404 lines
15 KiB
Markdown
Executable File
404 lines
15 KiB
Markdown
Executable File
# 增强版实体-关系提取规范
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> 基于70+维结构化提取的实体关系扩展方案
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> 创建时间: 2026-03-18
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---
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## 当前70+维中的实体关系定义
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### 现有 entities 字段
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```json
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"entities": [
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{"name": "基因/蛋白名称", "type": "gene/domain/database", "species": "物种", "description": "描述"}
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]
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```
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**问题**:
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- `type` 只有简单的3种类型
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- 缺少表型、代谢物、处理/胁迫等实体类型
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- 没有标准化的实体分类体系
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### 现有 relations 字段
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```json
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"relations": [
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{"source": "源实体", "target": "目标实体", "type": "关系类型", "description": "描述"}
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]
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```
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**问题**:
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- `type` 没有预定义的关系类型列表
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- 缺少调控关系、表达关系等生物学关系
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---
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## 增强版实体类型定义
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### 1. 核心实体类型 (Core Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **基因** | `gene` | name, symbol, id, family, chromosome, position | FtSPL1, AtSPL15 |
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| **蛋白质** | `protein` | name, accession, domain, molecular_weight, localization | FtSPL1蛋白 |
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| **基因家族** | `gene_family` | name, symbol, member_count, conserved_domain | SPL, NLR, MYB |
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### 2. 物种相关实体 (Organism Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **物种** | `organism` | scientific_name, common_name, taxonomy_id, clade | Fagopyrum tataricum (苦荞) |
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| **品种/品系** | `cultivar` | name, parent_organism, traits | 特定品种 |
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| **比较物种** | `reference_organism` | name, evolutionary_distance, genome_version | Arabidopsis thaliana |
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### 3. 表型与性状 (Phenotype Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **表型** | `phenotype` | name, trait_category, observable, measurement | 花发育、果实大小 |
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| **性状** | `trait` | name, quantitative/qualitative, heritability | 株高、产量 |
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| **发育阶段** | `developmental_stage` | name, tissue_type, age/days | 开花期、果实成熟期 |
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### 4. 实验处理 (Treatment Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **处理/胁迫** | `treatment` | name, type, duration, intensity, conditions | 干旱处理、盐胁迫、ABA处理 |
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| **激素** | `hormone` | name, concentration, application_method | ABA, GA3, IAA |
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| **环境因子** | `environmental_factor` | name, value, unit | 温度、光照强度 |
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### 5. 分子实体 (Molecular Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **代谢物** | `metabolite` | name, class, pathway, detection_method | 花青素、黄酮类 |
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| **miRNA** | `mirna` | name, sequence, target_genes | miR156, miR529 |
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| **转录因子** | `transcription_factor` | name, family, binding_motif | FtSPL1 (SPL家族) |
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| **启动子元件** | `promoter_element` | name, sequence, position, function | GTAC motif (SPL结合位点) |
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| **结构域** | `protein_domain` | name, pfam_id, function, conservation | SBP domain (PF03110) |
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### 6. 生物过程 (Process Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **生物过程** | `biological_process` | name, go_terms, pathway | 花发育、果实成熟、胁迫响应 |
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| **信号通路** | `signaling_pathway` | name, components, trigger | SPL-miR156通路 |
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| **调控网络** | `regulatory_network` | name, nodes, edges_count | SPL调控网络 |
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### 7. 数据与资源 (Data Entities)
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| 实体类型 | 类型标识 | 属性 | 示例 |
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|----------|----------|------|------|
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| **数据集** | `dataset` | accession, type, source, tissue, treatment | GSE111937 |
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| **基因组区域** | `genomic_region` | chromosome, start, end, strand, type | 基因座位置 |
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| **共线性区块** | `syntenic_block` | chromosome, genes, conservation_score | 共线性区域 |
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---
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## 增强版关系类型定义
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### 1. 调控关系 (Regulatory Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **正向调控** | `activates` | A → B | A激活B的表达或活性 | SPL9 → miR156 |
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| **负向调控** | `inhibits` | A → B | A抑制B的表达或活性 | miR156 → SPL |
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| **调控** | `regulates` | A → B | A调控B（方向不明确） | SPL regulates flowering |
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| **转录激活** | `transcriptionally_activates` | A → B | A转录因子激活B基因 | SPL → FT |
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| **转录抑制** | `transcriptionally_represses` | A → B | A转录因子抑制B基因 | SPL → TFL |
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| **翻译调控** | `translationally_regulates` | A → B | A调控B的翻译 | miRNA → mRNA |
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### 2. 包含关系 (Hierarchical Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **属于** | `belongs_to` | A → B | A属于B类别 | FtSPL1 belongs_to SPL family |
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| **包含** | `contains` | A → B | A包含B | SPL family contains FtSPL1 |
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| **部分** | `part_of` | A → B | A是B的一部分 | SBP domain part_of SPL protein |
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| **成员** | `member_of` | A → B | A是B的成员 | FtSPL1 member_of SPL family |
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| **子类** | `subclass_of` | A → B | A是B的子类 | SPL15 subclass_of SPL family |
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### 3. 表达关系 (Expression Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **表达于** | `expressed_in` | gene → tissue | 基因在组织中表达 | FtSPL1 expressed_in flower |
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| **上调** | `upregulated_in` | gene → condition | 基因在条件下上调 | FtSPL9 upregulated_in drought |
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| **下调** | `downregulated_in` | gene → condition | 基因在条件下下调 | FtSPL2 downregulated_in salt |
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| **诱导表达** | `induced_by` | gene → treatment | 基因被处理诱导 | FtSPL1 induced_by ABA |
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| **抑制表达** | `repressed_by` | gene → treatment | 基因被处理抑制 | FtSPL3 repressed_by GA |
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| **时序表达** | `temporally_expressed` | gene → stage | 基因在发育阶段表达 | FtSPL expressed_at flowering |
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### 4. 功能关系 (Functional Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **参与** | `involved_in` | gene → process | 基因参与生物过程 | FtSPL involved_in flowering |
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| **控制** | `controls` | gene → phenotype | 基因控制表型 | FtSPL16 controls fruit_size |
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| **影响** | `affects` | gene → trait | 基因影响性状 | FtSPL affects plant_height |
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| **介导** | `mediates` | gene → response | 基因介导响应 | FtSPL mediates stress_response |
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| **促进** | `promotes` | gene → process | 基因促进过程 | FtSPL promotes flowering |
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| **抑制** | `represses` | gene → process | 基因抑制过程 | SPL represses juvenile_phase |
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### 5. 进化关系 (Evolutionary Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **同源** | `homologous_to` | gene ↔ gene | 基因同源 | FtSPL1 homologous_to AtSPL1 |
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| **直系同源** | `orthologous_to` | gene ↔ gene | 直系同源 | FtSPL1 orthologous_to AtSPL1 |
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| **旁系同源** | `paralogous_to` | gene ↔ gene | 旁系同源 | FtSPL1 paralogous_to FtSPL2 |
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| **来源于** | `derived_from` | gene → gene | 基因来源于 | FtSPL derived_from duplication |
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| **复制** | `duplicated_to` | gene → gene | 基因复制为 | SPL1 duplicated_to SPL2 |
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| **共线性** | `syntenic_with` | gene ↔ gene | 基因共线性 | FtSPL1 syntenic_with GmSPL1 |
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### 6. 互作关系 (Interaction Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **互作** | `interacts_with` | protein ↔ protein | 蛋白互作 | FtSPL1 interacts_with FtSPL2 |
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| **结合** | `binds_to` | protein → DNA/metabolite | 蛋白结合 | SPL binds_to GTAC_motif |
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| **磷酸化** | `phosphorylates` | kinase → substrate | 激酶磷酸化底物 | kinase phosphorylates SPL |
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| **去磷酸化** | `dephosphorylates` | phosphatase → substrate | 磷酸酶去磷酸化 | phosphatase dephosphorylates SPL |
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| **切割** | `cleaves` | enzyme → substrate | 酶切割底物 | Dicer cleaves pre-miRNA |
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### 7. 数据关系 (Data Relations)
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| 关系类型 | 关系标识 | 方向 | 描述 | 示例 |
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|----------|----------|------|------|------|
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| **来源于** | `originated_from` | data → organism | 数据来源于物种 | Dataset originated_from 苦荞 |
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| **测序** | `sequenced_from` | data → tissue | 数据测序自组织 | RNA-seq sequenced_from flower |
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| **注释** | `annotated_in` | gene → database | 基因注释于数据库 | FtSPL1 annotated_in TAIR |
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| **存储于** | `stored_in` | data → database | 数据存储于数据库 | GSE111937 stored_in GEO |
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---
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## 增强版JSON Schema示例
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### 完整实体示例
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```json
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{
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"entities": [
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{
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"id": "FtSPL1",
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"name": "FtSPL1",
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"type": "gene",
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"symbol": "FtSPL1",
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"species": "Fagopyrum tataricum",
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"family": "SPL",
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"chromosome": "Chr1",
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"position": "123456-123890",
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"strand": "+",
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"description": "SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 1 in tartary buckwheat"
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},
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{
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"id": "SPL_family",
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"name": "SPL transcription factor family",
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"type": "gene_family",
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"symbol": "SPL",
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"member_count": 24,
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"conserved_domain": "SBP domain (PF03110)",
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"description": "SQUAMOSA PROMOTER BINDING PROTEIN-LIKE family"
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},
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{
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"id": "Fagopyrum_tataricum",
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"name": "Fagopyrum tataricum",
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"type": "organism",
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"common_name": "Tartary buckwheat",
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"common_name_cn": "苦荞",
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"taxonomy_id": "NCBI:txid321",
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"clade": "Eudicots",
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"description": "Tartary buckwheat, an important pseudocereal crop"
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},
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{
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"id": "flower_development",
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"name": "flower development",
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"type": "phenotype",
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"trait_category": "developmental",
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"observable": true,
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"description": "Process of flower formation and development"
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},
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{
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"id": "drought_stress",
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"name": "drought stress",
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"type": "treatment",
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"treatment_type": "abiotic_stress",
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"duration": "7 days",
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"intensity": "severe",
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"description": "Water deficit treatment"
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},
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{
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"id": "PF03110",
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"name": "SBP domain",
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"type": "protein_domain",
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"pfam_id": "PF03110",
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"function": "DNA binding",
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"conservation": "highly conserved in plants",
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"description": "SQUAMOSA PROMOTER BINDING PROTEIN domain"
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}
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],
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"relations": [
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{
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"id": "rel_1",
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"source": "FtSPL1",
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"target": "SPL_family",
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"type": "member_of",
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"description": "FtSPL1 is a member of SPL family",
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"confidence": "high",
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"evidence": "phylogenetic analysis"
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},
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{
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"id": "rel_2",
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"source": "FtSPL1",
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"target": "Fagopyrum_tataricum",
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"type": "belongs_to",
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"description": "FtSPL1 belongs to tartary buckwheat",
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"confidence": "high",
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"evidence": "genome annotation"
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},
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{
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"id": "rel_3",
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"source": "FtSPL1",
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"target": "flower_development",
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"type": "involved_in",
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"description": "FtSPL1 is involved in flower development",
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"confidence": "medium",
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"evidence": "expression analysis"
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},
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{
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"id": "rel_4",
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"source": "FtSPL1",
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"target": "PF03110",
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"type": "contains",
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"description": "FtSPL1 protein contains SBP domain",
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"confidence": "high",
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"evidence": "Pfam annotation"
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},
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{
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"id": "rel_5",
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"source": "drought_stress",
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"target": "FtSPL1",
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"type": "upregulates",
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"description": "Drought stress upregulates FtSPL1 expression",
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"confidence": "medium",
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"evidence": "RNA-seq data"
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}
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]
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}
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```
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---
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## 与现有70+维的整合建议
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### 方案1: 扩展现有字段
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保持现有 `entities` 和 `relations` 字段，但增强其内容规范：
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```json
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{
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"entities": [
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{
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"id": "唯一标识",
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"name": "实体名称",
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"type": "gene|protein|organism|phenotype|treatment|metabolite|process|...",
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"species": "物种",
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"attributes": {},
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"description": "描述"
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}
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],
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"relations": [
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{
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"id": "关系唯一标识",
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"source": "源实体ID",
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"target": "目标实体ID",
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"type": "activates|inhibits|regulates|expressed_in|involved_in|...",
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"description": "关系描述",
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"confidence": "high|medium|low",
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"evidence": "证据来源"
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}
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]
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}
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```
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### 方案2: 新增独立知识图谱字段
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在70+维之外新增 `knowledge_graph` 字段：
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```json
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{
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"knowledge_graph": {
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"nodes": [...], // 实体
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"edges": [...], // 关系
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"pathways": [...], // 通路
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"networks": [...] // 网络
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}
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}
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```
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### 方案3: 分层提取
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- **第一层**: 现有70+维（结构化信息）
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- **第二层**: 实体关系（知识图谱）
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- **第三层**: 通路网络（系统生物学）
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---
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## 实施建议
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### 1. 提示词修改
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在 `extraction_prompt.md` 中扩展 `entities` 和 `relations` 的定义：
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```markdown
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"entities": [
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{
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"id": "唯一标识符（如FtSPL1）",
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"name": "实体名称",
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"type": "实体类型：gene|protein|organism|phenotype|treatment|metabolite|process|gene_family|protein_domain|...",
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"species": "所属物种",
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"attributes": {},
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"description": "描述"
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}
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],
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"relations": [
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{
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"id": "关系唯一标识",
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"source": "源实体ID",
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"target": "目标实体ID",
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"type": "关系类型：activates|inhibits|regulates|expressed_in|upregulated_in|downregulated_in|involved_in|controls|homologous_to|orthologous_to|paralogous_to|member_of|contains|part_of|interacts_with|binds_to|...",
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"description": "关系描述",
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"confidence": "high|medium|low",
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"evidence": "证据来源"
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}
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]
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```
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### 2. 验证规则
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添加实体关系验证：
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- 实体ID必须唯一
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- 关系中的source和target必须存在于entities中
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- 关系类型必须符合预定义列表
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- 实体类型必须符合预定义列表
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### 3. 与知识库整合
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提取的实体关系可用于：
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- 构建知识图谱
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- 支持图检索
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- 发现新的基因-表型关联
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- 跨物种比较分析
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---
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## 总结
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| 方面 | 当前70+维 | 增强版建议 |
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|------|-----------|------------|
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| **实体类型** | 3种 (gene/domain/database) | 30+种 (基因、蛋白、物种、表型、处理、代谢物、过程等) |
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| **关系类型** | 未预定义 | 40+种 (调控、包含、表达、参与、进化、互作等) |
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| **属性完整性** | 基础 (name, type, species) | 丰富 (id, symbol, position, confidence, evidence等) |
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| **验证机制** | 无 | 有 (唯一性、类型检查、引用完整性) |
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| **应用场景** | 信息提取 | 知识图谱构建、图检索、通路分析 |
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**建议**: 采用**方案1**（扩展现有字段），保持向后兼容的同时增强实体关系表达能力。
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*文档创建: 2026-03-18*
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*基于: 70+维结构化提取规范 v1.0* |