DH{}DataHunter

Dataset from Zenodo · Langley, Andrew

SMILE: Systematic Microbiome Intelligence for Lost Ecosystems - Ancient Oral Microbiome Database v1.0

Open on Zenodo
License
CC BY 4.0commercial use allowedLicense text
This license allows commercial use. Usually you must credit the author; read the license for the exact terms.
Formats
CSV, JSON, SQL, MD
Size
6.3 MB
Updated
Apr 6, 2026

Description

SMILE (Systematic Microbiome Intelligence for Lost Ecosystems) is a curated relational database of ancient oral microbiome data derived from published archaeogenomic literature. Version 1.0 integrates data from 45 peer-reviewed publications (2014–2024), spanning 1,414 samples, 16,196 microbiome records, and 2,150 distinct taxa. Temporal coverage extends from approximately 102,000 BP (Pesturina Cave, Serbia — Neanderthal era) to the medieval period, with near-global geographic coverage (-175 to 178° longitude, -34 to 79° latitude). The corpus includes records for Bacteria (16,120), Archaea (53), Fungi (16), and Viruses (7), with 1,401 human host samples and 13 non-human host samples (bear, gorilla, reindeer). Authentication metric records (n=212) and methodological metadata entries (n=42) are included to support reproducibility and downstream filtering. Data were extracted using an LLM-assisted pipeline (Anthropic API: Haiku for pre/post-processing stages, Sonnet for structured extraction) applied to primary literature, with multilingual extraction coverage including English, Japanese, French, and Russian sources. All extraction scripts are available at…

Description from Zenodo, shortened.

Files (10)

  • CSVpublications.csv1.9 kB
  • JSONdataset_summary.json1 kB
  • CSVsamples.csv211 kB
  • CSVauthentication_metrics.csv12 kB
  • CSVpooled_analysis_members.csv3.1 kB
  • CSVpooled_analyses.csv7.1 kB
  • CSVmicrobiome_records.csv2.6 MB
  • SQLsmile_dump.sql3.5 MB
  • CSVmethodological_metadata.csv21 kB
  • MDREADME_zenodo.md3.8 kB

DataHunter does not store or host these files: every link leads to the original source. Check the license there before using the data.

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