| { | |
| "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." | |
| } | |
| ] | |
| } | |