Add MicrobeKG audited-20260928 Parquet tables and dataset card

LICENSE

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+MicrobeKG Source-Specific Terms
+Snapshot: audited-20260928
+Notice prepared: 2026-09-29
+
+1. Scope
+This notice describes the licensing of a compilation of third-party and derived
+knowledge-graph records. It does not substitute for, expand, or override the
+licenses, database rights, or other applicable terms of the original sources.
+It is not a blanket grant of rights to third-party material.
+
+2. Source terms
+Reuse and redistribution of a record are subject to the applicable terms of its
+contributing sources and any permissions obtained from their rights holders.
+SOURCE_TERMS.md and source_terms.json identify sources, links to terms or source
+publications, review status, and outstanding questions. Those reviews are not
+themselves grants of permission. The original sources' applicable terms control.
+
+Preserve source attribution, evidence identifiers, and applicable notices.
+For records with multiple sources, retain all contributing-source information.
+Derived conflict records remain connected to their underlying source evidence.
+Dropping a source label does not establish that the remaining content is free of
+that source's rights or restrictions.
+
+3. Known qualifications
+HMDB states that commercial use and redistribution require explicit permission
+and acknowledgment. The CTD authors describe free non-commercial availability
+and a license requirement for commercial downloading. Exact snapshot terms and
+redistribution permissions must be considered separately where unresolved.
+Other sources also retain their own terms and attribution requirements.
+
+4. Compilation status
+This complete graph package is prepared for local author review. Permission for
+unrestricted public redistribution of the entire compilation has not been
+established. An "other" license tag, a non-commercial label, private hosting, or
+gated access does not create any missing upstream permission. This notice adds
+no restriction to material that is independently available under broader rights.
+
+5. Software
+The MIT license in the separate MicrobeKG code repository applies to the software
+within its stated scope. It does not relicense the third-party graph content.
+
+6. Scientific interpretation
+The graph retains source-dependent assertions and evidence classes. Inclusion
+does not imply endorsement by a data provider or confirmation of an association,
+a causal mechanism, or a therapeutic effect.

README.md

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+---
+pretty_name: MicrobeKG
+language:
+- en
+license: other
+license_name: microbekg-source-specific-terms
+license_link: LICENSE
+size_categories:
+- 1M<n<10M
+tags:
+- knowledge-graph
+- microbiome
+- biology
+- graph-machine-learning
+- link-prediction
+configs:
+- config_name: edges
+  default: true
+  data_files:
+  - split: full
+    path: data/edges/*.parquet
+- config_name: nodes
+  data_files:
+  - split: full
+    path: data/nodes/*.parquet
+---
+
+# MicrobeKG
+
+MicrobeKG connects microorganisms, metabolites, substrates, diseases, host genes,
+and interventions in a heterogeneous knowledge graph. Records retain source and
+evidence fields for graph querying, resource analysis, and hypothesis generation.
+
+This package contains the **audited-20260928** graph: **3,647,004 assertion rows**,
+**67,485 typed nodes**, **25 relation labels**, and **31 typed relation patterns**.
+It is a lossless Parquet export prepared on 2026-09-29.
+
+**Data terms:** the graph incorporates third-party sources with different terms.
+The `other` label refers to [source-specific terms](LICENSE), not a blanket open
+license. See [SOURCE_TERMS.md](SOURCE_TERMS.md) for source attribution, current
+contribution counts, review dates, and unresolved redistribution permissions.
+The software repository's MIT license does not license these third-party data.
+
+## Contents and loading
+
+| Configuration | Split | Rows | Files |
+|---|---|---:|---|
+| `edges` | `full` | 3,647,004 | 8 Parquet shards |
+| `nodes` | `full` | 67,485 | 1 Parquet file |
+
+`full` means the complete table. It is not a training or evaluation partition.
+Shards preserve the original row order and contain at most 500,000 rows. The files
+use Zstandard compression and row groups of at most 65,536 rows.
+
+```python
+from datasets import load_dataset
+
+repo_id = "YOUR_HF_USERNAME/MicrobeKG"  # replace with the actual dataset repository
+edges = load_dataset(repo_id, "edges", split="full")
+nodes = load_dataset(repo_id, "nodes", split="full")
+
+# Read progressively without materializing the entire table.
+edge_stream = load_dataset(repo_id, "edges", split="full", streaming=True)
+print(next(iter(edge_stream)))
+```
+
+For a private repository, first run `hf auth login` with an account that has access.
+For reproducible work, pass `revision="<dataset-commit-sha>"` to `load_dataset`.
+To use downloaded Parquet directly:
+
+```python
+import pyarrow.dataset as ds
+
+edges = ds.dataset("data/edges", format="parquet")
+subset = edges.to_table(
+    columns=["head_id", "relation", "tail_id", "source", "evidence"],
+    filter=(ds.field("head_type") == "microbe")
+           & (ds.field("tail_type") == "disease"),
+)
+```
+
+## Schema
+
+All columns are UTF-8 strings. Empty cells remain empty strings, and identifiers
+retain their original prefixes and formatting. See [schema.json](schema.json).
+
+| Table | Column | Meaning |
+|---|---|---|
+| edges | `head_id`, `head_type` | Identifier and type of the subject node |
+| edges | `relation` | Directed relation label |
+| edges | `tail_id`, `tail_type` | Identifier and type of the object node |
+| edges | `confidence` | Source-specific score or label, retained verbatim; not a calibrated probability |
+| edges | `species_source` | Source organism/context label, retained verbatim |
+| edges | `source` | Source labels; multiple labels can be separated by `\|` |
+| edges | `evidence` | Source evidence, identifiers, and provenance, retained verbatim |
+| edges | `evidence_type` | Evidence-class labels, potentially combined with `\|` |
+| nodes | `node_id` | Original canonical identifier |
+| nodes | `node_type` | One of the six entity types below |
+| nodes | `node_name` | Recorded display label; may be an identifier-derived label |
+| nodes | `source_databases` | Source labels associated with the node |
+
+**Node identity is `(node_type, node_id)`.** The same chemical identifier can occur
+as both a substrate and a metabolite. Join edges to nodes using both the identifier
+and type, rather than `node_id` alone. Evidence text may contain delimiters with
+different meanings; it should not be interpreted as a single list of source labels.
+
+| Node type | Count |
+|---|---:|
+| metabolite | 25,366 |
+| host_gene | 19,907 |
+| microbe | 15,821 |
+| disease | 5,212 |
+| substrate | 1,057 |
+| intervention | 122 |
+
+The microbe count includes taxonomic ranks and genome bins; it is not a species
+count. The build audit flags identifier-derived display labels for 19,907 host
+genes, 252 metabolites, and 14 substrates. These cells are populated, not missing;
+the original labels and typed graph connections are retained without name imputation.
+
+## Sources and preparation
+
+The graph integrates 18 upstream source labels, including curated association
+databases, metabolic resources, taxonomy/ontology resources, and literature-derived
+records. `cross_source_conflict` is an additional derived label. Source-labelled
+counts overlap when a row cites multiple sources and should not be summed as
+distinct graph assertions. `Lit44` is a historical source identifier; this snapshot
+contains retained assertions from 18 studies under that label.
+
+The audited snapshot harmonizes typed identifiers and relation labels and preserves
+evidence and disagreement records. This export does not change, filter, rescore,
+or impute any graph field. Source TSV hashes, Parquet hashes, file sizes, and counts
+are recorded in [manifest.json](manifest.json). Independently checked row equality,
+typed endpoint integrity, and statistics are recorded in [validation.json](validation.json)
+and [statistics.json](statistics.json).
+
+## Scope and appropriate use
+
+Use the graph for evidence-aware retrieval, graph exploration, and development of
+research methods. Distinguish observed associations, computationally inferred
+metabolic capabilities, curated biochemical records, and ontology relations.
+Associations and graph paths alone do not establish causation or clinical efficacy.
+Source coverage, research attention, organism resolution, and evidence density are
+uneven; missing edges should not be assumed to be confirmed negative findings.
+
+This package contains graph tables, not raw participant-level clinical records,
+sequencing reads, upstream database dumps, model checkpoints, or benchmark splits.
+Previously reported benchmark results use the frozen reference graph and splits;
+they are not new measurements on this audited export. Define and document suitable
+splits and leakage controls when evaluating methods on this snapshot.
+
+## Attribution and related code
+
+Code: [MicrobeKG-dataset_split_task](https://github.com/ZachGu-00/MicrobeKG-dataset_split_task).
+The code repository documents the scope of its reference graph construction and
+evaluation tools; this export is not a claim of complete upstream reconstruction.
+
+When citing the resource, include **MicrobeKG, audited-20260928**, the actual
+Hugging Face repository URL, and the immutable dataset commit used. Also acknowledge
+the relevant original data providers listed in [SOURCE_TERMS.md](SOURCE_TERMS.md).
+No DOI or publication identifier has been assigned by this packaging operation.
+Questions about this package can be filed in the linked code repository's Issues.

SHA256SUMS

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+4a16cc7c2cf2bb7609fe2eead1c7448721a71912c00db429396ccc34d9bae720  LICENSE
+be6c4a9724d8c60389cdaeac628be5358d4a96f59e175fd3bde46837a4c2f1d2  manifest.json
+52f9304aaec48846d4bdbb289c18d26a5e4e1c44099a1cc884dfc0b77c043afa  README.md
+3d7387d322fb52bdf90c728d7124c35266cad101ab0310c0f90246b37a37b548  schema.json
+dc7bb60624711ffc407637c4ff0c63c82af10e6a9bfa230e65295d6e91960e0b  source_terms.json
+23ff9d63272697f1a9edc1e16d5665bb04b7630885b467f19d31ca7fcb71b258  SOURCE_TERMS.md
+e8fba96c599de091ddbf20586c67e90ecfcf793717927f12cae3f63547688e02  statistics.json
+3d8a068e79ddaaf9fe0b3efdb3b9bd0415136ef2c8e7b379237653d01ec25044  validation.json

SOURCE_TERMS.md

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+# Sources, attribution, and licensing observations
+
+Counts refer to audited-20260928 and were independently recomputed from the exported records.
+They count assertion rows carrying each source label; multi-source rows contribute to more than one count.
+The 19 labels consist of 18 upstream labels and one derived conflict label.
+
+This is a source-terms record, not an unrestricted public redistribution license.
+`verified` / `verified_terms` indicate a located statement, not clearance for every possible use.
+`pending` means the applicable permission has not been established, not that reuse is forbidden.
+`partial` means the located statement does not yet establish the exact downloaded payload's terms.
+`restricted` / `restricted_pending_snapshot` preserve known qualifications.
+Publication licensing and database or supplementary-table licensing may differ.
+
+The earlier source review was dated 2026-09-18. Only HMDB and CTD were refreshed on 2026-09-29
+for this packaging task; dates below do not imply a new review of the other providers.
+See [source_terms.json](source_terms.json) for the machine-readable record and [LICENSE](LICENSE) for scope.
+
+| Source label | Labelled assertions | Status | Terms observation | Last checked | Evidence |
+|---|---:|---|---|---|---|
+| AGORA2 | 1,496,721 | partial | MIT on repository; downloaded SBML scope needs confirmation | 2026-09-18 | [Provider / publication](https://github.com/VirtualMetabolicHuman/AGORA2) |
+| BugSigDB | 15,197 | verified | ODC-BY-1.0 | 2026-09-18 | [Provider / publication](https://bugsigdb.org/Project:About) |
+| CTD | 124,973 | restricted | Non-commercial access; commercial download license | 2026-09-29 | [Provider / publication](https://academic.oup.com/nar/article/53/D1/D1328/7816860) |
+| Disbiome | 6,715 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://disbiome.ugent.be/) |
+| GMMAD | 1,046,640 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC10464125/) |
+| GMrepo_v3 | 19,849 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://gmrepo.humangut.info/) |
+| HMDAD | 407 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](http://www.cuilab.cn/hmdad) |
+| HMDB | 850,148 | restricted_pending_snapshot | Official terms require explicit permission and acknowledgment for commercial use and redistribution. | 2026-09-29 | [Provider / publication](https://www.hmdb.ca/downloads) |
+| Lit44 | 1,941 | pending | Per-article extracted factual assertions; heterogeneous terms | 2026-09-18 | Study identifiers in each record's evidence |
+| MeSH | 8,076 | verified_terms | NLM MeSH Terms and Conditions | 2026-09-18 | [Provider / publication](https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html) |
+| NCBI_Taxonomy | 58,610 | verified_terms | NCBI government-information policy, subject to third-party notices | 2026-09-18 | [Provider / publication](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
+| NJC19 | 5,042 | partial | Dryad dataset terms; snapshot license confirmation pending | 2026-09-18 | [Provider / publication](https://datadryad.org/dataset/doi:10.5061/dryad.dr7sqv9v8) |
+| Peryton | 3,439 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://dianalab.e-ce.uth.gr/peryton/) |
+| Piccinno_2025 | 191 | pending | Source/supplement-specific terms to confirm | 2026-09-18 | [Provider / publication](https://doi.org/10.1038/s41591-025-03693-9) |
+| Thomas_2019 | 52 | pending | Source/supplement-specific terms to confirm | 2026-09-18 | [Provider / publication](https://doi.org/10.1038/s41591-019-0405-7) |
+| cross_source_conflict | 1,054 | derived | Derived; preserve all contributing-source restrictions | 2026-09-18 | [Provider / publication](https://github.com/ZachGu-00/MicrobeKG-dataset_split_task/blob/2324306309e8851596b443e2711fef4b1bf41d66/scripts/step_merge_kg.py) |
+| gutMDisorder_v2 | 2,041 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://bio-computing.hrbmu.edu.cn/gutMDisorder/) |
+| gutMGene | 4,771 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://bio-computing.hrbmu.edu.cn/gutmgene/) |
+| mBodyMap | 8,252 | pending | No explicit data license established | 2026-09-18 | [Provider / publication](https://mbodymap.microbiome.cloud/) |
+
+## Source-specific notes
+
+- **AGORA2**: Repository redirects model downloads to VMH; preserve model attribution and confirm SBML terms.
+- **BugSigDB**: Data licensing section explicitly covers database reuse; preserve attribution and notices.
+- **CTD**: The authors describe free non-commercial availability and a commercial download license. This does not establish unrestricted bulk redistribution of the derived graph.
+- **Disbiome**: Download access and article availability do not establish redistribution rights.
+- **GMMAD**: Database paper located; exact downloaded-table terms still required.
+- **GMrepo_v3**: Confirm terms for the v3 phenotype and abundance exports used here.
+- **HMDAD**: Confirm original association table license.
+- **HMDB**: Commercial restriction verified in current official page text. Exact source snapshot and applicable redistribution permission remain to be confirmed.
+- **Lit44**: Historical source label. Retained assertion evidence contains study identifiers; exact article/supplement terms require per-study review. Full texts are not included.
+- **MeSH**: Acknowledge NLM; no endorsement; identify frozen version (local source desc2026.xml.gz).
+- **NCBI_Taxonomy**: Acknowledge NCBI and retain snapshot/version information; not a blanket license for other NCBI-hosted resources.
+- **NJC19**: Exact upstream dataset and NJC19 archive located; retain Lim et al. 2020 citation.
+- **Peryton**: Confirm downloadable associations terms separately from paper license.
+- **Piccinno_2025**: Confirm license and third-party notices for the exact MaAsLin2/phylogenetic/meta-analysis tables.
+- **Thomas_2019**: Confirm exact supplement identity and reuse terms; not inferred from another article.
+- **cross_source_conflict**: Conflict mining is original processing; underlying evidence remains source-governed.
+- **gutMDisorder_v2**: Freely accessible resource does not establish an unrestricted data license.
+- **gutMGene**: Confirm terms for the three downloaded interaction tables.
+- **mBodyMap**: Confirm terms for phenotype/body-site/species exports.
+
+## Attribution
+
+Acknowledge MicrobeKG and the original providers whose records are used. Follow each provider's
+requested citation and preserve the source/evidence fields. MeSH and NCBI inclusion does not
+imply endorsement by NLM, NCBI, or the United States government. This package does not change
+upstream licensing conditions or certify that all third-party permissions have been obtained.

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manifest.json

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+{
+  "dataset": "MicrobeKG",
+  "graph_version": "audited-20260928",
+  "package_version": "2026-09-29",
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+  "compression": "zstd",
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+  "scope": "Complete audited graph tables; no benchmark splits or model results.",
+  "split_name": "full",
+  "tables": {
+    "nodes": {
+      "rows": 67485,
+      "columns": [
+        "node_id",
+        "node_type",
+        "node_name",
+        "source_databases"
+      ],
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+        "source",
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+  "license": "other",
+  "license_name": "microbekg-source-specific-terms",
+  "publication_status": "Local package; source redistribution review remains incomplete.",
+  "software": {
+    "pyarrow": "25.0.1"
+  },
+  "parquet_bytes": 21484308,
+  "source_tsv_bytes": 693793669
+}

schema.json

@@ -0,0 +1,88 @@
+{
+  "graph_version": "audited-20260928",
+  "encoding": "UTF-8",
+  "empty_cells": "Preserved as empty strings, never inferred as null or NaN.",
+  "columns": {
+    "edges": [
+      {
+        "name": "head_id",
+        "type": "string"
+      },
+      {
+        "name": "head_type",
+        "type": "string"
+      },
+      {
+        "name": "relation",
+        "type": "string"
+      },
+      {
+        "name": "tail_id",
+        "type": "string"
+      },
+      {
+        "name": "tail_type",
+        "type": "string"
+      },
+      {
+        "name": "confidence",
+        "type": "string"
+      },
+      {
+        "name": "species_source",
+        "type": "string"
+      },
+      {
+        "name": "source",
+        "type": "string"
+      },
+      {
+        "name": "evidence",
+        "type": "string"
+      },
+      {
+        "name": "evidence_type",
+        "type": "string"
+      }
+    ],
+    "nodes": [
+      {
+        "name": "node_id",
+        "type": "string"
+      },
+      {
+        "name": "node_type",
+        "type": "string"
+      },
+      {
+        "name": "node_name",
+        "type": "string"
+      },
+      {
+        "name": "source_databases",
+        "type": "string"
+      }
+    ]
+  },
+  "node_key": [
+    "node_type",
+    "node_id"
+  ],
+  "edge_joins": {
+    "head": {
+      "head_type": "node_type",
+      "head_id": "node_id"
+    },
+    "tail": {
+      "tail_type": "node_type",
+      "tail_id": "node_id"
+    }
+  },
+  "confidence": "Source-specific text, including labels and numeric-looking values; not a uniform probability.",
+  "source": "Multiple source labels can be separated by |; retain all labels.",
+  "evidence": "Original free-form evidence and provenance; preserve verbatim.",
+  "node_name": "Recorded display label, which may equal the identifier or its suffix.",
+  "splits": {
+    "full": "Complete graph table; not a benchmark train/validation/test split."
+  }
+}

source_terms.json

@@ -0,0 +1,200 @@
+{
+  "graph_version": "audited-20260928",
+  "count_date": "2026-09-29",
+  "counts_overlap": true,
+  "public_redistribution_review_complete": false,
+  "sources": [
+    {
+      "source": "AGORA2",
+      "current_labelled_assertions": 1496721,
+      "license_observation": "MIT on repository; downloaded SBML scope needs confirmation",
+      "status": "partial",
+      "evidence_url": "https://github.com/VirtualMetabolicHuman/AGORA2",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Repository redirects model downloads to VMH; preserve model attribution and confirm SBML terms."
+    },
+    {
+      "source": "BugSigDB",
+      "current_labelled_assertions": 15197,
+      "license_observation": "ODC-BY-1.0",
+      "status": "verified",
+      "evidence_url": "https://bugsigdb.org/Project:About",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Data licensing section explicitly covers database reuse; preserve attribution and notices."
+    },
+    {
+      "source": "CTD",
+      "current_labelled_assertions": 124973,
+      "license_observation": "Non-commercial access; commercial download license",
+      "status": "restricted",
+      "evidence_url": "https://academic.oup.com/nar/article/53/D1/D1328/7816860",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-29",
+      "notes": "The authors describe free non-commercial availability and a commercial download license. This does not establish unrestricted bulk redistribution of the derived graph.",
+      "check_method": "Read Data availability in the CTD authors' 2025 update."
+    },
+    {
+      "source": "Disbiome",
+      "current_labelled_assertions": 6715,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://disbiome.ugent.be/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Download access and article availability do not establish redistribution rights."
+    },
+    {
+      "source": "GMMAD",
+      "current_labelled_assertions": 1046640,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10464125/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Database paper located; exact downloaded-table terms still required."
+    },
+    {
+      "source": "GMrepo_v3",
+      "current_labelled_assertions": 19849,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://gmrepo.humangut.info/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm terms for the v3 phenotype and abundance exports used here."
+    },
+    {
+      "source": "HMDAD",
+      "current_labelled_assertions": 407,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "http://www.cuilab.cn/hmdad",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm original association table license."
+    },
+    {
+      "source": "HMDB",
+      "current_labelled_assertions": 850148,
+      "license_observation": "Official terms require explicit permission and acknowledgment for commercial use and redistribution.",
+      "status": "restricted_pending_snapshot",
+      "evidence_url": "https://www.hmdb.ca/downloads",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-29",
+      "notes": "Commercial restriction verified in current official page text. Exact source snapshot and applicable redistribution permission remain to be confirmed.",
+      "check_method": "Official download/about page text returned by web search; direct page access unavailable."
+    },
+    {
+      "source": "Lit44",
+      "current_labelled_assertions": 1941,
+      "license_observation": "Per-article extracted factual assertions; heterogeneous terms",
+      "status": "pending",
+      "evidence_url": "",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Historical source label. Retained assertion evidence contains study identifiers; exact article/supplement terms require per-study review. Full texts are not included."
+    },
+    {
+      "source": "MeSH",
+      "current_labelled_assertions": 8076,
+      "license_observation": "NLM MeSH Terms and Conditions",
+      "status": "verified_terms",
+      "evidence_url": "https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Acknowledge NLM; no endorsement; identify frozen version (local source desc2026.xml.gz)."
+    },
+    {
+      "source": "NCBI_Taxonomy",
+      "current_labelled_assertions": 58610,
+      "license_observation": "NCBI government-information policy, subject to third-party notices",
+      "status": "verified_terms",
+      "evidence_url": "https://www.ncbi.nlm.nih.gov/home/about/policies/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Acknowledge NCBI and retain snapshot/version information; not a blanket license for other NCBI-hosted resources."
+    },
+    {
+      "source": "NJC19",
+      "current_labelled_assertions": 5042,
+      "license_observation": "Dryad dataset terms; snapshot license confirmation pending",
+      "status": "partial",
+      "evidence_url": "https://datadryad.org/dataset/doi:10.5061/dryad.dr7sqv9v8",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Exact upstream dataset and NJC19 archive located; retain Lim et al. 2020 citation."
+    },
+    {
+      "source": "Peryton",
+      "current_labelled_assertions": 3439,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://dianalab.e-ce.uth.gr/peryton/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm downloadable associations terms separately from paper license."
+    },
+    {
+      "source": "Piccinno_2025",
+      "current_labelled_assertions": 191,
+      "license_observation": "Source/supplement-specific terms to confirm",
+      "status": "pending",
+      "evidence_url": "https://doi.org/10.1038/s41591-025-03693-9",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm license and third-party notices for the exact MaAsLin2/phylogenetic/meta-analysis tables."
+    },
+    {
+      "source": "Thomas_2019",
+      "current_labelled_assertions": 52,
+      "license_observation": "Source/supplement-specific terms to confirm",
+      "status": "pending",
+      "evidence_url": "https://doi.org/10.1038/s41591-019-0405-7",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm exact supplement identity and reuse terms; not inferred from another article."
+    },
+    {
+      "source": "cross_source_conflict",
+      "current_labelled_assertions": 1054,
+      "license_observation": "Derived; preserve all contributing-source restrictions",
+      "status": "derived",
+      "evidence_url": "https://github.com/ZachGu-00/MicrobeKG-dataset_split_task/blob/2324306309e8851596b443e2711fef4b1bf41d66/scripts/step_merge_kg.py",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Conflict mining is original processing; underlying evidence remains source-governed."
+    },
+    {
+      "source": "gutMDisorder_v2",
+      "current_labelled_assertions": 2041,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://bio-computing.hrbmu.edu.cn/gutMDisorder/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Freely accessible resource does not establish an unrestricted data license."
+    },
+    {
+      "source": "gutMGene",
+      "current_labelled_assertions": 4771,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://bio-computing.hrbmu.edu.cn/gutmgene/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm terms for the three downloaded interaction tables."
+    },
+    {
+      "source": "mBodyMap",
+      "current_labelled_assertions": 8252,
+      "license_observation": "No explicit data license established",
+      "status": "pending",
+      "evidence_url": "https://mbodymap.microbiome.cloud/",
+      "original_review_date": "2026-09-18",
+      "last_terms_check_date": "2026-09-18",
+      "notes": "Confirm terms for phenotype/body-site/species exports."
+    }
+  ]
+}

statistics.json

@@ -0,0 +1,258 @@
+{
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+    "mBodyMap": 8252
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+  "source_counts_overlap": true,
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+}

validation.json

@@ -0,0 +1,56 @@
+{
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+  "checked_date": "2026-09-29",
+  "method": "Independent Python csv parser vs every Parquet cell, preserving row order.",
+  "tables": {
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+      "all_cells_equal": true,
+      "empty_strings_by_column": {
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+        "node_name": 0,
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+      "source_sha256_matches": true,
+      "parquet_hashes_match": true
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+      "all_cells_equal": true,
+      "empty_strings_by_column": {
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+        "relation": 0,
+        "tail_id": 0,
+        "tail_type": 0,
+        "confidence": 0,
+        "species_source": 0,
+        "source": 0,
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+        "evidence_type": 0
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+      "source_sha256_matches": true,
+      "parquet_hashes_match": true
+    }
+  },
+  "huggingface_local_load": {
+    "nodes": {
+      "split": "full",
+      "rows": 67485,
+      "all_shards_read": true
+    },
+    "edges": {
+      "split": "full",
+      "rows": 3647004,
+      "all_shards_read": true
+    }
+  },
+  "typed_node_keys_unique": true,
+  "missing_typed_endpoints": 0,
+  "statistics_match_audited_and_independent_counts": true,
+  "dataset_card_parsed": true,
+  "remote_upload_performed": false,
+  "remote_viewer_verified": false,
+  "passed": true
+}