{
  "id": "CofactorMech:copper",
  "name": "copper(2+)",
  "chemical_id": "CHEBI:29036",
  "categories": [
    "METAL_ION"
  ],
  "description": "copper(2+) is represented by the precise ChEBI entity CHEBI:29036. Cofactor roles are chemical-context annotations; ingredient links describe chemical supply and do not establish uptake, bioavailability or a requirement for every organism.",
  "evidence": [
    {
      "reference": "https://www.ebi.ac.uk/chebi/CHEBI:29036",
      "title": "ChEBI CHEBI:29036",
      "claim": "ChEBI assigns a cofactor, coenzyme or prosthetic-group role to CHEBI:29036.",
      "locator": "JSON Pointer /roles_classification",
      "source_license": "CC-BY-4.0"
    }
  ],
  "related_records": [
    {
      "corpus": "mediaingredientmech",
      "identifier": "CHEBI:49553",
      "relation": "SUPPLIED_BY",
      "basis": "The source is a chemically specified salt containing this metal in the +2 oxidation state; supply is chemical composition, not proof of uptake, cellular availability or enzyme occupancy.",
      "source_version": "0529fc6bc065bfa04aba0aed234f6b0cfad6a142",
      "source_path": "data/ingredients/mapped/Cucl2.yaml",
      "source_url": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Cucl2.yaml",
      "status": "PROVISIONAL",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Cucl2.yaml",
          "title": "MIM ingredient identity",
          "claim": "The cited ingredient is mapped to CHEBI:49553; this is a compound-identity assertion, not a bioavailability measurement.",
          "locator": "JSON Pointer /identifier",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.ebi.ac.uk/chebi/CHEBI:49553",
          "title": "ChEBI CHEBI:49553",
          "claim": "The source compound contains the metal in oxidation state +2, corresponding to CHEBI:29036; supply does not imply enzyme occupancy.",
          "locator": "JSON Pointer /ontology_relations",
          "source_license": "CC-BY-4.0"
        }
      ]
    },
    {
      "corpus": "mediaingredientmech",
      "identifier": "CHEBI:86318",
      "relation": "SUPPLIED_BY",
      "basis": "The source is a chemically specified salt containing this metal in the +2 oxidation state; supply is chemical composition, not proof of uptake, cellular availability or enzyme occupancy.",
      "source_version": "0529fc6bc065bfa04aba0aed234f6b0cfad6a142",
      "source_path": "data/ingredients/mapped/Cucl2_X_2_H2o.yaml",
      "source_url": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Cucl2_X_2_H2o.yaml",
      "status": "PROVISIONAL",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Cucl2_X_2_H2o.yaml",
          "title": "MIM ingredient identity",
          "claim": "The cited ingredient is mapped to CHEBI:86318; this is a compound-identity assertion, not a bioavailability measurement.",
          "locator": "JSON Pointer /identifier",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.ebi.ac.uk/chebi/CHEBI:86318",
          "title": "ChEBI CHEBI:86318",
          "claim": "The exact source salt or hydrate supplies the chemical component represented by CHEBI:49553; this is a composition relationship.",
          "locator": "JSON Pointer /ontology_relations",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.ebi.ac.uk/chebi/CHEBI:49553",
          "title": "ChEBI CHEBI:49553",
          "claim": "The parent salt contains the metal in oxidation state +2; the resulting ion is CHEBI:29036.",
          "locator": "JSON Pointer /ontology_relations",
          "source_license": "CC-BY-4.0"
        }
      ]
    },
    {
      "corpus": "mediaingredientmech",
      "identifier": "CHEBI:91245",
      "relation": "SUPPLIED_BY",
      "basis": "The source is a chemically specified salt containing this metal in the +2 oxidation state; supply is chemical composition, not proof of uptake, cellular availability or enzyme occupancy.",
      "source_version": "0529fc6bc065bfa04aba0aed234f6b0cfad6a142",
      "source_path": "data/ingredients/mapped/Cucl2_X_5_H2o.yaml",
      "source_url": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Cucl2_X_5_H2o.yaml",
      "status": "PROVISIONAL",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/MediaIngredientMech/blob/0529fc6bc065bfa04aba0aed234f6b0cfad6a142/data/ingredients/mapped/Cucl2_X_5_H2o.yaml",
          "title": "MIM ingredient identity",
          "claim": "The cited ingredient is mapped to CHEBI:91245; this is a compound-identity assertion, not a bioavailability measurement.",
          "locator": "JSON Pointer /identifier",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.ebi.ac.uk/chebi/CHEBI:91245",
          "title": "ChEBI CHEBI:91245",
          "claim": "The exact source salt or hydrate supplies the chemical component represented by CHEBI:49553; this is a composition relationship.",
          "locator": "JSON Pointer /ontology_relations",
          "source_license": "CC-BY-4.0"
        },
        {
          "reference": "https://www.ebi.ac.uk/chebi/CHEBI:49553",
          "title": "ChEBI CHEBI:49553",
          "claim": "The parent salt contains the metal in oxidation state +2; the resulting ion is CHEBI:29036.",
          "locator": "JSON Pointer /ontology_relations",
          "source_license": "CC-BY-4.0"
        }
      ]
    },
    {
      "corpus": "proteintraitsmech",
      "identifier": "proteintraitsmech:COFACTOR_REQ_CHEBI_29036",
      "relation": "REQUIRED_BY",
      "basis": "Conceptual requirement coverage: this PTM trait defines the requirement for the same ChEBI chemical. It is not an organism-level or enzyme-level measurement.",
      "source_version": "8d08b33cfbee1e9d1c2fdb2211b82b49dd0c8b1f",
      "source_path": "data/traits/function/cofactor_requirement/chebi/copper-2-chebi29036.yaml",
      "source_url": "https://github.com/CultureBotAI/proteintraitsmech/blob/8d08b33cfbee1e9d1c2fdb2211b82b49dd0c8b1f/data/traits/function/cofactor_requirement/chebi/copper-2-chebi29036.yaml",
      "status": "VERIFIED",
      "evidence": [
        {
          "reference": "https://github.com/CultureBotAI/proteintraitsmech/blob/8d08b33cfbee1e9d1c2fdb2211b82b49dd0c8b1f/data/traits/function/cofactor_requirement/chebi/copper-2-chebi29036.yaml",
          "title": "PTM cofactor-requirement concept",
          "claim": "The target is a CLASS trait with an explicit cross-reference to this chemical, rather than a measured protein observation.",
          "locator": "JSON Pointer /xrefs",
          "source_license": "CC-BY-4.0"
        }
      ]
    }
  ],
  "research_gaps": [
    {
      "corpus": "pathwaymech",
      "reason": "No exact-identifier cofactor-use or production link verified in the complete 282-record PathwayMech snapshot. Related broader/narrower chemical forms are not substituted. Exact Cu(2+) occurrences were inhibition or activation observations; the SOD1 cofactor is the broader copper-cation entity CHEBI:23378."
    },
    {
      "corpus": "proteintraitsmech",
      "reason": "The curated PTM link covers a cofactor-requirement concept only. A separately sourced, named enzyme exemplar requiring this exact chemical has not been curated in this seed record."
    }
  ],
  "curation_history": [
    {
      "timestamp": "2026-11-09T01:42:27Z",
      "curator": "cofactor-stream-c",
      "action": "CREATE",
      "summary": "Curate initial source-backed cofactor and scoped cross-corpus links",
      "history_file": "history/records/copper/2026-11-09T014227Z-cofactor-stream-c-447118.yaml"
    }
  ]
}