| # 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. | |