reference/AGENT_CONNECTION.json

{
  "connection_type": "msc_aging_agent_corpus",
  "connection_version": "2.1.0",
  "corpus_revision": "corpus-v2026.06.7",
  "single_entry_point": true,
  "description": "Single connection manifest for the MSC Aging Agent Corpus. Agents should use the live Research API on Hugging Face Space for queries, hypothesis testing, and statistical reruns. The Dataset remains the data archive; the Space is the query layer.",
  "urls": {
    "agent_api_base": "https://S4MPL3BI4S-msc-aging-corpus-api.hf.space",
    "agent_api_openapi": "https://S4MPL3BI4S-msc-aging-corpus-api.hf.space/docs",
    "agent_api_research": "https://S4MPL3BI4S-msc-aging-corpus-api.hf.space/research",
    "connection_manifest_hf": "https://huggingface.co/datasets/S4MPL3BI4S/msc-aging-agent-corpus/raw/corpus-v2026.06.7/reference/AGENT_CONNECTION.json",
    "connection_manifest_github": "https://raw.githubusercontent.com/SampleBias/MSC_Age_Research/main/reference/AGENT_CONNECTION.json",
    "corpus_home": "https://huggingface.co/datasets/S4MPL3BI4S/msc-aging-agent-corpus",
    "space_repo": "https://huggingface.co/spaces/S4MPL3BI4S/msc-aging-corpus-api",
    "agent_guide_hf": "https://huggingface.co/datasets/S4MPL3BI4S/msc-aging-agent-corpus/raw/corpus-v2026.06.7/AGENT_CONNECT.md"
  },
  "connect": {
    "preferred_mode": "live_api",
    "repo_id": "S4MPL3BI4S/msc-aging-agent-corpus",
    "repo_type": "dataset",
    "revision": "corpus-v2026.06.7",
    "space_id": "S4MPL3BI4S/msc-aging-corpus-api",
    "github_build_repo": "https://github.com/SampleBias/MSC_Age_Research",
    "curator": "James Utley, PhD",
    "organization": "Syndicate Laboratories"
  },
  "live_api": {
    "base_url": "https://S4MPL3BI4S-msc-aging-corpus-api.hf.space",
    "openapi": "/docs",
    "primary_endpoint": {
      "method": "POST",
      "path": "/research",
      "body_example": {
        "gene": "NDRG1",
        "dataset_id": "GSE39540",
        "species": "Homo sapiens",
        "actions": ["search", "rerun", "cite"]
      }
    },
    "endpoints": {
      "GET /": "Service metadata",
      "GET /health": "Liveness check",
      "GET /connect": "This connection manifest (from dataset)",
      "GET /manifest": "GEO cohort scope",
      "GET /search?gene=": "Cross-dataset biomarker hits",
      "GET /expression?gene=&dataset_id=": "Sample-level expression rows",
      "GET /rerun?gene=&dataset_id=": "Fresh OLS model for hypothesis testing",
      "GET /cite?gene=&datasets=": "APA citations",
      "POST /research": "Multi-step research workflow (recommended)"
    }
  },
  "bootstrap_load_order": [
    "reference/AGENT_CONNECTION.json",
    "POST https://S4MPL3BI4S-msc-aging-corpus-api.hf.space/research",
    "datasets/CORPUS_PROVENANCE.json",
    "reference/citations_apa.json",
    "datasets/hallmarks_of_aging/hallmark_definitions.csv",
    "datasets/hallmarks_of_aging/hallmark_dataset_index.csv"
  ],
  "python_client": {
    "install": "uv sync --group agent",
    "module": "msc_corpus",
    "connect": "from msc_corpus import connect; corpus = connect()",
    "http_example": "import requests; requests.post('https://S4MPL3BI4S-msc-aging-corpus-api.hf.space/research', json={'gene':'NDRG1','dataset_id':'GSE39540','actions':['search','rerun','cite']}).json()"
  },
  "research_capabilities": {
    "biomarker_discovery": {
      "api": "GET /search?gene={symbol}",
      "method": "corpus.search_gene(gene_symbol)",
      "returns": "Cross-dataset beta, p_value, q_value, model_formula, species, aging_axis"
    },
    "statistical_rerun": {
      "api": "GET /rerun?gene={symbol}&dataset_id={GSE}",
      "method": "corpus.rerun_model(gene_symbol, dataset_id)",
      "returns": "Fresh OLS coefficients, p_values, R-squared, n_samples"
    },
    "hypothesis_workflow": {
      "api": "POST /research",
      "method": "corpus.research(gene_symbol, dataset_id=..., actions=[...])",
      "returns": "Combined search, optional expression, rerun, mechanism, cite payload"
    },
    "hallmarks_of_aging": {
      "tables": [
        "datasets/hallmarks_of_aging/hallmark_definitions.csv",
        "datasets/hallmarks_of_aging/hallmark_dataset_index.csv",
        "datasets/hallmarks_of_aging/hallmark_gene_evidence.csv"
      ],
      "framework_citation": "López-Otín et al. (2023). Hallmarks of aging: An expanding universe. Cell, 186(2), 243–278. https://doi.org/10.1016/j.cell.2022.11.001"
    }
  },
  "example_research_flow": [
    "POST /research {\"gene\":\"NDRG1\",\"dataset_id\":\"GSE39540\",\"actions\":[\"search\",\"rerun\",\"cite\"]}",
    "Load hallmark_dataset_index.csv filtered by hallmark_id=cellular_senescence for ranked senescence GEO series",
    "Interpret rerun.p_values for the aging-axis coefficient",
    "Read manifest interpretation_caution before cross-dataset claims",
    "Include citations from response plus López-Otín 2023 when using hallmark framework"
  ],
  "agent_instruction": "You are connected to the MSC Aging Agent Corpus via the Hugging Face Space API. Use POST /research for hypothesis workflows. Load datasets/hallmarks_of_aging/ for twelve-hallmark MSC dataset ranking. Always rerun statistics via /rerun or /research rather than trusting cached p-values alone for new claims. Cite Utley (2026) for corpus use plus upstream GEO publications returned by /cite."
}