Phase 4 — Strict full/core reconciliation

### 4.1 Shared-slot derivation (runtime, not hand-maintained)

Shared slots were derived at runtime with LinkML `SchemaView` by intersecting
`class_induced_slots("Dataset")` with `class_induced_slots("CoreDataset")`:

- `CoreDataset` induced slots: **79**
- Shared with `Dataset`: **77**
- Schema-identical (same induced range and cardinality): **76**
- Projected (range differs): **1** — `resources` (`Dataset` in full, `CoreDataset` in core)
- Core-only: **2** — `distributions`, `dialect`
- Full-only: **17** — `citation`, `collection_consents`, `collection_notifications`,
  `consent_revocations`, `direct_collection`, `file_collections`, `parent_datasets`,
  `participant_compensation`, `participant_privacy`, `related_datasets`, `relationships`,
  `splits`, `subsets`, `third_party_sharing`, `total_file_count`, `total_size_bytes`, `variables`

The core record was generated by projecting the Phase 3-corrected full record through this derived
intersection, so identity holds by construction rather than by transcription.

### 4.2 Slot counts

| | populated top-level slots |
|---|---|
| Full (`Dataset`) | **74** |
| Core (`CoreDataset`) | **63** |
| Full slots outside the core schema | 11 — `collection_consents`, `collection_notifications`, `consent_revocations`, `direct_collection`, `participant_compensation`, `participant_privacy`, `relationships`, `splits`, `subsets`, `third_party_sharing`, `variables` |

74 − 11 = 63. The difference is entirely accounted for by the core schema's field inventory; no
content was dropped for length and none was condensed.

### 4.3 Schema-identical slots

All 76 schema-identical slots satisfy both requirements:

- **Identical presence** — each is present in both files or absent from both.
- **Deep value identity** — parsed YAML values are equal, including every nested mapping value and
  every list item in the same order.

This holds for the narrative fields as well. Core does not condense, paraphrase, reorder, or omit
any shared content: the long device descriptions in `collection_mechanisms` (20 objects), the
`known_limitations` and `known_biases` narratives, and the multi-item `version_access` history are
byte-for-byte the same content in both records.

No synchronization pass was required. `--sync-core` was **not** run; the pair passed the independent
check on the first attempt, because core was generated as a projection of the corrected full record.

### 4.4 Projected and related content — semantic review

**`resources` (projection, `Dataset` → `CoreDataset`).**
Two resource objects, matched by `id`, with equal coverage in both files:

| id | present in full | present in core | nested slots |
|---|---|---|---|
| `…fairhub.3#public-access-tier` | yes | yes | `id`, `name`, `title`, `description` |
| `…fairhub.3#controlled-access-tier` | yes | yes | `id`, `name`, `title`, `description` |

Every nested slot used is schema-identical between `Dataset` and `CoreDataset`, and each value is
deeply identical across the pair. No full-only nested slot was populated on either resource, so the
projection drops nothing. Semantically the two resources partition the release by access tier and
agree with `description`, `sensitive_elements`, and `regulatory_restrictions.confidentiality_level:
restricted` in both files.

**`file_collections` → `distributions` (related representations).**
Both are empty. The Healthsheet contains no file-level evidence — no file names, counts, byte sizes,
checksums, formats, encodings, or directory paths — so `file_collections`, `total_file_count`, and
`total_size_bytes` are absent from full and `distributions` is absent from core. There is nothing to
map and therefore no possible conflict in names, descriptions, paths, formats, compression,
checksums, byte counts, access URLs, or release scope. Access-point information that *is* supported
lives in the schema-identical `distribution_formats` slot, which is deeply identical across the pair.

**`total_file_count` / `total_size_bytes` vs distribution-level values.** Not applicable; all are
absent. No scope comparison is possible or needed.

**`dialect`, formats, `is_tabular`.** `dialect` is absent from core: the bundle states no delimiter,
header, or quoting convention. No `FormatEnum` or `MediaTypeEnum` value is asserted anywhere in
either record, because the bundle names modality families (tabular, imaging, physiological
signal/waveform) and the DICOM and OMOP standards, but no concrete file format. `is_tabular: false`
is present and identical in both files and agrees with that description — the dataset spans imaging
and waveform data and is not purely tabular — and it does not conflict with `dialect` being absent
or with the absence of format assertions.

**Top-level identity, version, and access facts vs nested content.** Checked across the pair and
within each file: `id` / `doi` / `version` / `status` / `page` / `publisher` / `license` agree with
`version_access` (including `latest_version_doi`), `distribution_dates`, `distribution_formats`,
`license_and_use_terms`, `updates`, and the two access-tier `resources`. `third_party_sharing`
(`is_shared: true`) is full-only, and it does not contradict anything in core: core carries the same
public-distribution fact through `distribution_formats`, `license_and_use_terms`, and
`resources[0]`.

**Historical vs current release.** Version 1 (204 participants, May 2024), version 2 (1067
participants, November 2024), and version 3 (2280 participants, November 2025) are recorded as an
explicit version history inside `version_access`, not as competing values of `version` or of
`instances[0].counts`. The differing participant counts are therefore a documented progression, not
a contradiction. The same applies to the dropped Snellen visual acuity variables, which are recorded
as a version-to-version change in `version_access.version_details`, in
`instances[0].missing_information`, and (full-only) in `variables[0].quality_notes`.

**Unresolved contradictions within or between the two records: none.**

### 4.5 Files changed

| File | Change |
|---|---|
| `…/claudecode_agent_healthsheet/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d.yaml` | created in Phase 1; corrected in Phase 3 (F1–F5) |
| `…/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d_core.yaml` | created in Phase 2; regenerated in Phase 3 from the corrected full record |
| `…/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_provenance.yaml` | written by `d4d provenance record` after Phase 4 |
| `…/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_reconciliation.md` | this report |

Nothing outside these four paths was created or modified.

### 4.6 Commands run

```bash
# Phase 1 / Phase 3 validation of the full record
poetry run linkml-validate -s src/data_sheets_schema/schema/data_sheets_schema_all.yaml \
  -C Dataset data/d4d_concatenated/claudecode_agent_healthsheet/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d.yaml
poetry run linkml-term-validator validate-data \
  data/d4d_concatenated/claudecode_agent_healthsheet/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d.yaml \
  --schema src/data_sheets_schema/schema/data_sheets_schema_all.yaml --target-class Dataset

# Phase 2 / Phase 3 validation of the core record
poetry run linkml-validate -s src/data_sheets_schema/schema/data_sheets_schema_core_all.yaml \
  -C CoreDataset data/d4d_concatenated/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d_core.yaml
poetry run linkml-term-validator validate-data \
  data/d4d_concatenated/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d_core.yaml \
  --schema src/data_sheets_schema/schema/data_sheets_schema_core_all.yaml --target-class CoreDataset

# Phase 4 schema-derived pair consistency (no --sync-core needed)
poetry run python -m data_sheets_schema.d4d_pair_consistency \
  --full data/d4d_concatenated/claudecode_agent_healthsheet/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d.yaml \
  --core data/d4d_concatenated/claudecode_agent_healthsheet_core/2026-07-28_claude-opus-5-deprimed_rep1/AI_READI_d4d_core.yaml

# Live provenance record
poetry run d4d provenance record --project AI_READI --method claudecode_agent_healthsheet \
  --label 2026-07-28_claude-opus-5-deprimed_rep1 \
  --input-bundle data/preprocessed/concatenated/AI_READI_healthsheet_only.txt
```

### 4.7 Final results

| Check | Result |
|---|---|
| Full — LinkML schema validation (`Dataset`) | **PASS** — No issues found |
| Full — ontology term validation | **PASS** |
| Core — LinkML schema validation (`CoreDataset`) | **PASS** — No issues found |
| Core — ontology term validation | **PASS** |
| Pair consistency (schema-derived, no sync) | **PASS** — 76 schema-identical slots; projected slots = `['resources']` |
| Projected / related content semantic review | **complete, 0 unresolved contradictions** |
| Provenance boundary | **clean** — no prior-run D4D, evaluation, or reconciliation artifact read |
| Live provenance record | present, `record_mode: live` |

**Outcome:** the pair reconciles cleanly. Five source-audit corrections (F1–F5) were applied to the
full record and propagated to core by regeneration; no divergence between the two records remained
at Phase 4, and no synchronization pass was required.
