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

Opis

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…

Opis sa Zenodo, skraćen.

Fajlovi (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

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