# Neo4j 知识图谱 Schema 设计

## 实体类型 (Nodes)

### 1. GeneFamily (基因家族)
```cypher
(:GeneFamily {
  name: string,           // 基因家族名称，如 "SPL"
  full_name: string,      // 全称，如 "SQUAMOSA PROMOTER BINDING PROTEIN-LIKE"
  description: string,    // 描述
  pfam_ids: [string],     // 相关Pfam ID
  interpro_ids: [string]  // 相关InterPro ID
})
```

### 2. Gene (基因)
```cypher
(:Gene {
  id: string,             // 基因ID，如 "FtSPL1"
  name: string,           // 基因名称
  species: string,        // 物种
  chromosome: string,     // 染色体位置
  start: int,             // 起始位置
  end: int,               // 终止位置
  strand: string,         // 正负链
  sequence: string        // 序列（可选）
})
```

### 3. Species (物种)
```cypher
(:Species {
  name: string,           // 物种名，如 "Solanum lycopersicum"
  common_name: string,    // 常用名，如 "Tomato"
  taxonomy_id: string     // NCBI Taxonomy ID
})
```

### 4. PhylogenyGroup (系统发育分组)
```cypher
(:PhylogenyGroup {
  name: string,           // 分组名，如 "Group_I"
  gene_family: string,    // 所属基因家族
  description: string     // 分组描述
})
```

### 5. Domain (蛋白结构域)
```cypher
(:Domain {
  name: string,           // 结构域名，如 "SBP"
  pfam_id: string,        // Pfam ID
  description: string     // 描述
})
```

### 6. Motif (Motif)
```cypher
(:Motif {
  id: string,             // Motif ID
  name: string,           // Motif名称
  pattern: string         // 序列模式
})
```

### 7. Publication (文献)
```cypher
(:Publication {
  doi: string,            // DOI
  pmid: string,           // PubMed ID
  pmcid: string,          // PMC ID
  title: string,          // 标题
  authors: [string],      // 作者列表
  year: int,              // 发表年份
  journal: string         // 期刊
})
```

## 关系类型 (Relationships)

### 1. BELONGS_TO (基因属于家族)
```cypher
(g:Gene)-[:BELONGS_TO]->(gf:GeneFamily)
```

### 2. FROM_SPECIES (基因来自物种)
```cypher
(g:Gene)-[:FROM_SPECIES]->(s:Species)
```

### 3. IN_GROUP (基因在分组中)
```cypher
(g:Gene)-[:IN_GROUP]->(pg:PhylogenyGroup)
```

### 4. HAS_DOMAIN (基因有结构域)
```cypher
(g:Gene)-[:HAS_DOMAIN {count: int, positions: [string]}]->(d:Domain)
```

### 5. HAS_MOTIF (基因有Motif)
```cypher
(g:Gene)-[:HAS_MOTIF {position: int, score: float}]->(m:Motif)
```

### 6. ORTHOLOG (直系同源)
```cypher
(g1:Gene)-[:ORTHOLOG {identity: float, coverage: float}]->(g2:Gene)
```

### 7. PARALOG (旁系同源)
```cypher
(g1:Gene)-[:PARALOG {identity: float, coverage: float}]->(g2:Gene)
```

### 8. COEXPRESSED (共表达)
```cypher
(g1:Gene)-[:COEXPRESSED {correlation: float, tissue: string}]->(g2:Gene)
```

### 9. CITED_IN (基因家族被文献引用)
```cypher
(gf:GeneFamily)-[:CITED_IN {confidence: float}]->(p:Publication)
```

## 索引设计

```cypher
// 基因ID索引
CREATE INDEX gene_id_idx FOR (g:Gene) ON (g.id);

// 基因家族名称索引
CREATE INDEX family_name_idx FOR (gf:GeneFamily) ON (gf.name);

// 物种名称索引
CREATE INDEX species_name_idx FOR (s:Species) ON (s.name);

// 文献DOI索引
CREATE INDEX publication_doi_idx FOR (p:Publication) ON (p.doi);
```

## Cypher 查询示例

### 查询某基因家族的所有基因
```cypher
MATCH (gf:GeneFamily {name: 'SPL'})<-[:BELONGS_TO]-(g:Gene)
RETURN g.id, g.name
```

### 查询某分组的所有基因
```cypher
MATCH (pg:PhylogenyGroup {name: 'Group_I'})<-[:IN_GROUP]-(g:Gene)
RETURN g.id, g.name
```

### 查询两个基因的共表达关系
```cypher
MATCH (g1:Gene {id: 'FtSPL1'})-[c:COEXPRESSED]-(g2:Gene {id: 'FtSPL2'})
RETURN c.correlation, c.tissue
```