161 lines
3.7 KiB
Markdown
Executable File
161 lines
3.7 KiB
Markdown
Executable File
# Neo4j 知识图谱 Schema 设计
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## 实体类型 (Nodes)
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### 1. GeneFamily (基因家族)
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```cypher
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(:GeneFamily {
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name: string, // 基因家族名称，如 "SPL"
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full_name: string, // 全称，如 "SQUAMOSA PROMOTER BINDING PROTEIN-LIKE"
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description: string, // 描述
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pfam_ids: [string], // 相关Pfam ID
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interpro_ids: [string] // 相关InterPro ID
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})
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```
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### 2. Gene (基因)
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```cypher
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(:Gene {
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id: string, // 基因ID，如 "FtSPL1"
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name: string, // 基因名称
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species: string, // 物种
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chromosome: string, // 染色体位置
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start: int, // 起始位置
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end: int, // 终止位置
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strand: string, // 正负链
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sequence: string // 序列（可选）
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})
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```
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### 3. Species (物种)
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```cypher
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(:Species {
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name: string, // 物种名，如 "Solanum lycopersicum"
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common_name: string, // 常用名，如 "Tomato"
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taxonomy_id: string // NCBI Taxonomy ID
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})
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```
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### 4. PhylogenyGroup (系统发育分组)
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```cypher
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(:PhylogenyGroup {
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name: string, // 分组名，如 "Group_I"
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gene_family: string, // 所属基因家族
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description: string // 分组描述
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})
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```
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### 5. Domain (蛋白结构域)
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```cypher
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(:Domain {
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name: string, // 结构域名，如 "SBP"
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pfam_id: string, // Pfam ID
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description: string // 描述
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})
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```
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### 6. Motif (Motif)
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```cypher
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(:Motif {
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id: string, // Motif ID
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name: string, // Motif名称
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pattern: string // 序列模式
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})
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```
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### 7. Publication (文献)
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```cypher
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(:Publication {
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doi: string, // DOI
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pmid: string, // PubMed ID
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pmcid: string, // PMC ID
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title: string, // 标题
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authors: [string], // 作者列表
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year: int, // 发表年份
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journal: string // 期刊
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})
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```
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## 关系类型 (Relationships)
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### 1. BELONGS_TO (基因属于家族)
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```cypher
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(g:Gene)-[:BELONGS_TO]->(gf:GeneFamily)
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```
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### 2. FROM_SPECIES (基因来自物种)
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```cypher
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(g:Gene)-[:FROM_SPECIES]->(s:Species)
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```
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### 3. IN_GROUP (基因在分组中)
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```cypher
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(g:Gene)-[:IN_GROUP]->(pg:PhylogenyGroup)
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```
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### 4. HAS_DOMAIN (基因有结构域)
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```cypher
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(g:Gene)-[:HAS_DOMAIN {count: int, positions: [string]}]->(d:Domain)
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```
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### 5. HAS_MOTIF (基因有Motif)
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```cypher
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(g:Gene)-[:HAS_MOTIF {position: int, score: float}]->(m:Motif)
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```
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### 6. ORTHOLOG (直系同源)
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```cypher
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(g1:Gene)-[:ORTHOLOG {identity: float, coverage: float}]->(g2:Gene)
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```
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### 7. PARALOG (旁系同源)
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```cypher
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(g1:Gene)-[:PARALOG {identity: float, coverage: float}]->(g2:Gene)
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```
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### 8. COEXPRESSED (共表达)
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```cypher
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(g1:Gene)-[:COEXPRESSED {correlation: float, tissue: string}]->(g2:Gene)
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```
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### 9. CITED_IN (基因家族被文献引用)
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```cypher
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(gf:GeneFamily)-[:CITED_IN {confidence: float}]->(p:Publication)
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```
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## 索引设计
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```cypher
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// 基因ID索引
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CREATE INDEX gene_id_idx FOR (g:Gene) ON (g.id);
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// 基因家族名称索引
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CREATE INDEX family_name_idx FOR (gf:GeneFamily) ON (gf.name);
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// 物种名称索引
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CREATE INDEX species_name_idx FOR (s:Species) ON (s.name);
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// 文献DOI索引
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CREATE INDEX publication_doi_idx FOR (p:Publication) ON (p.doi);
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```
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## Cypher 查询示例
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### 查询某基因家族的所有基因
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```cypher
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MATCH (gf:GeneFamily {name: 'SPL'})<-[:BELONGS_TO]-(g:Gene)
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RETURN g.id, g.name
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```
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### 查询某分组的所有基因
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```cypher
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MATCH (pg:PhylogenyGroup {name: 'Group_I'})<-[:IN_GROUP]-(g:Gene)
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RETURN g.id, g.name
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```
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### 查询两个基因的共表达关系
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```cypher
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MATCH (g1:Gene {id: 'FtSPL1'})-[c:COEXPRESSED]-(g2:Gene {id: 'FtSPL2'})
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RETURN c.correlation, c.tissue
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```
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