{
  "id": "AssayMech:methyl-red-test",
  "name": "methyl red test",
  "record_kind": "ONTOLOGY_ASSAY_CONCEPT",
  "categories": [
    "MICROBIAL_CHARACTERIZATION"
  ],
  "description": "An ontology assay concept for testing sustained acidic products of glucose fermentation.",
  "limitations": [
    "This is an assay concept, with no organism or strain result asserted.",
    "METPO supplies a conceptual definition, not a complete executable protocol, validated threshold or performance estimate."
  ],
  "evidence": [
    {
      "reference": "https://github.com/berkeleybop/metpo/blob/800c9d27913158efdf466edf2cd710dbf1ce893f/metpo.json",
      "title": "METPO ontology at commit 800c9d27913158efdf466edf2cd710dbf1ce893f",
      "claim": "The selected class defines the named assay; its identity alone is not an organism-level positive or negative result.",
      "locator": "/graphs/0/nodes/1403",
      "source_license": "CC-BY-4.0"
    }
  ],
  "ontology_groundings": [
    {
      "term_id": "METPO:1005013",
      "term_name": "methyl red test",
      "entity_type": "CLASS",
      "relation": "ASSAY_IDENTITY",
      "source_version": "800c9d27913158efdf466edf2cd710dbf1ce893f",
      "source_path": "metpo.json",
      "source_url": "https://github.com/berkeleybop/metpo/blob/800c9d27913158efdf466edf2cd710dbf1ce893f/metpo.json",
      "evidence": [
        {
          "reference": "https://github.com/berkeleybop/metpo/blob/800c9d27913158efdf466edf2cd710dbf1ce893f/metpo.json",
          "title": "METPO ontology at commit 800c9d27913158efdf466edf2cd710dbf1ce893f",
          "claim": "The pinned node is the named assay parent, distinct from its positive and negative outcome classes.",
          "locator": "/graphs/0/nodes/1403",
          "source_license": "CC-BY-4.0"
        }
      ]
    }
  ],
  "research_gaps": [
    {
      "scope": "cmmmech",
      "reason": "No source-backed correspondence between this assay concept and a specific CMM mechanism was established for this seed."
    },
    {
      "scope": "controls",
      "reason": "The selected METPO definition does not establish an assay-specific positive/negative control protocol."
    },
    {
      "scope": "protocol_parameters",
      "reason": "Reagent concentrations, incubation conditions, decision thresholds and performance characteristics require a separately sourced operational protocol."
    },
    {
      "scope": "method",
      "reason": "The selected definition identifies the biological transformation but does not specify an operational detection method."
    },
    {
      "scope": "measurement",
      "reason": "Detection chemistry, response scale and a positive/negative decision rule are not established by the selected definition."
    }
  ],
  "curation_history": [
    {
      "timestamp": "2026-11-09T02:38:32Z",
      "curator": "assay-stream-c",
      "action": "CREATE",
      "summary": "Curate initial sourced assay concept or scoped operational assay",
      "history_file": "history/records/methyl-red-test/2026-11-09T023832Z-assay-stream-c-2cb5df.yaml"
    }
  ]
}