fix:sample/plate 之前的开发
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彭帅
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docs/architecture/00-overall-data-architecture.md
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docs/architecture/00-overall-data-architecture.md
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# BrAPI Test Server 总体数据架构图
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本文档把 4 个模块串成一张总览图：
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```text
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Core -> Germplasm/Seed -> Phenotyping -> Genotyping
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```
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对应的模块文档：
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| 模块 | 文档 | 核心作用 |
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| --- | --- | --- |
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| Core | `core-data-flow.md` | crop、program、trial、study、location、person 等基础上下文 |
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| Germplasm/Seed | `04-germplasm-seed-data-flow.md` | germplasm、breeding_method、seed_lot、cross、pedigree、attribute |
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| Phenotyping | `02-phenotyping-data-flow.md` | observation_unit、observation_variable、event、image、observation |
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| Genotyping | `03-genotyping-data-flow.md` | sample、plate、reference、variantset、variant、callset、allele_call |
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## 总体结论
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整个数据模型的主干是：
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```text
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Core: crop -> program -> trial -> study
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Germplasm: breeding_method -> germplasm -> cross / seed_lot / pedigree / attribute
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Phenotyping: study + germplasm/seed_lot/cross -> observation_unit -> observation
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Genotyping: observation_unit/study -> sample -> callset -> allele_call
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Genotyping: reference_set -> variantset -> variant -> allele_call
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```
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`study` 是 Core 到 Phenotyping/Genotyping 的主桥；`germplasm` 是 Germplasm/Seed 到 Phenotyping/Genotyping 的主桥；`observation_unit` 是 Phenotyping 到 Genotyping 的主桥。
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## 总架构图
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```mermaid
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flowchart TD
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subgraph CORE["Core 基础上下文"]
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CROP["crop<br/>作物"]
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PERSON["person<br/>人员"]
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PROGRAM["program<br/>项目"]
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LOCATION["location<br/>地点"]
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TRIAL["trial<br/>试验批次"]
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SEASON["season<br/>季节"]
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STUDY["study<br/>研究/试验实施单元"]
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LIST["list / list_item<br/>通用列表"]
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CROP --> PROGRAM
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PERSON --> PROGRAM
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PROGRAM --> TRIAL
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CROP --> TRIAL
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PROGRAM --> LOCATION
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CROP --> LOCATION
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TRIAL --> STUDY
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PROGRAM --> STUDY
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CROP --> STUDY
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LOCATION --> STUDY
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SEASON --> STUDY
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PERSON --> LIST
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end
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subgraph GERM["Germplasm / Seed 种质与种子"]
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BM["breeding_method<br/>育种方法"]
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GERMPLASM["germplasm<br/>种质"]
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GAD["germplasm_attribute_definition<br/>属性定义"]
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GAV["germplasm_attribute_value<br/>属性值"]
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CP["crossing_project<br/>杂交项目"]
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CROSS["cross_entity<br/>Cross / PlannedCross"]
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XP["cross_parent<br/>杂交亲本"]
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PEDNODE["pedigree_node<br/>系谱节点"]
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PEDEDGE["pedigree_edge<br/>系谱边"]
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SEEDLOT["seed_lot<br/>种子批次"]
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MIX["seed_lot_content_mixture<br/>批次组成"]
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TX["seed_lot_transaction<br/>批次流转"]
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BM --> GERMPLASM
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GAD --> GAV
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GERMPLASM --> GAV
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CP --> CROSS
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CROSS --> XP
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GERMPLASM --> XP
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CROSS --> CROSS_PLANNED["cross_entity<br/>planned cross 自关联"]
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GERMPLASM --> PEDNODE
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CP --> PEDNODE
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PEDNODE --> PEDEDGE
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PEDEDGE --> PEDNODE2["pedigree_node<br/>父本/子代节点"]
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GERMPLASM --> MIX
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CROSS --> MIX
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MIX --> SEEDLOT
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SEEDLOT --> TX
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TX --> SEEDLOT
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end
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subgraph PHENO["Phenotyping 表型"]
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ONTOLOGY["ontology<br/>本体"]
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TRAIT["trait<br/>性状"]
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METHOD["method<br/>方法"]
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SCALE["scale<br/>标尺"]
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OV["observation_variable<br/>观测变量"]
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OU["observation_unit<br/>观测单元"]
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EVENT["event<br/>事件"]
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IMAGE["image<br/>图像"]
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OBS["observation<br/>观测值"]
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ONTOLOGY --> TRAIT
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ONTOLOGY --> METHOD
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ONTOLOGY --> SCALE
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TRAIT --> OV
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METHOD --> OV
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SCALE --> OV
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OU --> OBS
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OV --> OBS
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EVENT --> OU
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OU --> IMAGE
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IMAGE --> OBS
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end
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subgraph GENO["Genotyping 基因型"]
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PLATE["plate<br/>样本板"]
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SAMPLE["sample<br/>样本"]
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REFSET["reference_set<br/>参考集"]
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REF["reference<br/>参考序列"]
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REFB["reference_bases<br/>参考片段"]
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VARSET["variantset<br/>变异集合"]
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VARIANT["variant<br/>变异位点"]
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CALLSET["callset<br/>样本调用集合"]
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CALL["allele_call<br/>基因型结果"]
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GMAP["genome_map<br/>遗传图谱"]
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LG["linkageGroup<br/>连锁群"]
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MP["marker_position<br/>图谱位置"]
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PLATE --> SAMPLE
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SAMPLE --> CALLSET
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CALLSET --> CALL
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REFSET --> REF
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REF --> REFB
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REFSET --> VARSET
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VARSET --> VARIANT
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REFSET --> VARIANT
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VARIANT --> CALL
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GMAP --> LG
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LG --> MP
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VARIANT --> MP
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end
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CROP --> GERMPLASM
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CROP --> GAD
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TRAIT --> GAD
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METHOD --> GAD
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SCALE --> GAD
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ONTOLOGY --> GAD
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PROGRAM --> CP
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PROGRAM --> SEEDLOT
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LOCATION --> SEEDLOT
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STUDY --> OU
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TRIAL --> OU
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PROGRAM --> OU
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CROP --> OU
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GERMPLASM --> OU
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SEEDLOT --> OU
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CROSS --> OU
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STUDY --> EVENT
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STUDY --> OBS
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TRIAL --> OBS
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PROGRAM --> OBS
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CROP --> OBS
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STUDY --> PLATE
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TRIAL --> PLATE
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PROGRAM --> PLATE
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STUDY --> SAMPLE
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TRIAL --> SAMPLE
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PROGRAM --> SAMPLE
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OU --> SAMPLE
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GERMPLASM --> REFSET
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STUDY --> VARSET
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CROP --> GMAP
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```
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## 跨模块关键桥接关系
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| 桥接点 | 连接模块 | 说明 |
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| --- | --- | --- |
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| `crop` | Core -> Germplasm/Pheno/Geno | 作物维度贯穿 program、trial、study、germplasm、变量、图谱 |
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| `program` | Core -> Germplasm/Seed/Pheno/Geno | 项目维度连接 crossing_project、seed_lot、observation_unit、sample、plate |
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| `trial` | Core -> Pheno/Geno | 试验批次维度连接 study、observation_unit、observation、sample、plate |
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| `study` | Core -> Pheno/Geno | 最重要的实验上下文，连接 observation_unit、event、observation、sample、plate、variantset |
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| `germplasm` | Germplasm -> Pheno/Geno | 种质可连接 observation_unit、cross_parent、seed_lot_content_mixture、reference_set |
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| `seed_lot` | Germplasm/Seed -> Pheno | SeedLot 可作为 observation_unit 的材料来源 |
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| `cross_entity` | Germplasm/Seed -> Pheno | Cross/PlannedCross 可作为 observation_unit 或 seed_lot_content_mixture 的来源 |
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| `observation_unit` | Pheno -> Geno | 表型观测单元可生成或关联 genotyping sample |
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| `sample` | Geno 内部入口 | 从 observation_unit/study/trial/program 进入 callset 和 allele_call |
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| `variant` | Geno 内部位点 | 与 allele_call、marker_position 连接，承载基因型结果定位 |
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## 推荐整体录入顺序
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1. 录入 Core 基础上下文：`crop`、`person`、`program`、`location`、`trial`、`season`、`study`。
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2. 录入 Germplasm 上游：`breeding_method`、`germplasm_attribute_definition` 依赖的 `trait/method/scale/ontology`。
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3. 录入 `germplasm`，再补充 `germplasm_attribute_value`、donor、origin、institute、synonym、taxon 等扩展信息。
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4. 如果涉及杂交，录入 `crossing_project`、`cross_entity`、`cross_parent`；计划杂交使用 `cross_entity.planned` 和 `planned_cross_id` 自关联表达。
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5. 录入 Seed 数据：`seed_lot`、`seed_lot_content_mixture`、`seed_lot_transaction`。
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6. 录入 Phenotyping 定义：`ontology`、`trait`、`method`、`scale`、`observation_variable`。
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7. 录入 Phenotyping 实体与事实：`observation_unit`、`event`、`image`、`observation`。
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8. 录入 Genotyping 样本入口：`plate`、`sample`。
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9. 录入 Genotyping 参考和变异：`reference_set`、`reference`、`reference_bases`、`variantset`、`variant`。
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10. 录入 Genotyping 结果：`callset`、`callset_variant_sets`、`allele_call`。
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11. 如需遗传图谱定位，录入 `genome_map`、`linkageGroup`、`marker_position`。
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## 模块边界速记
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| 模块 | 根节点 | 主要事实表 | 向外输出 |
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| --- | --- | --- | --- |
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| Core | `crop/program/trial/study` | `study` | 给所有业务模块提供上下文 |
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| Germplasm/Seed | `germplasm` | `germplasm_attribute_value`, `seed_lot_content_mixture`, `seed_lot_transaction`, `cross_parent`, `pedigree_edge` | 给 Pheno 提供材料来源，给 Geno 提供 reference source |
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| Phenotyping | `observation_unit` | `observation` | 给 Geno 提供 sample 的观测对象来源 |
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| Genotyping | `sample`, `variant` | `allele_call` | 输出样本在位点上的 genotype 结果 |
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## 关键注意点
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1. `study` 是大多数实验数据的上下文入口；如果数据要进入 Pheno 或 Geno，通常都应该能追溯到 `study`。
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2. `germplasm` 描述种质主数据，`seed_lot` 描述库存批次；二者通过 `seed_lot_content_mixture` 间接关联。
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3. `plannedcross` 没有独立数据库表，落库在 `cross_entity`，通过 `planned` 和 `planned_cross_id` 表达。
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4. `observation_unit` 可以关联 `germplasm`、`seed_lot`、`cross_entity`，是材料进入表型观测的入口。
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5. `sample` 可以从 `observation_unit` 来，也冗余关联 `study/trial/program`，是基因型流程入口。
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6. `allele_call` 是最终 genotype 结果表，连接 `callset` 与 `variant`。
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7. `additional_info` 和 `external_references` 是跨模块通用扩展表，主图中未展开，以免遮挡主干关系。
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