{"title_zh":"SciOmni MCP 服务目录","title_en":"SciOmni MCP Service Directory","description_zh":"SciOmni 提供的远程 Model Context Protocol 服务目录。","description_en":"Directory of remote Model Context Protocol services provided by SciOmni.","documentation":["/marrvel/info","/vep/info","/clinvar/info","/monarch/info","/gnomad/info","/opentargets/info","/pubmed/info","/uniprot/info","/pharmgkb/info","/ensembl/info","/ncbi-datasets/info","/reactome/info","/string/info","/materials-project/info","/matlab/info"],"health":"/health","services":[{"id":"marrvel","name":"MARRVEL-MCP","endpoint":"https://mcp.sciomni.ai/marrvel","transport":"MCP Streamable HTTP","description_zh":"面向孟德尔遗传病与罕见病研究的 MCP 服务。它帮助 AI 助手查询和整合基因、变异、疾病表型、模式生物同源基因、组织表达、药物靶点及生物医学文献证据。","description_en":"An MCP service for Mendelian and rare-disease research. It enables AI assistants to query and synthesize evidence about genes, variants, disease phenotypes, model-organism orthologs, tissue expression, drug targets, and biomedical literature.","paper":{"title":"MARRVEL-MCP: An agentic interface for Mendelian disease discovery via tool-augmented context engineering","journal":"The American Journal of Human Genetics","online_date":"2026-05-21","issue_date":"2026-06-04","doi":"10.1016/j.ajhg.2026.04.012","doi_url":"https://doi.org/10.1016/j.ajhg.2026.04.012","pubmed_url":"https://pubmed.ncbi.nlm.nih.gov/42167217/"},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠，以停止空闲容器计算并降低成本。访问服务目录、说明接口或 /health 不会启动 Container。休眠后的首次 MCP 请求需要等待冷启动，实测约10秒。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to stop idle container compute and reduce cost. Viewing the directory, documentation, or /health does not start the Container. The first MCP request after sleep incurs a cold start, measured at about 10 seconds."}},{"id":"vep","name":"SciOmni-VEP-MCP","endpoint":"https://mcp.sciomni.ai/vep","transport":"MCP Streamable HTTP","description_zh":"面向Sentieon Engineer Agent三级分析的变异功能注释服务，支持GRCh38和GRCh37上的坐标/等位基因、VCF样式变异、HGVS和rsID注释。该MCP适配层由SciOmni自建和维护，底层 VEP REST 接口与注释数据由 Ensembl 维护。","description_en":"Variant-effect annotation service for tertiary analysis by the Sentieon Engineer Agent. It supports coordinate/allele, VCF-like, HGVS, and rsID inputs on GRCh38 and GRCh37. The MCP adapter is built and maintained by SciOmni. The underlying VEP REST API and annotation data are maintained by Ensembl.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层VEP REST接口、注释数据及发布周期由Ensembl维护。本服务不是Ensembl官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. Ensembl maintains the underlying VEP REST API, annotation data, and release lifecycle. This is not an official Ensembl MCP server.","mcp_adapter":"SciOmni","vep_rest_and_annotation_data":"Ensembl","official_ensembl_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/vep/info或/health不会启动VEP Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /vep/info, or /health does not start the VEP Container; the first request after sleep incurs a cold-start delay."}},{"id":"clinvar","name":"SciOmni-ClinVar-MCP","endpoint":"https://mcp.sciomni.ai/clinvar","transport":"MCP Streamable HTTP","description_zh":"面向Sentieon Engineer Agent三级分析的ClinVar变异临床意义检索服务，支持自由文本、基因、HGVS、疾病、VCV/RCV/SCV和rsID查询。该MCP适配层由SciOmni自建和维护，底层 ClinVar 数据与 NCBI/NLM API 由 NCBI/NLM 维护。","description_en":"ClinVar interpretation-evidence service for tertiary analysis by the Sentieon Engineer Agent. It supports free text, gene, HGVS, condition, VCV/RCV/SCV, and rsID queries. The MCP adapter is built and maintained by SciOmni. The underlying ClinVar data and NCBI/NLM APIs are maintained by NCBI/NLM.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层ClinVar数据、Clinical Tables与Variation Services API由NCBI/NLM维护。本服务不是NCBI官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. NCBI/NLM maintains the underlying ClinVar data, Clinical Tables, and Variation Services APIs. This is not an official NCBI MCP server.","mcp_adapter":"SciOmni","data_and_apis":"NCBI/NLM","official_ncbi_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/clinvar/info或/health不会启动ClinVar Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /clinvar/info, or /health does not start the ClinVar Container; the first request after sleep incurs a cold-start delay."}},{"id":"monarch","name":"SciOmni-HPO-Monarch-MCP","endpoint":"https://mcp.sciomni.ai/monarch","transport":"MCP Streamable HTTP","description_zh":"面向罕见病三级分析的HPO表型、疾病、基因与语义相似性服务。该MCP适配层由SciOmni自建和维护；Monarch Initiative 维护知识图谱与 API，HPO及其他上游资源由各自项目维护。","description_en":"HPO phenotype, disease, gene, and semantic-similarity service for rare-disease tertiary analysis. The MCP adapter is built and maintained by SciOmni. The Monarch Initiative maintains the knowledge graph and API; HPO and other upstream resources are maintained by their respective projects.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；Monarch Initiative维护知识图谱与API，HPO项目维护人类表型本体。Monarch实体接口返回5xx时，HP:术语详情回退到EMBL-EBI OLS；Monarch semsim返回5xx时，表型集合比较及疾病/基因排序回退到镜像内固定版本PyHPO 4.0.0，并明确标记来源、算法和非等价性。通用关联查询仍不回退。本服务不是Monarch官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. The Monarch Initiative maintains the knowledge graph and API, while the HPO project maintains the Human Phenotype Ontology. On Monarch entity API 5xx errors, HP: term details fall back to EMBL-EBI OLS. On Monarch semsim 5xx errors, phenotype-set comparison and disease/gene ranking fall back to pinned PyHPO 4.0.0 data in the image, with explicit provenance, algorithm, and non-equivalence markers. Generic association queries still have no fallback. This is not an official Monarch MCP server.","mcp_adapter":"SciOmni","knowledge_graph_and_api":"Monarch Initiative","hpo":"Human Phenotype Ontology project","official_monarch_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/monarch/info或/health不会启动Monarch Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /monarch/info, or /health does not start the Monarch Container; the first request after sleep incurs a cold-start delay."}},{"id":"gnomad","name":"SciOmni-gnomAD-MCP","endpoint":"https://mcp.sciomni.ai/gnomad","transport":"MCP Streamable HTTP","description_zh":"面向三级分析的人群频率、亚群频率、基因约束和覆盖度服务。","description_en":"Population frequency, ancestry frequency, gene constraint, and coverage service for tertiary analysis.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由gnomAD/Broad Institute维护。本服务不是gnomAD/Broad Institute官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. gnomAD/Broad Institute maintains the underlying data and APIs. This is not an official gnomAD/Broad Institute MCP server.","mcp_adapter":"SciOmni","data_and_api":"gnomAD/Broad Institute","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/gnomad/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /gnomad/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"opentargets","name":"SciOmni-Open-Targets-MCP","endpoint":"https://mcp.sciomni.ai/opentargets","transport":"MCP Streamable HTTP","description_zh":"基因-疾病、GWAS、药物和机制证据查询服务。","description_en":"Target-disease, GWAS, drug, and mechanism evidence service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由Open Targets维护。本服务不是Open Targets官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. Open Targets maintains the underlying data and APIs. This is not an official Open Targets MCP server.","mcp_adapter":"SciOmni","data_and_api":"Open Targets","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/opentargets/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /opentargets/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"pubmed","name":"SciOmni-PubMed-MCP","endpoint":"https://mcp.sciomni.ai/pubmed","transport":"MCP Streamable HTTP","description_zh":"PubMed检索、摘要、引用关系和PMC开放获取元数据服务。","description_en":"PubMed search, abstract, citation-link, and PMC open-access metadata service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由NCBI/NLM维护。本服务不是NCBI/NLM官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. NCBI/NLM maintains the underlying data and APIs. This is not an official NCBI/NLM MCP server.","mcp_adapter":"SciOmni","data_and_api":"NCBI/NLM","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/pubmed/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /pubmed/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"uniprot","name":"SciOmni-UniProt-MCP","endpoint":"https://mcp.sciomni.ai/uniprot","transport":"MCP Streamable HTTP","description_zh":"蛋白功能、结构域、序列特征、FASTA和UniRef服务。","description_en":"Protein function, domain, sequence-feature, FASTA, and UniRef service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由UniProt Consortium维护。本服务不是UniProt Consortium官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. UniProt Consortium maintains the underlying data and APIs. This is not an official UniProt Consortium MCP server.","mcp_adapter":"SciOmni","data_and_api":"UniProt Consortium","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/uniprot/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /uniprot/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"pharmgkb","name":"SciOmni-PharmGKB-MCP","endpoint":"https://mcp.sciomni.ai/pharmgkb","transport":"MCP Streamable HTTP","description_zh":"药物基因组学临床注释、剂量指南和药品标签服务，底层使用当前ClinPGx REST API。","description_en":"Pharmacogenomic clinical annotation, dosing-guideline, and drug-label service backed by the current ClinPGx REST API.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由PharmGKB维护。本服务不是PharmGKB官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. PharmGKB maintains the underlying data and APIs. This is not an official PharmGKB MCP server.","mcp_adapter":"SciOmni","data_and_api":"PharmGKB","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/pharmgkb/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /pharmgkb/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"ensembl","name":"SciOmni-Ensembl-MCP","endpoint":"https://mcp.sciomni.ai/ensembl","transport":"MCP Streamable HTTP","description_zh":"基因、转录本、变异标识符、基因组区域和交叉引用解析服务。","description_en":"Gene, transcript, variation identifier, genomic region, and cross-reference resolution service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由Ensembl维护。本服务不是Ensembl官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. Ensembl maintains the underlying data and APIs. This is not an official Ensembl MCP server.","mcp_adapter":"SciOmni","data_and_api":"Ensembl","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/ensembl/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /ensembl/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"ncbi-datasets","name":"SciOmni-NCBI-Datasets-MCP","endpoint":"https://mcp.sciomni.ai/ncbi-datasets","transport":"MCP Streamable HTTP","description_zh":"参考组装accession、版本、物种和taxonomy元数据服务。","description_en":"Reference assembly accession, version, organism, and taxonomy metadata service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由NCBI维护。本服务不是NCBI官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. NCBI maintains the underlying data and APIs. This is not an official NCBI MCP server.","mcp_adapter":"SciOmni","data_and_api":"NCBI","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/ncbi-datasets/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /ncbi-datasets/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"reactome","name":"SciOmni-Reactome-MCP","endpoint":"https://mcp.sciomni.ai/reactome","transport":"MCP Streamable HTTP","description_zh":"Reactome通路、事件、实体通路归属和事件参与者服务。","description_en":"Reactome pathway, event, entity-membership, and participant service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由Reactome维护。本服务不是Reactome官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. Reactome maintains the underlying data and APIs. This is not an official Reactome MCP server.","mcp_adapter":"SciOmni","data_and_api":"Reactome","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/reactome/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /reactome/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"string","name":"SciOmni-STRING-MCP","endpoint":"https://mcp.sciomni.ai/string","transport":"MCP Streamable HTTP","description_zh":"STRING蛋白互作、网络边和功能富集服务。","description_en":"STRING protein-interaction, network-edge, and functional-enrichment service.","maintenance":{"zh":"SciOmni负责MCP适配、Cloudflare部署和路由；底层数据与API由STRING Consortium维护。本服务不是STRING Consortium官方MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. STRING Consortium maintains the underlying data and APIs. This is not an official STRING Consortium MCP server.","mcp_adapter":"SciOmni","data_and_api":"STRING Consortium","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m","sleep_zh":"空闲 15 分钟后自动休眠以降低成本。访问服务目录、/string/info或/health不会启动Container；休眠后的首次请求会有冷启动延迟。","sleep_en":"Automatically sleeps after 15 minutes of inactivity to reduce cost. Viewing the directory, /string/info, or /health does not start the Container; the first request after sleep incurs a cold-start delay."}},{"id":"materials-project","name":"SciOmni-Materials-Project-MCP","endpoint":"https://mcp.sciomni.ai/materials-project","transport":"MCP Streamable HTTP","description_zh":"面向 Msagent 的 Materials Project 只读证据源，用于材料结构发现、既有标准化计算信息对比和计算前筛选，为后续计算分析提供支撑。","description_en":"Read-only Materials Project evidence for structure discovery, comparison with existing standardized computed properties, and pre-compute screening that supports later calculation and analysis.","maintenance":{"zh":"SciOmni 负责 MCP 适配、Cloudflare 部署和路由；Materials Project 维护上游数据库与 API。本服务不是 Materials Project 官方 MCP。","en":"SciOmni maintains the MCP adapter, Cloudflare deployment, and routing. Materials Project maintains the upstream database and API. This is not an official Materials Project MCP server.","mcp_adapter":"SciOmni","data_and_api":"Materials Project","official_upstream_mcp":false},"runtime":{"platform":"Cloudflare Containers","instance_type":"lite","max_instances":3,"load_balancing":"random shard routing","stateless_http":true,"sleep_after":"15m"}},{"id":"matlab","name":"SciOmni-MATLAB-MCP","endpoint":"https://mcp.sciomni.ai/matlab","transport":"MCP Streamable HTTP","description_zh":"面向 SciOmni 底层 worker/HPC 集群 MATLAB 运行时的受控远程 MCP 入口。Cloudflare 只承担私有网关、鉴权、路由和审计边界；实际 MATLAB 进程、工作目录和许可证均在 SciOmni worker 集群侧管理。","description_en":"A controlled remote MCP entrypoint for MATLAB runtimes on the SciOmni worker/HPC cluster. Cloudflare provides only the private gateway, authentication, routing, and audit boundary; MATLAB processes, working directories, and license use are managed by the SciOmni worker cluster.","maintenance":{"zh":"SciOmni 负责 Cloudflare MCP 网关、集群适配和路由；MathWorks 维护 MATLAB 与官方 matlab/matlab-mcp-server。本服务不是 MathWorks 官方托管 MCP，且不会在 Cloudflare Worker 内运行 MATLAB。","en":"SciOmni maintains the Cloudflare MCP gateway, cluster adapter, and routing. MathWorks maintains MATLAB and the official matlab/matlab-mcp-server. This is not an official MathWorks-hosted MCP service, and MATLAB does not run inside the Cloudflare Worker.","mcp_adapter":"SciOmni","matlab_runtime":"SciOmni worker/HPC cluster","upstream_reference":"https://github.com/matlab/matlab-mcp-server","official_mathworks_hosted_mcp":false},"runtime":{"platform":"Cloudflare Worker private proxy to SciOmni worker/HPC cluster","cloudflare_container":false,"backend_secret":"MATLAB_MCP_BACKEND_URL","backend_auth_secret":"MATLAB_MCP_BACKEND_TOKEN","client_auth_secret":"MATLAB_MCP_CLIENT_TOKEN","platform_adapter":"Enabled when SCIOMNI_API_KEY, MATLAB_MCP_PROJECT_ID, MATLAB_MCP_WORKER_ID, and MATLAB pipeline ids are configured.","state_model":"stateless gateway; cluster or SciOmni Pipeline owns MATLAB session lifecycle","timeout_owner":"cluster worker adapter","license_boundary":"Do not share one MATLAB MCP process across multiple users unless MathWorks licensing explicitly allows centralized/shared use."}}]}