生物TcgaMcp
目的：使用TCGA分析工具演示MCP服务器
安装了此软件包并在以下位置安装了合适的配置文件 ~/.config/mcptools/config.json 这包括
{
"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()"]
}
}
}然后
library(ellmer)
ch = chat_openai(model="gpt-4o")
ch$set_tools(mcptools::mcp_tools()) # need biocTcgaMcp 0.0.2 for improved type list tool
cc = type_array(type_object(codes = type_string(description = "TCGA tumor type codes"),
types = type_string(description = "TCGA tumor study names"))
ch$chat_structured("What tumor types are available in TCGA?", type=cc)应该返回一个data.frame。 chat_structured 不是必需的，但会创造 呼叫R会话中的值。
> ch$chat_structured("What tumor types are available in TCGA?", type=cc)
codes types
1 ACC Adrenocortical carcinoma
2 BLCA Bladder Urothelial Carcinoma
3 BRCA Breast invasive carcinoma
4 CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
5 CHOL Cholangiocarcinoma
6 COAD Colon adenocarcinoma
7 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
8 ESCA Esophageal carcinoma
9 GBM Glioblastoma multiforme
10 HNSC Head and Neck squamous cell carcinoma
11 KICH Kidney Chromophobe
12 KIRC Kidney renal clear cell carcinoma
13 KIRP Kidney renal papillary cell carcinoma
14 LAML Acute Myeloid Leukemia
15 LGG Brain Lower Grade Glioma
16 LIHC Liver hepatocellular carcinoma
17 LUAD Lung adenocarcinoma
18 LUSC Lung squamous cell carcinoma
19 MESO Mesothelioma
20 OV Ovarian serous cystadenocarcinoma
21 PAAD Pancreatic adenocarcinoma
22 PCPG Pheochromocytoma and Paraganglioma
23 PRAD Prostate adenocarcinoma
24 READ Rectum adenocarcinoma
25 SARC Sarcoma
26 SKCM Skin Cutaneous Melanoma
27 STAD Stomach adenocarcinoma
28 TGCT Testicular Germ Cell Tumors
29 THCA Thyroid carcinoma
30 THYM Thymoma
31 UCEC Uterine Corpus Endometrial Carcinoma
32 UCS Uterine Carcinosarcoma
33 UVM Uveal Melanoma此包中定义的用于回答上述查询的工具可以 直接运行 biocTcgaMcp::list_cancer_types() 并返回一个data.frame 33排。
非MCP查询结果：
> ch = chat_openai(model="gpt-4o")
> ch$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.这并不太令人满意，因为我们知道有33种肿瘤类型。
此软件包的目的是完善工具定义和提示设计，以便我们 出错的风险很低。