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    16 repositories

    • env-embeddings

      Public
      Simple experiment to compare ENVO similarity to google embedding cosine similarity
      monarchinitiativeai4curation
      monarchinitiativeai4curation
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•15•4•Updated Feb 1, 2026Feb 1, 2026

    • cyberian

      Public
      A Python CLI wrapper for running AI coder agents (claude code, gemini-cli, etc)
      monarchinitiativeai4curation
      monarchinitiativeai4curation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•1•7•Updated Jan 27, 2026Jan 27, 2026

    • mcp_literature_eval

      Public
      Evaluation of MCPs that retrieve scientific literature
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•2•5•Updated Dec 17, 2025Dec 17, 2025

    • biosample-enricher

      Public
      Infer AI-friendly environmental and geographic metadata about biosamples from multiple authoritative sources
      pythonbioinformaticsgeospatial
      pythonbioinformaticsgeospatialclickmulti-providerpydanticenvironmental-databiosamplemetadata-enrichment
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•61•0•Updated Nov 25, 2025Nov 25, 2025

    • artl-mcp

      Public archive
      ARCHIVED - replaced by contextualizer-ai/artl-mcp
      mcpai4curationcontextualizer-ai
      mcpai4curationcontextualizer-ai
      Python
      •
      MIT License
      •0•2•42•1•Updated Nov 3, 2025Nov 3, 2025

    • to-duckdb

      Public
      tools for converting content in other databases (like Biosamples in MongoDB) to DuckDB
      Makefile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•7•0•Updated Sep 20, 2025Sep 20, 2025

    • fitness-mcp

      Public
      Example mcp to query a file for growth conditions about a gene/locus ID
      Python
      •0•0•9•1•Updated Sep 18, 2025Sep 18, 2025

    • .github

      Public
      0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • gene-function-review

      Public
      Demonstration of AI review of existing functional annotations
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•1•2•0•Updated Sep 17, 2025Sep 17, 2025

    • gold-tools

      Public
      tools for ingesting GOLD metadata (Biosamples, Studies, Projects) into MongoDB and flattening into something like DuckDB or Parquet. Adds some semantic realignm…
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•0•Updated Sep 16, 2025Sep 16, 2025

    • ncbi-tools

      Public
      tools for ingesting NCBI metadata (Biosamples, Bioprojects, SRA metadata) into MongoDB and flattening into something like DuckDB or Parquet. Adds some minimal c…
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 15, 2025Sep 15, 2025

    • crawl-first

      Public
      Deterministic biosample enrichment for LLM-ready data preparation; optional PydanticAI agentic assessment
      Python
      •
      MIT License
      •0•0•29•1•Updated Sep 9, 2025Sep 9, 2025

    • ols-mcp

      Public
      An MCP for retrieving information from the Ontology Lookup Service
      mcp
      mcp
      Python
      •
      MIT License
      •2•7•1•0•Updated Aug 5, 2025Aug 5, 2025

    • metabolome-mcp

      Public
      Model Context Protocol (MCP) Server for Metabolomic data
      Python
      •
      Other
      •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • weather-mcp

      Public
      MCP interface for historical and normalized weather data
      mcp
      mcp
      Python
      •
      Other
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • landuse-mcp

      Public
      mcp
      mcp
      Python
      •
      MIT License
      •1•0•2•0•Updated Jul 15, 2025Jul 15, 2025
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