Bioctcgamcp

🚀 biocTcgaMcp

biocTcgaMcp 用于演示一个具备 TCGA 分析工具的 MCP 服务器，为 TCGA 相关分析提供支持。

🚀 快速开始

配置文件准备

安装本包后，需要在 ~/.config/mcptools/config.json 处准备一个合适的配置文件，文件内容如下：

{
  "mcpServers": {
    "r-mcptools": {
      "command": "Rscript",
      "args": ["-e", "mcptools::mcp_server()"]
    },
    "r-btw": {
      "command": "Rscript",
      "args": ["-e", "btw::btw_mcp_server()"]
    },
    "r-tcga": {
      "command": "Rscript",
      "args": ["-e", "biocTcgaMcp::btcga_mcp_server()"]
    }
  }
}

代码示例

基础用法

library(ellmer)
ch = chat_openai(model="gpt-4o")
ch$set_tools(mcptools::mcp_tools())  # 需要 biocTcgaMcp 0.0.2 以使用改进的类型列表工具
cc = type_array(type_object(codes = type_string(description = "TCGA tumor type codes"), 
         types = type_string(description = "TCGA tumor study names"))
ch$chat_structured("What tumor types are available in TCGA?", type=cc)

上述代码运行后应返回一个数据框。chat_structured 不是必需的，但它会在调用的 R 会话中创建一个值。例如：

> ch$chat_structured("What tumor types are available in TCGA?", type=cc)
   codes                                                            types
1    ACC                                         Adrenocortical carcinoma
2   BLCA                                     Bladder Urothelial Carcinoma
3   BRCA                                        Breast invasive carcinoma
4   CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
5   CHOL                                               Cholangiocarcinoma
6   COAD                                             Colon adenocarcinoma
7   DLBC                  Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
8   ESCA                                             Esophageal carcinoma
9    GBM                                          Glioblastoma multiforme
10  HNSC                            Head and Neck squamous cell carcinoma
11  KICH                                               Kidney Chromophobe
12  KIRC                                Kidney renal clear cell carcinoma
13  KIRP                            Kidney renal papillary cell carcinoma
14  LAML                                           Acute Myeloid Leukemia
15   LGG                                         Brain Lower Grade Glioma
16  LIHC                                   Liver hepatocellular carcinoma
17  LUAD                                              Lung adenocarcinoma
18  LUSC                                     Lung squamous cell carcinoma
19  MESO                                                     Mesothelioma
20    OV                                Ovarian serous cystadenocarcinoma
21  PAAD                                        Pancreatic adenocarcinoma
22  PCPG                               Pheochromocytoma and Paraganglioma
23  PRAD                                          Prostate adenocarcinoma
24  READ                                            Rectum adenocarcinoma
25  SARC                                                          Sarcoma
26  SKCM                                          Skin Cutaneous Melanoma
27  STAD                                           Stomach adenocarcinoma
28  TGCT                                      Testicular Germ Cell Tumors
29  THCA                                                Thyroid carcinoma
30  THYM                                                          Thymoma
31  UCEC                             Uterine Corpus Endometrial Carcinoma
32   UCS                                           Uterine Carcinosarcoma
33   UVM                                                   Uveal Melanoma

本包中定义的用于回答上述查询的工具可以直接使用 biocTcgaMcp::list_cancer_types() 运行，它会返回一个包含 33 行的数据框。

💡 非 MCP 查询结果示例

> ch = chat_openai(model="gpt-4o")
> ch$chat("What are the tumor types studied in TCGA?")
The Cancer Genome Atlas (TCGA) was a large-scale project aimed at cataloging genetic mutations responsible for 
different types of cancer using genome sequencing and bioinformatics. TCGA studied a wide variety of tumor types, 
including but not limited to:

1. **Breast Invasive Carcinoma (BRCA)**
2. **Lung Adenocarcinoma (LUAD)**
3. **Lung Squamous Cell Carcinoma (LUSC)**
4. **Prostate Adenocarcinoma (PRAD)**
5. **Kidney Renal Clear Cell Carcinoma (KIRC)**
6. **Thyroid Carcinoma (THCA)**
7. **Stomach Adenocarcinoma (STAD)**
8. **Liver Hepatocellular Carcinoma (LIHC)**
9. **Colorectal Adenocarcinoma (COADREAD)**
10. **Brain Lower Grade Glioma (LGG)**
11. **Glioblastoma Multiforme (GBM)**
12. **Ovarian Serous Cystadenocarcinoma (OV)**
13. **Pancreatic Adenocarcinoma (PAAD)**
14. **Bladder Urothelial Carcinoma (BLCA)**
15. **Head and Neck Squamous Cell Carcinoma (HNSC)**
16. **Uterine Corpus Endometrial Carcinoma (UCEC)**
17. **Skin Cutaneous Melanoma (SKCM)**
18. **Esophageal Carcinoma (ESCA)**
19. **Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC)**
20. **Acute Myeloid Leukemia (LAML)**
21. **Kidney Renal Papillary Cell Carcinoma (KIRP)**
22. **Kidney Chromophobe (KICH)**
23. **Uveal Melanoma (UVM)**
24. **Mesothelioma (MESO)**
25. **Pheochromocytoma and Paraganglioma (PCPG)**
26. **Thymoma (THYM)**
27. **Adrenocortical Carcinoma (ACC)**
28. **Cholangiocarcinoma (CHOL)**

These tumor types were selected for their prevalence and mortality rates, as well as their scientific and clinical 
importance. The data collected from TCGA has been crucial in advancing the understanding of the genomic underpinnings 
of cancer.

这个结果不太令人满意，因为我们知道 TCGA 中有 33 种肿瘤类型。

本包的目的是优化工具定义和提示设计，降低出错的风险。