PubChem 工具¶
Configuration File: pubchem_tools.json
Tool Type: Local
Tools Count: 18
本页面包含在``pubchem_tools.json``配置文件中定义的所有工具。
可用工具¶
**PubChem_get_CID_by_SMILES**（类型：PubChemRESTTool）¶
通过SMILES字符串检索对应的CID列表。
PubChem_get_CID_by_SMILES 工具规范
工具信息：
名称:
PubChem_get_CID_by_SMILES类型:
PubChemRESTTool描述：通过SMILES字符串检索对应的CID列表。
参数：
``smiles``（字符串）（必填）SMILES 表达式（例如：”CC(=O)OC1=CC=CC=C1C(=O)O” 对应于阿司匹林）。
示例用法：
query = {
"name": "PubChem_get_CID_by_SMILES",
"arguments": {
"smiles": "example_value"
}
}
result = tu.run(query)
**PubChem_get_CID_by_compound_name**（类型：PubChemRESTTool）¶
Search PubChem by compound name to get CID(s). This is the PRIMARY tool for looking up a drug or …
PubChem_get_CID_by_compound_name 工具规范
工具信息：
名称:
PubChem_get_CID_by_compound_name类型:
PubChemRESTToolDescription: Search PubChem by compound name to get CID(s). This is the PRIMARY tool for looking up a drug or chemical by name (e.g., ‘cytarabine’, ‘aspirin’, ‘metformin’, ‘venetoclax’) to obtain PubChem Compound IDs. Use the returned CID with other PubChem tools for properties, patents, etc. Only works with chemical/drug names, not disease names.
参数：
name(string) (optional) Chemical compound name (e.g., “Aspirin”, “Acetaminophen”) or IUPAC name. Do not use disease names or medical conditions.compound_name(string) (optional) Alias for name. The compound name to look up.
示例用法：
query = {
"name": "PubChem_get_CID_by_compound_name",
"arguments": {
}
}
result = tu.run(query)
PubChem_get_assay_active_compounds (Type: PubChemRESTTool)¶
Get CIDs of compounds that are ACTIVE in a bioassay. Returns compound IDs that passed the activit…
PubChem_get_assay_active_compounds tool specification
工具信息：
Name:
PubChem_get_assay_active_compounds类型:
PubChemRESTToolDescription: Get CIDs of compounds that are ACTIVE in a bioassay. Returns compound IDs that passed the activity threshold. Use for hit identification from HTS screens.
参数：
aid(integer) (required) PubChem BioAssay ID
示例用法：
query = {
"name": "PubChem_get_assay_active_compounds",
"arguments": {
"aid": 10
}
}
result = tu.run(query)
PubChem_get_assay_description (Type: PubChemRESTTool)¶
Get bioassay description and metadata by AID. Returns assay name, source, protocol, target inform…
PubChem_get_assay_description tool specification
工具信息：
Name:
PubChem_get_assay_description类型:
PubChemRESTToolDescription: Get bioassay description and metadata by AID. Returns assay name, source, protocol, target information, activity outcomes, and data columns. Essential for understanding what an assay measures before retrieving results.
参数：
aid(integer) (required) PubChem BioAssay ID (e.g., 1000, 504526)
示例用法：
query = {
"name": "PubChem_get_assay_description",
"arguments": {
"aid": 10
}
}
result = tu.run(query)
PubChem_get_assay_dose_response (Type: PubChemRESTTool)¶
Get dose-response data from a bioassay. Returns concentration-response curves for tested compound…
PubChem_get_assay_dose_response tool specification
工具信息：
Name:
PubChem_get_assay_dose_response类型:
PubChemRESTToolDescription: Get dose-response data from a bioassay. Returns concentration-response curves for tested compounds. Essential for determining IC50/EC50 values. Limited to dose-response type assays.
参数：
aid(integer) (required) PubChem BioAssay ID (must be a dose-response assay)
示例用法：
query = {
"name": "PubChem_get_assay_dose_response",
"arguments": {
"aid": 10
}
}
result = tu.run(query)
PubChem_get_assay_summary (Type: PubChemRESTTool)¶
Get summary statistics for a bioassay by AID. Returns counts of active/inactive compounds, target…
PubChem_get_assay_summary tool specification
工具信息：
Name:
PubChem_get_assay_summary类型:
PubChemRESTToolDescription: Get summary statistics for a bioassay by AID. Returns counts of active/inactive compounds, target information, and assay metadata. Useful for quick assessment of assay size and hit rate.
参数：
aid(integer) (required) PubChem BioAssay ID
示例用法：
query = {
"name": "PubChem_get_assay_summary",
"arguments": {
"aid": 10
}
}
result = tu.run(query)
PubChem_get_assay_targets (Type: PubChemRESTTool)¶
Get protein/gene targets for a bioassay. Returns GI numbers, protein names, gene IDs, and gene sy…
PubChem_get_assay_targets tool specification
工具信息：
Name:
PubChem_get_assay_targets类型:
PubChemRESTToolDescription: Get protein/gene targets for a bioassay. Returns GI numbers, protein names, gene IDs, and gene symbols. Critical for understanding what molecular targets an assay screens against.
参数：
aid(integer) (required) PubChem BioAssay ID
示例用法：
query = {
"name": "PubChem_get_assay_targets",
"arguments": {
"aid": 10
}
}
result = tu.run(query)
PubChem_get_assays_for_compound_active (Type: PubChemRESTTool)¶
Get AIDs of assays where a compound is ACTIVE. Returns list of bioassay IDs where the compound sh…
PubChem_get_assays_for_compound_active tool specification
工具信息：
Name:
PubChem_get_assays_for_compound_active类型:
PubChemRESTToolDescription: Get AIDs of assays where a compound is ACTIVE. Returns list of bioassay IDs where the compound showed activity. Use to understand a compound’s target profile.
参数：
cid(integer) (required) PubChem Compound ID
示例用法：
query = {
"name": "PubChem_get_assays_for_compound_active",
"arguments": {
"cid": 10
}
}
result = tu.run(query)
**PubChem_get_associated_patents_by_CID**（类型：PubChemRESTTool）¶
获取与特定化合物CID相关的专利列表。
PubChem_get_associated_patents_by_CID 工具规格说明
工具信息：
名称：
PubChem_get_associated_patents_by_CID类型:
PubChemRESTTool描述：获取与特定化合物CID相关的专利列表。
参数：
``cid``（整数）（必填）用于查询的PubChem化合物ID，例如2244（阿司匹林）。
示例用法：
query = {
"name": "PubChem_get_associated_patents_by_CID",
"arguments": {
"cid": 10
}
}
result = tu.run(query)
**PubChem_get_compound_2D_image_by_CID**（类型：PubChemRESTTool）¶
通过CID获取化合物的二维结构图像（PNG格式）。
PubChem_get_compound_2D_image_by_CID 工具规格说明
工具信息：
名称：
PubChem_get_compound_2D_image_by_CID类型:
PubChemRESTTool描述：通过CID获取化合物的二维结构图像（PNG格式）。
参数：
``cid``（整数）（必填）用于获取图像的化合物ID，例如 2244。
image_size(string) (required) Optional parameter, image size, like “200x200” (default).
示例用法：
query = {
"name": "PubChem_get_compound_2D_image_by_CID",
"arguments": {
"cid": 10,
"image_size": "example_value"
}
}
result = tu.run(query)
PubChem_get_compound_bioactivity (Type: PubChemRESTTool)¶
Get bioassay results summary for a compound by CID. Returns all assays the compound was tested in…
PubChem_get_compound_bioactivity tool specification
工具信息：
Name:
PubChem_get_compound_bioactivity类型:
PubChemRESTToolDescription: Get bioassay results summary for a compound by CID. Returns all assays the compound was tested in, activity outcomes (active/inactive), and target information. Critical for understanding compound’s biological profile.
参数：
cid(integer) (required) PubChem Compound ID
示例用法：
query = {
"name": "PubChem_get_compound_bioactivity",
"arguments": {
"cid": 10
}
}
result = tu.run(query)
**PubChem_get_compound_properties_by_CID**（类型：PubChemRESTTool）¶
通过 CID（化合物 ID）获取一组指定的分子属性，例如分子量，…
PubChem_get_compound_properties_by_CID 工具规范
工具信息：
名称:
PubChem_get_compound_properties_by_CID类型:
PubChemRESTTool描述：通过CID（化合物ID）获取一组指定的分子属性，例如分子量、IUPAC名称、规范SMILES。
参数：
``cid``（整数）（必填）用于查询的PubChem化合物ID，例如2244（阿司匹林）。
示例用法：
query = {
"name": "PubChem_get_compound_properties_by_CID",
"arguments": {
"cid": 10
}
}
result = tu.run(query)
**PubChem_get_compound_synonyms_by_CID**（类型：PubChemREST工具）¶
获取基于CID的化合物完整同义词列表。
PubChem_get_compound_synonyms_by_CID 工具规范
工具信息：
名称:
PubChem_get_compound_synonyms_by_CID类型:
PubChemRESTTool描述：获取化合物CID的完整同义词列表。
参数：
``cid``（整数）（必填）用于查询化合物的同义词，例如 2244。
示例用法：
query = {
"name": "PubChem_get_compound_synonyms_by_CID",
"arguments": {
"cid": 10
}
}
result = tu.run(query)
**PubChem_get_compound_xrefs_by_CID**（类型：PubChemREST工具）¶
通过CID获取化合物的外部参考（XRefs），包括指向ChEBI、DrugBank、KEGG等的链接。
PubChem_get_compound_xrefs_by_CID 工具规范
工具信息：
名称:
PubChem_get_compound_xrefs_by_CID类型:
PubChemRESTTool描述：通过CID获取化合物的外部参考（XRefs），包括链接到ChEBI、DrugBank、KEGG等。
参数：
``cid``（整数）（必填）用于查询外部引用的化合物ID，例如：2244。
``xref_types``（数组）（必填）要查询的外部数据库类型列表，例如：[“RegistryID”, “RN”, “PubMedID”]。
示例用法：
query = {
"name": "PubChem_get_compound_xrefs_by_CID",
"arguments": {
"cid": 10,
"xref_types": ["item1", "item2"]
}
}
result = tu.run(query)
PubChem_search_assays_by_target_gene (Type: PubChemRESTTool)¶
Search bioassays by target gene symbol. Returns AIDs of assays that screen against the specified …
PubChem_search_assays_by_target_gene tool specification
工具信息：
Name:
PubChem_search_assays_by_target_gene类型:
PubChemRESTToolDescription: Search bioassays by target gene symbol. Returns AIDs of assays that screen against the specified gene. Example: USP2 returns assays targeting USP2 protease.
参数：
gene_symbol(string) (required) Gene symbol to search (e.g., EGFR, USP2, TP53)
示例用法：
query = {
"name": "PubChem_search_assays_by_target_gene",
"arguments": {
"gene_symbol": "example_value"
}
}
result = tu.run(query)
PubChem_search_assays_by_type (Type: PubChemRESTTool)¶
Search bioassays by assay type. Types: screening (HTS), confirmatory, doseresponse, summary, cell…
PubChem_search_assays_by_type tool specification
工具信息：
Name:
PubChem_search_assays_by_type类型:
PubChemRESTToolDescription: Search bioassays by assay type. Types: screening (HTS), confirmatory, doseresponse, summary, cellbased, biochemical, invivo, invitro. Returns list of matching AIDs.
参数：
assay_type(string) (required) Type of assay to search for
示例用法：
query = {
"name": "PubChem_search_assays_by_type",
"arguments": {
"assay_type": "example_value"
}
}
result = tu.run(query)
**PubChem_search_compounds_by_similarity**（类型：PubChemRESTTool）¶
按相似度搜索（Tanimoto系数），返回相似度高于…的化合物CID列表
PubChem_search_compounds_by_similarity 工具规格说明
工具信息：
名称：
PubChem_search_compounds_by_similarity类型:
PubChemRESTToolDescription: Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above threshold to given SMILES molecule. Returns up to max_results CIDs (default 10).
参数：
``smiles``（字符串）（必填）目标分子的SMILES表达式。
threshold(number) (required) Similarity threshold (between 0 and 1), e.g., 0.9 means 90% similarity.max_results(integer) (optional) Maximum number of CIDs to return (default: 10, max: 10000).
示例用法：
query = {
"name": "PubChem_search_compounds_by_similarity",
"arguments": {
"smiles": "example_value",
"threshold": "example_value"
}
}
result = tu.run(query)
**PubChem_按子结构搜索化合物**（类型：PubChemRESTTool）¶
Search for CIDs in PubChem that contain the given substructure (SMILES). Returns up to max_result…
PubChem_按子结构搜索化合物 工具规范
工具信息：
名称：
PubChem_search_compounds_by_substructure类型:
PubChemRESTToolDescription: Search for CIDs in PubChem that contain the given substructure (SMILES). Returns up to max_results CIDs (default 10).
参数：
``smiles``（字符串）（必填）子结构的SMILES表示（例如，“c1ccccc1”对应苯环）。
max_results(integer) (optional) Maximum number of CIDs to return (default: 10, max: 10000).
示例用法：
query = {
"name": "PubChem_search_compounds_by_substructure",
"arguments": {
"smiles": "example_value"
}
}
result = tu.run(query)