iSynth 反应数据规范：完整字段说明

如何使用

人工贡献使用简化表格；AI、实验室软件和平台对接使用 Reaction JSON。JSON Schema 约束数据交换和校验，不要求用户手填全部字段，也不等同于数据库表结构。

每次实验生成一条 Reaction → 校验并核对原文 → 上传到私有草稿 → 查看反应预览 → 提交审核。上传时每条记录序列化为 reaction_record 列中的 JSON 字符串，作者、来源与许可在数据集信息中单独填写。

网页提供反应结构、阶段条件和测量结果视图，同时保留原始文件与完整 JSONL 下载。发布且检索准备完成后，可通过 MCP 查询并读取完整记录。

论文提取

JSON Schema（Draft 2020-12）定义字段、类型与嵌套结构；模型输出的是符合它的反应 JSON 数据，不是 Schema 本身。示例按字段说明顺序展示，JSON 对象的键顺序不影响校验；segments 数组顺序表示实验先后。

提供论文正文、补充信息及本页。每次实验输出一个 Reaction；多次实验使用 JSONL，每行一个对象。未报告的可选字段省略，来源不清楚的描述保留为文字。

先核对结构，再校验物料引用、量值与测量归属，最后回查原文。MCP 可先调用 get_reaction_contract(view="extraction")，再调用 validate_reaction_records；校验不保存数据。无法打开链接的模型可直接使用下载规范包中的文件。

填写约定

• 常规范围使用 lower、upper 和 unit，例如 20–25 °C 写为 {"lower":20,"upper":25,"unit":"°C"}。单侧界限使用 value 与 qualifier，例如 <0 °C。特殊边界表述保留在 raw。
• 自定义参数完整保存于 JSONB。登记参数的名称、类型、单位和位置后，可通过 API/MCP 的 parameter_filters 筛选；先用 get_parameter_catalog 查询支持范围。同组条件须匹配同一阶段，缺失或单位不明的值不参与数值筛选。参数登记表：/schemas/reaction-parameter-registry.json。
• 手性位点说明本次考察的位置，比较对象说明数值的含义：ee/er 比较完整的一对对映体，de/dr 比较所述非对映体。多个手性中心仍可测 ee/er；固定其余中心只改变一个中心，通常属于 de/dr。
• stereocentres 使用原文位次，不等于 SMILES 原子序号。多位点、天然产物或分组比例须保留原文比较对象；不从位点列表推断异构体分组。
• 一个 JSON 对象对应一次实验，统一使用 materials、initial_state、segments、products 和 measurements。
• materials 定义投入物料，products 定义产物；起始投料和后续加料均使用 Charge，用量与浓度并列填写。
• 普通反应通常一个阶段，一锅多步按顺序增加阶段。未报告阶段信息时，segments 填空数组。
• 阶段条件填 conditions，未填写的沿用前值；duration 只属于当前阶段。操作及定性观察填 text。仅原文明示的阶段产物填本段 products，阶段测量填本段 measurements；最终结果填根对象，不重复填入最后一个阶段。
• Charge.material 引用投入物料编号；Measurement.subject 引用被测物料或产物编号。所有指标统一使用 measurements。
• 保留来源单位。value 与 unit 表示量值；无法拆分时可以只填 raw。
• 补充结构化属性统一填 parameters；补充文字统一填 text。后续阶段省略条件会沿用前值，null 明确停止沿用，不表示数值 0。
• 已有 1.8.0、1.7.0、1.6.0、1.5.0、1.4.0、1.3.0、1.2.0、1.1.0、1.0.0 记录继续按原规则读取，原始数据不改写。

Reaction

一次实验统一记录物料、起始投料、反应阶段和结果。普通反应填写一个阶段，一锅多步按顺序增加阶段。

对象示例

{
  "schema_version": "1.9.0",
  "reaction_identifier": "EXP-0001",
  "materials": [
    {
      "id": "alcohol",
      "identifiers": [
        {
          "type": "SMILES",
          "value": "CCO"
        }
      ],
      "role": "reactant"
    },
    {
      "id": "reagent",
      "identifiers": [
        {
          "type": "NAME",
          "value": "acetic anhydride"
        }
      ],
      "role": "reagent"
    }
  ],
  "initial_state": {
    "inputs": [
      {
        "material": "alcohol",
        "amount": {
          "value": 0.25,
          "unit": "mmol",
          "raw": "0.25 mmol"
        }
      },
      {
        "material": "reagent"
      }
    ]
  },
  "segments": [
    {
      "conditions": {
        "temperature": {
          "value": 25,
          "unit": "°C",
          "raw": "25 °C"
        }
      }
    }
  ],
  "products": [
    {
      "id": "product",
      "identifiers": [
        {
          "type": "SMILES",
          "value": "CCOC(C)=O"
        }
      ]
    }
  ],
  "measurements": [
    {
      "subject": "product",
      "type": "yield",
      "value": {
        "value": 80,
        "scale": "percent",
        "raw": "80%"
      }
    }
  ],
  "provenance": {
    "reference": "Fictional teaching record; Example A"
  },
  "text": "Fictional format illustration, not a measured result. Unreported amounts, method and calculation bases are omitted."
}

"1.9.0"

"EXP-0001"

[
  {
    "id": "alcohol",
    "identifiers": [
      {
        "type": "SMILES",
        "value": "CCO"
      }
    ],
    "role": "reactant"
  },
  {
    "id": "reagent",
    "identifiers": [
      {
        "type": "NAME",
        "value": "acetic anhydride"
      }
    ],
    "role": "reagent"
  }
]

{
  "inputs": [
    {
      "material": "alcohol",
      "amount": {
        "value": 0.25,
        "unit": "mmol",
        "raw": "0.25 mmol"
      }
    },
    {
      "material": "reagent"
    }
  ]
}

[
  {
    "conditions": {
      "temperature": {
        "value": 25,
        "unit": "°C",
        "raw": "25 °C"
      }
    }
  }
]

[
  {
    "id": "product_1",
    "identifiers": [
      {
        "type": "SMILES",
        "value": "C[C@H](O)c1ccccc1"
      }
    ],
    "role": "desired_product",
    "text": "Isolated target product",
    "parameters": {
      "reported_stereochemistry": "(S)"
    }
  }
]

[
  {
    "subject": "reactant_1",
    "type": "conversion",
    "value": {
      "value": 90,
      "scale": "percent"
    },
    "text": "Determined by GC."
  }
]

{
  "reference": "Fictional teaching record; Example A"
}

"Fictional format illustration, not a measured result. Unreported amounts, method and calculation bases are omitted."

{
  "run_id": "RUN-0001"
}

Identifier

SMILES / INCHI 保存结构，INCHIKEY 保存结构索引键，NAME 保存名称或缩写（如 DCM），CUSTOM 保存论文内编号（如 1a，需保留来源位置）。同一物料可有多个有据可查的标识；不从名称或编号猜结构。

对象示例

{
  "type": "SMILES",
  "value": "CCO"
}

"SMILES"

"CCO"

Quantity

一个量值，例如 {"value":1,"unit":"mmol"}。用于用量、温度、时间或测量值；raw 可保留原文。

对象示例

[
  {
    "value": 25,
    "unit": "°C"
  },
  {
    "unit": "°C",
    "raw": "20–25 °C",
    "lower": 20,
    "upper": 25
  },
  {
    "value": 25,
    "unit": "°C",
    "raw": "25 ± 2 °C",
    "uncertainty": 2
  },
  {
    "value": 5,
    "scale": "percent",
    "raw": "<5%",
    "qualifier": "<"
  }
]

25

"percent"

"°C"

"20–25 °C"

"<"

20

25

2

Material

投入物料的结构、名称与角色；用量和浓度填写在投料项 Charge 中。

对象示例

{
  "id": "reactant_1",
  "identifiers": [
    {
      "type": "SMILES",
      "value": "CCO"
    }
  ],
  "role": "reactant",
  "is_limiting": true,
  "text": "Ethanol used as the limiting reactant",
  "parameters": {
    "purity": "99.5%"
  }
}

"reactant_1"

[
  {
    "type": "SMILES",
    "value": "CCO"
  }
]

"reactant"

true

"Ethanol used as the limiting reactant"

{
  "purity": "99.5%"
}

Charge

一项投料：material 指向投入物料，amount 记录用量，concentration 记录本次所用试剂的浓度或配方。

对象示例

{
  "material": "reagent_1",
  "amount": {
    "value": 2,
    "unit": "mL"
  },
  "concentration": {
    "raw": "2.5 M solution in hexanes"
  }
}

"reagent_1"

{
  "value": 2,
  "unit": "mL"
}

{
  "raw": "2.5 M solution in hexanes"
}

Conditions

反应条件。后续阶段省略的条件沿用前值；null 是 JSON 空值，表示停止沿用该条件，并不表示数值 0。持续时间填 Segment.duration。

对象示例

{
  "temperature": {
    "value": 25,
    "unit": "°C"
  },
  "pressure": {
    "value": 1,
    "unit": "atm"
  },
  "atmosphere": "nitrogen",
  "parameters": {
    "humidity": {
      "raw": "40% RH"
    },
    "light_source_type": "blue LED",
    "wavelength": "450 nm"
  }
}

{
  "value": 25,
  "unit": "°C"
}

{
  "value": 1,
  "unit": "atm"
}

"nitrogen"

{
  "milling_frequency": {
    "value": 30,
    "unit": "Hz"
  }
}

InitialState

反应开始时已投入的物料和条件。inputs 引用 materials 中的编号；溶剂也作为物料填写。

对象示例

{
  "inputs": [
    {
      "material": "reactant_1",
      "amount": {
        "value": 1,
        "unit": "mmol",
        "raw": "1 mmol"
      }
    },
    {
      "material": "solvent_1",
      "amount": {
        "value": 2,
        "unit": "mL",
        "raw": "2 mL"
      }
    }
  ],
  "conditions": {
    "temperature": {
      "value": 0,
      "unit": "°C"
    }
  },
  "text": "The starting materials were charged at 0 °C."
}

[
  {
    "material": "reactant_1",
    "amount": {
      "value": 1,
      "unit": "mmol",
      "raw": "1 mmol"
    }
  },
  {
    "material": "solvent_1",
    "amount": {
      "value": 2,
      "unit": "mL",
      "raw": "2 mL"
    }
  }
]

{
  "temperature": {
    "value": 0,
    "unit": "°C"
  }
}

"The starting materials were charged at 0 °C."

Segment

按顺序记录投料、条件、时间、操作与观察。通常填写这些信息即可；原文另有阶段产物或定量结果时，再填写 products 或 measurements。

对象示例

{
  "added_materials": [
    {
      "material": "reagent_1",
      "amount": {
        "value": 1,
        "unit": "mmol"
      }
    }
  ],
  "conditions": {
    "temperature": {
      "value": 0,
      "unit": "°C"
    }
  },
  "duration": {
    "value": 1,
    "unit": "h"
  },
  "text": "The reagent was added dropwise. The solution turned yellow."
}

[
  {
    "material": "reagent_1",
    "amount": {
      "value": 1,
      "unit": "mmol"
    }
  }
]

{
  "temperature": {
    "value": 0,
    "unit": "°C"
  }
}

{
  "value": 1,
  "unit": "h"
}

"The reagent was added dropwise. The solution turned yellow and a precipitate formed."

[
  {
    "id": "intermediate_1",
    "identifiers": [
      {
        "type": "NAME",
        "value": "Intermediate A (source label)"
      }
    ],
    "role": "intermediate"
  }
]

[
  {
    "subject": "reactant_1",
    "type": "conversion",
    "value": {
      "value": 90,
      "scale": "percent"
    },
    "text": "Determined by GC."
  }
]

Product

产物的结构、角色与补充属性。测量值统一填写在所属反应或阶段的 measurements，通过 subject 引用此产物编号。

对象示例

{
  "id": "product_1",
  "identifiers": [
    {
      "type": "SMILES",
      "value": "C[C@H](O)c1ccccc1"
    }
  ],
  "role": "desired_product",
  "text": "Isolated target product",
  "parameters": {
    "reported_stereochemistry": "(S)"
  }
}

"product_1"

[
  {
    "type": "SMILES",
    "value": "C[C@H](O)c1ccccc1"
  }
]

"desired_product"

"Isolated target product"

{
  "reported_stereochemistry": "(S)"
}

Measurement

一项测量：被测对象 subject、指标 type、数值 value 及补充说明。同一对象的多个指标或多次测量分别填写。

对象示例

{
  "subject": "product_1",
  "type": "ee",
  "value": {
    "value": 96,
    "scale": "percent",
    "raw": "96%"
  },
  "stereocentres": "(2R,5S)",
  "basis": "(2R,5S):(2S,5R)",
  "text": "Isolated target diastereomer fraction analysed by chiral HPLC."
}

"reactant_1"

"ee"

{
  "value": 96,
  "scale": "percent",
  "raw": "96%"
}

"5S"

"(2R,5S):(2S,5R)"

"Isolated product analysed by chiral HPLC."

Provenance

文章来源：论文 DOI 与文献引用。实验原始文件由平台另行保存。

对象示例

{
  "doi": "10.1234/isynth.example",
  "reference": "Fictional article for documentation examples"
}

"10.1234/isynth.example"

"Fictional article for documentation examples"

完整的一锅多步示例

{
  "schema_version": "1.9.0",
  "reaction_identifier": "EXP-0002",
  "materials": [
    {
      "id": "reactant_1",
      "identifiers": [
        {
          "type": "SMILES",
          "value": "C[C@H](O)c1ccccc1"
        }
      ],
      "role": "reactant"
    },
    {
      "id": "reagent_1",
      "identifiers": [
        {
          "type": "SMILES",
          "value": "CC(=O)OC(C)=O"
        }
      ],
      "role": "reagent"
    },
    {
      "id": "solvent_1",
      "identifiers": [
        {
          "type": "SMILES",
          "value": "CC#N"
        }
      ],
      "role": "solvent"
    }
  ],
  "initial_state": {
    "inputs": [
      {
        "material": "reactant_1",
        "amount": {
          "value": 1,
          "unit": "mmol",
          "raw": "1 mmol"
        }
      },
      {
        "material": "solvent_1",
        "amount": {
          "value": 2,
          "unit": "mL",
          "raw": "2 mL"
        }
      }
    ],
    "conditions": {
      "temperature": {
        "value": 0,
        "unit": "°C"
      }
    }
  },
  "segments": [
    {
      "added_materials": [
        {
          "material": "reagent_1",
          "amount": {
            "value": 1,
            "unit": "mmol"
          }
        }
      ],
      "duration": {
        "value": 1,
        "unit": "h"
      },
      "text": "The reagent was added dropwise at 0 °C, and the solution turned yellow. After 1 h, an aliquot was taken for HPLC.",
      "measurements": [
        {
          "subject": "reactant_1",
          "type": "conversion",
          "value": {
            "value": 95,
            "scale": "percent",
            "raw": "95 %"
          },
          "text": "Method: HPLC."
        }
      ]
    },
    {
      "added_materials": [
        {
          "material": "reagent_1",
          "amount": {
            "value": 1,
            "unit": "mmol"
          }
        }
      ],
      "conditions": {
        "temperature": {
          "value": 80,
          "unit": "°C"
        }
      },
      "duration": {
        "value": 3,
        "unit": "h"
      },
      "text": "The same mixture was heated to 80 °C for 3 h."
    }
  ],
  "products": [
    {
      "id": "product_1",
      "identifiers": [
        {
          "type": "SMILES",
          "value": "CC(=O)O[C@H](C)c1ccccc1"
        }
      ]
    }
  ],
  "measurements": [
    {
      "subject": "product_1",
      "type": "yield",
      "value": {
        "value": 80,
        "scale": "percent",
        "raw": "80 %"
      },
      "text": "Method: isolated."
    },
    {
      "subject": "product_1",
      "type": "ee",
      "value": {
        "value": 94,
        "scale": "percent",
        "raw": "94 %"
      },
      "text": "Method: chiral HPLC."
    }
  ],
  "workup": "The reaction mixture was worked up and purified as reported.",
  "provenance": {
    "reference": "Fictional documentation fixture. All quantities and observations illustrate format only; no experiment or source paper is claimed."
  },
  "text": "FORMAT EXAMPLE ONLY. Not a laboratory instruction or a reported experimental result."
}