Ppi 工具

Configuration File: ppi_tools.json Tool Type: Local Tools Count: 4

此页面包含在``ppi_tools.json``配置文件中定义的所有工具。

可用工具

STRING_functional_enrichment (Type: STRINGRESTTool)

Identify enriched biological functions, pathways, and processes for a protein set using STRING (S…

STRING_functional_enrichment tool specification

工具信息：

  • Name: STRING_functional_enrichment

  • 类型: STRINGRESTTool

  • Description: Identify enriched biological functions, pathways, and processes for a protein set using STRING (Search Tool for Retrieval of Interacting Genes/Proteins) database. Performs statistical enrichment analysis against GO (Gene Ontology) terms, KEGG pathways, Reactome pathways, and other annotation databases. Returns significantly enriched terms with FDR-corrected p-values. Minimum 3-4 proteins required for meaningful statistical analysis. No API key required. Use for: discovering pathways enriched in protein network, identifying biological processes, finding shared functions among proteins, interpreting omics data (proteomics, interactomics), hypothesis generation.

参数：

  • protein_ids (array) (required) List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins recommended for meaningful enrichment.

  • ``species``（整数）（可选）NCBI分类学ID（默认值：9606，表示人类）

  • category (string) (optional) Enrichment category: ‘Process’ (GO Biological Process), ‘Component’ (GO Cellular Component), ‘Function’ (GO Molecular Function), ‘KEGG’, ‘Reactome’, ‘WikiPathways’, ‘COMPARTMENTS’, ‘TISSUES’, ‘DISEASES’

示例用法：

query = {
    "name": "STRING_functional_enrichment",
    "arguments": {
        "protein_ids": ["item1", "item2"]
    }
}
result = tu.run(query)

**STRING_get_protein_interactions**（类型：STRINGRESTTool）

Alternative method to retrieve protein interactions from STRING (Search Tool for Retrieval of Int…

STRING_get_protein_interactions工具规格

工具信息：

  • 名称: STRING_get_protein_interactions

  • 类型: STRINGRESTTool

  • Description: Alternative method to retrieve protein interactions from STRING (Search Tool for Retrieval of Interacting Genes/Proteins). Provides similar functionality to STRING_get_network but may return different response format. Recommend using STRING_get_network for most analyses - more commonly used and better documented. No API key required. Use for: alternative interaction retrieval if get_network has issues, specific data format requirements, compatibility with legacy code.

参数：

  • ``protein_ids``（数组）（必填）蛋白质标识符列表（UniProt ID、基因名称等）

  • ``species``（整数）（可选）NCBI分类学ID（默认值：9606，表示人类）

  • ``confidence_score``（数字）（可选）最低置信分数（0-1，默认值：0.4）

  • ``limit``（整数）（可选）返回的最大交互数量（默认值：50）

  • ``network_type``（字符串）（可选）网络类型（“完整”、“物理”、“功能”）

示例用法：

query = {
    "name": "STRING_get_protein_interactions",
    "arguments": {
        "protein_ids": ["item1", "item2"]
    }
}
result = tu.run(query)

STRING_map_identifiers (Type: STRINGRESTTool)

Map protein identifiers to STRING (Search Tool for Retrieval of Interacting Genes/Proteins) datab…

STRING_map_identifiers tool specification

工具信息：

  • Name: STRING_map_identifiers

  • 类型: STRINGRESTTool

  • Description: Map protein identifiers to STRING (Search Tool for Retrieval of Interacting Genes/Proteins) database IDs. Essential first step before using other STRING tools - converts your protein names (gene symbols, UniProt IDs, Ensembl IDs) to STRING’s internal identifiers. STRING database contains 14M+ proteins from 5,000+ organisms with functional association networks. No API key required (public API with rate limits). Use for: preparing protein lists for network analysis, converting between identifier types, validating protein names exist in STRING, batch identifier conversion.

参数：

  • protein_ids (array) (required) List of protein identifiers to map (UniProt IDs, gene names, Ensembl IDs, RefSeq IDs)

  • species (integer) (optional) NCBI taxonomy ID (default: 9606 for human, 10090 for mouse)

  • limit (integer) (optional) Maximum number of matches per identifier (default: 1)

  • echo_query (integer) (optional) Include query identifier in response (1=yes, 0=no, default: 1)

示例用法：

query = {
    "name": "STRING_map_identifiers",
    "arguments": {
        "protein_ids": ["item1", "item2"]
    }
}
result = tu.run(query)

STRING_ppi_enrichment (Type: STRINGRESTTool)

Test if your protein set has more interactions than expected by chance (PPI = Protein-Protein Int…

STRING_ppi_enrichment tool specification

工具信息：

  • Name: STRING_ppi_enrichment

  • 类型: STRINGRESTTool

  • Description: Test if your protein set has more interactions than expected by chance (PPI = Protein-Protein Interaction enrichment). Compares observed interactions in your network to random expectation - significant enrichment suggests proteins work together functionally. Returns enrichment p-value and expected vs observed interaction counts. Useful for validating that your protein list forms a real functional module rather than random proteins. No API key required. Use for: validating protein complex predictions, testing if proteins form functional module, quality control for network analysis, distinguishing real complexes from random protein lists, assessing functional coherence.

参数：

  • protein_ids (array) (required) List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins required.

  • ``species``（整数）（可选）NCBI分类学ID（默认值：9606，表示人类）

  • confidence_score (number) (optional) Minimum confidence score for counting interactions (0-1, default: 0.4)

示例用法：

query = {
    "name": "STRING_ppi_enrichment",
    "arguments": {
        "protein_ids": ["item1", "item2"]
    }
}
result = tu.run(query)