从微生物 → 代谢物 → 基因 → 信号通路 → 疾病，并且关联 Association 节点 保存证据、观察信息等元数据。下面我给你一个 标准化建模方案。
:Association
{id:"A001", evidence:"PMID:123456"}
:Taxonomy
{name:"Bacteroides"}
:Metabolomics
{name:"Butyrate"}
:Gene
{name:"CYP1A1"}
:Pathway
{name:"TLR signaling"}
:Disease
{name:"Obesity"}
:Study
{pmid:"123456", title:"..."}
:SUBJECT
:OBJECT
:OBSERVED_IN
:EVIDENCED_IN
:PRODUCES_METABOLITE
:REGULATES_GENE
:PARTICIPATES_IN_PATHWAY
:PATHWAY_ASSOCIATED_WITH
假设：
Bacteroides fragilis
Butyrate
CYP1A1
TLR signaling
Obesity
PMID:123456
// 节点 MERGE (microbe:Taxonomy {name:"Bacteroides fragilis"}) MERGE (met:Metabolomics {name:"Butyrate"}) MERGE (gene:Gene {name:"CYP1A1"}) MERGE (pathway:Pathway {name:"TLR signaling"}) MERGE (disease:Disease {name:"Obesity"}) MERGE (study:Study {pmid:"123456", title:"..."}) // Association 节点 CREATE (assoc:Association {id:"A001", description:"Bacteroides fragilis produces Butyrate, upregulates CYP1A1, participates in TLR signaling, affects Obesity"}) // 关系 MERGE (microbe)-[:SUBJECT]->(assoc) MERGE (assoc)-[:OBJECT]->(disease) MERGE (assoc)-[:OBSERVED_IN]->(study) MERGE (assoc)-[:EVIDENCED_IN]->(study) // 生物学链条 MERGE (microbe)-[:PRODUCES_METABOLITE]->(met) MERGE (met)-[:REGULATES_GENE {direction:"up"}]->(gene) MERGE (gene)-[:PARTICIPATES_IN_PATHWAY]->(pathway) MERGE (pathway)-[:PATHWAY_ASSOCIATED_WITH]->(disease)
查询微生物对肥胖的因果链：
MATCH (m:Taxonomy)-[:PRODUCES_METABOLITE]->(met:Metabolomics) -[:REGULATES_GENE]->(g:Gene) -[:PARTICIPATES_IN_PATHWAY]->(p:Pathway) -[:PATHWAY_ASSOCIATED_WITH]->(d:Disease {name:"Obesity"}) RETURN m.name, met.name, g.name, p.name, d.name
查询文献支持的 Association：
MATCH (assoc:Association)-[:SUBJECT]->(m:Taxonomy), (assoc)-[:OBJECT]->(d:Disease), (assoc)-[:EVIDENCED_IN]->(s:Study) RETURN assoc.description, m.name, d.name, s.pmid
✅ 优点
Association