# RO-Crate Normalization — CM4AI

Generated by `d4d rocrate normalize`. Raw inputs are never modified;
re-running over unchanged inputs reproduces these outputs exactly.

## Inputs

- `linkml`: `data/ro-crate_packages/CM4AI/crate/ro-crate-linkml.yaml`
- `metadata`: `data/ro-crate_packages/CM4AI/crate/ro-crate-metadata.json`
- `datasheet`: `data/ro-crate_packages/CM4AI/crate/ro-crate-datasheet.html`
- `score`: `data/ro-crate_packages/CM4AI/crate/ai_ready_score.json`

## Outputs

- `d4d`: `data/ro-crate_packages/CM4AI/processed/CM4AI_crate_d4d.yaml`
- `metadata_reduced`: `data/ro-crate_packages/CM4AI/processed/CM4AI_crate_metadata_reduced.json`

## Validation

- `CM4AI_crate_d4d.yaml`: **PASS**

## Changes (25)

| Step | Action | Detail | Before | After |
|------|--------|--------|--------|-------|
| schema-reconcile | remap | `bytes` -> `total_size_bytes` | bytes: 21880281392742 | total_size_bytes: 21880281392742 |
| schema-reconcile | drop-redundant | `encoding` absent from schema; duplicates `distribution_formats` | [".d", ".d directory group", ".tsv", ".xml", "TSV", "csv", "executable", "fastq.gz", "h5", "h5ad", "image/jpeg", "pdf", "unknown"] |  |
| schema-reconcile | drop-redundant | `format` absent from schema; duplicates `distribution_formats` | [".d", ".d directory group", ".tsv", ".xml", "TSV", "csv", "executable", "fastq.gz", "h5", "h5ad", "image/jpeg", "pdf", "unknown"] |  |
| compression | drop | slot is single-valued with range CompressionEnum (bzip2\|compress\|gzip\|lzma\|tar\|xz\|zip); supplied value is neither. Codecs are not inferred from file extensions. | [".d", ".d directory group", ".tsv", ".xml", "TSV", "csv", "executable", "fastq.gz", "h5", "h5ad", "image/jpeg", "pdf", "unknown"] |  |
| creators | mint-surrogate-id | 12 organization(s) named without an identifier; Organization.id is required, so a local `urn:d4d:org:` surrogate was minted. Carries no external authority; not a ROR/GRID claim. | affiliation name only | urn:d4d:org:kth-royal-institute-of-technology, urn:d4d:org:simon-fraser-university, urn:d4d:org:stanford-university |
| creators | resolve | 38 reference(s) resolved to name + affiliation from in-crate Person entities; 0 unresolved. `@id` renamed to `id`, ORCID retained. | 47 entries, 38 ref-only | [{"id": "https://orcid.org/0000-0003-4060-7360", "name": "Clark, T", "affiliations": [{"id": "urn:d4d:org:university-of-virginia", "name": "University of Virgi… |
| created_by | flatten | slot range is string but a 47-item list was supplied; resolved and joined into one string (47 names) | 47 entries | Clark, T, Parker, J, Al Manir, S, Axelsson, U, Ballllosero Navarro, F, Chinn, B, Churas, CP, Dailamy, A, Doctor, Y, Fall, J, Forget, A, Gao, J, Hansen, JN, Hu,… |
| reduce-metadata | collapse | `hasPart` on Cell Maps for Artificial Intelligence - June 2026 Data Rele… | 60 entries | summary of 60 |
| reduce-metadata | collapse | `hasPart` on EndoTag AP-MS Profiling of Chromatin Modifier Interactome R… | 560 entries | summary of 560 |
| reduce-metadata | collapse | `https://w3id.org/EVI#outputs` on EndoTag AP-MS Profiling of Chromatin Modifier Interactome R… | 555 entries | summary of 555 |
| reduce-metadata | collapse | `https://w3id.org/EVI#inputs` on EndoTag AP-MS Profiling of Chromatin Modifier Interactome R… | 117 entries | summary of 117 |
| reduce-metadata | collapse | `hasPart` on EndoTag-AP-MS Profiling of Chromatin Modifier Interactome R… | 723 entries | summary of 723 |
| reduce-metadata | collapse | `https://w3id.org/EVI#outputs` on EndoTag-AP-MS Profiling of Chromatin Modifier Interactome R… | 718 entries | summary of 718 |
| reduce-metadata | collapse | `https://w3id.org/EVI#inputs` on EndoTag-AP-MS Profiling of Chromatin Modifier Interactome R… | 138 entries | summary of 138 |
| reduce-metadata | collapse | `hasPart` on Paclitaxel IF Images | 18,625 entries | summary of 18,625 |
| reduce-metadata | collapse | `https://w3id.org/EVI#outputs` on Paclitaxel IF Images | 17,685 entries | summary of 17,685 |
| reduce-metadata | collapse | `hasPart` on Untreated IF Images | 16,845 entries | summary of 16,845 |
| reduce-metadata | collapse | `https://w3id.org/EVI#outputs` on Untreated IF Images | 15,905 entries | summary of 15,905 |
| reduce-metadata | collapse | `hasPart` on Vorinostat IF Images | 18,789 entries | summary of 18,789 |
| reduce-metadata | collapse | `https://w3id.org/EVI#outputs` on Vorinostat IF Images | 17,849 entries | summary of 17,849 |
| reduce-metadata | collapse | `hasPart` on SEC-MS characterization of KOLF2 neuronal and cardiomyocyte… | 867 entries | summary of 867 |
| reduce-metadata | collapse | `hasPart` on SEC-MS of MDA-MB468 following treatment of vorinostat or pa… | 45 entries | summary of 45 |
| reduce-metadata | collapse | `https://w3id.org/EVI#outputs` on Perturbation Cell Atlas of Human Induced Pluripotent Stem C… | 103 entries | summary of 103 |
| reduce-metadata | collapse | `https://w3id.org/EVI#inputs` on Perturbation Cell Atlas of Human Induced Pluripotent Stem C… | 192 entries | summary of 192 |
| reduce-metadata | collapse | `https://w3id.org/EVI#inputs` on Perturbation Cell Atlas of Human Induced Pluripotent Stem C… | 90 entries | summary of 90 |
