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科研 MCP

公开生物与化学检索是进程内的原生 catalog（mcp_bio），不是 Python MCP 子进程，也不再附带 ketcher。默认 23 个连接器、247 个工具，覆盖约 80 个上游数据库。Agent 用 search_mcp_tools 发现、use_mcp_tool 调用。

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[ 001 ] How it works

进程内 catalog

桌面、CLI 与 ACP bridge 共用 crates/wisp-bio。默认 mcp_bio 挂全部已实现域；WISP_MCP_PKG=mcp_pubmed 可只挂一个域。

先发现，再调用

完整 schema 不会塞进每一轮提示词。说清数据库或目标即可，不要猜工具名。连接改动对新会话或空闲 Agent 重建生效。

自定义 MCP

设置 → 连接 → Add connection 可加本地命令或远程 URL（含 OAuth）。与这份原生 catalog 分开，密钥只进操作系统钥匙串。

KEGG / CADD / PanglaoDB / Sanger Cell Model Passports 带有学术或快照使用说明。ZINC SmallWorld 是公开 ZINC20 在售索引。PubMed 的开放获取标志不是再利用授权。结果几乎都是有界页，不是全库导出。

[ 002 ] 23 connectors

连接器一览

连接器	包名	工具	上游
BioMartBioMart	`mcp_biomart`	8	Ensembl BioMart, Ensembl usage terms
bioRxivbioRxiv	`mcp_biorxiv`	7	bioRxiv / medRxiv API
癌症模型Cancer Models	`mcp_cancer_models`	11	cBioPortal, Sanger Cell Model Passports
CellGuideCellGuide	`mcp_cellguide`	5	CZ CELLxGENE CellGuide
ChEMBLChEMBL	`mcp_chembl`	6	ChEMBL web services
化学Chemistry	`mcp_chemistry`	12	PubChem, ChEBI, Rhea, BindingDB
临床基因组学Clinical Genomics	`mcp_clinical_genomics`	20	CIViC, ClinGen, Open Targets
临床试验Clinical Trials	`mcp_clinical_trials`	6	ClinicalTrials.gov API
药品监管Drug Regulatory	`mcp_drug_regulatory`	7	openFDA Drugs@FDA, openFDA drug labels
表达Expression	`mcp_expression`	15	GTEx, PanglaoDB
基因与本体Genes Ontologies	`mcp_genes_ontologies`	10	MyGene.info, UniProt, OLS, QuickGO, Reactome, KEGG API and usage conditions
基因组Genomes	`mcp_genomes`	11	Ensembl REST, UCSC Genome Browser API
人类遗传学Human Genetics	`mcp_human_genetics`	14	GWAS Catalog, eQTL Catalogue, PheWeb
文献Literature	`mcp_literature`	9	OpenAlex, arXiv API, arXiv API usage terms
组学归档Omics Archives	`mcp_omics_archives`	17	NCBI GEO, ArrayExpress, MetaboLights, MGnify, PRIDE
蛋白注释Protein Annotation	`mcp_protein_annotation`	13	InterPro, Human Protein Atlas, STRING
PubMedPubMed	`mcp_pubmed`	7	PubMed, NCBI E-utilities, Europe PMC
调控Regulation	`mcp_regulation`	16	ENCODE, JASPAR, UniBind
研究资源Research Resources	`mcp_research_resources`	5	Antibody Registry, Grants.gov API
RNARNA	`mcp_rna`	9	Rfam API
结构与相互作用Structures Interactions	`mcp_structures_interactions`	16	RCSB PDB, AlphaFold DB, EMDB, Complex Portal, IntAct
变异Variants	`mcp_variants`	18	CADD API and usage conditions, gnomAD, ClinVar, dbSNP
ZINCZINC	`mcp_zinc`	5	ZINC / CartBlanche22, SmallWorld API

[ 003 ] mcp_biomart · 8

BioMartBioMart

通过 Ensembl BioMart 查询基因组注释、转换标识符并查找交叉引用。可先浏览数据库、物种数据集、属性和筛选条件，再获取查询结果。

Query Ensembl BioMart for genomic annotations, identifier translation and cross-references. Discover marts, species datasets, attributes and filters before retrieving a bounded result table.

Ensembl BioMart · Ensembl usage terms

工具	做什么
`list_marts`	列出 Ensembl BioMart 的 mart 数据库List Ensembl BioMart marts.
`list_datasets`	列出某个 mart 下的物种/数据集List datasets in one Ensembl BioMart mart.
`list_common_attributes`	列出数据集 Features 页上的常用属性List attributes on the Ensembl Genes Features page (attribute page feature_page) for a dataset.
`list_all_attributes`	列出数据集的全部 BioMart 属性（含同源、芯片页）List every BioMart attribute for a dataset.
`list_filters`	列出数据集可用的筛选条件List BioMart filters for a dataset.
`get_data`	按属性与筛选条件查询有界 TSV 结果表Query Ensembl BioMart for a bounded TSV table.
`get_translation`	在两个 BioMart 属性之间翻译单个标识符Translate one identifier between BioMart attributes (for example hgnc_symbol → ensembl_gene_id) by querying the dataset with an ID-list filter, not a full-ta…
`batch_translate`	一次把最多 200 个标识符在两个属性之间翻译Translate up to 200 identifiers between BioMart attributes in one ID-list query (from_attr must be a filter).

[ 004 ] mcp_biorxiv · 7

bioRxivbioRxiv

检索 bioRxiv、medRxiv 预印本，查看稿件版本与正式发表链接，并获取学科、资助方和使用统计。

Find bioRxiv and medRxiv preprints, inspect manuscript versions and publication links, and retrieve category, funder and usage summaries.

bioRxiv / medRxiv API

工具	做什么
`get_categories`	列出 bioRxiv Content API 接受的 27 个学科分类List the 27 bioRxiv subject categories accepted as the Content API category query parameter.
`get_content_statistics`	获取 bioRxiv 平台新稿与修订预印本计数Retrieve platform-wide bioRxiv new and revised preprint counts from the Content API summary endpoint.
`get_preprint`	按 DOI 取一篇 bioRxiv/medRxiv 预印本的全部版本Retrieve every version of one bioRxiv or medRxiv preprint by DOI from the Content API.
`get_usage_statistics`	获取摘要浏览、全文浏览和 PDF 下载次数Retrieve abstract-view, full-text-view and PDF-download counts from the Content API usage endpoint.
`search_by_funder`	按资助方 ROR 标识分页浏览预印本Page through preprints that declare a funder ROR identifier.
`search_preprints`	分页浏览 bioRxiv/medRxiv 预印本元数据（无关键词检索）Page through bioRxiv or medRxiv preprint metadata.
`search_published_preprints`	分页浏览预印本到期刊的发表链接Page through preprint-to-journal links from the Content API pubs endpoint, or from the bioRxiv-only publisher prefix endpoint.

[ 005 ] mcp_cancer_models · 11

癌症模型Cancer Models

浏览 cBioPortal 癌症研究、分子谱、样本和临床数据，以及 Sanger Cell Model Passports 中的癌症模型。

Explore cBioPortal cancer studies, molecular profiles, samples and clinical data, alongside Sanger Cell Model Passports for cancer models.

cBioPortal · Sanger Cell Model Passports

工具	做什么
`cbioportal_clinical_attributes`	列出某项 cBioPortal 研究的临床属性Catalogue clinical attributes for one cBioPortal study (patient- or sample-level; STRING or NUMBER).
`cbioportal_cna_in_gene`	取某基因在一项研究中的离散拷贝数（GISTIC −2..2）Discrete copy-number calls (GISTIC-style −2..2) for one gene in one cBioPortal study.
`cbioportal_get_study`	按 studyId 取一项 cBioPortal 研究的引用、平台样本数和分子谱Retrieve one cBioPortal study by studyId: citation, platform sample counts, and molecular profiles.
`cbioportal_list_studies`	列出公开的 cBioPortal 癌症基因组学研究List public cBioPortal cancer genomics studies.
`cbioportal_mutation_frequency`	比较 1–12 项研究中某基因的突变样本比例Compare the fraction of sequenced samples with at least one mutation in a gene across 1–12 cBioPortal studies.
`cbioportal_mutations_in_gene`	列出某基因在一项研究中的体细胞突变List somatic mutations for one HUGO symbol or Entrez gene ID in one cBioPortal study.
`gene_dependencies`	按 CMP 基因符号取 CRISPR 敲除依赖分数CRISPR knock-out dependency scores for one official CMP gene symbol.
`get_model`	按 SIDM 或精确名称取一个 Sanger Cell Model Passports 模型Retrieve one Sanger Cell Model Passports model by SIDM id (case-insensitive prefix) or exact name/synonym.
`list_models`	列出 Sanger Cell Model Passports 模型（可按组织/癌种过滤）List Sanger Cell Model Passports models (SIDM ids).
`search_genes`	按官方 CMP 符号搜索 Sanger 基因Search Sanger Cell Model Passports genes by official CMP symbol (GET /genes).
`search_models`	按关键词搜索 Sanger 细胞模型Search Sanger Cell Model Passports models.

[ 006 ] mcp_cellguide · 5

CellGuideCellGuide

基于 CZ CELLxGENE CellGuide 的图谱快照，浏览细胞类型、标记基因及其组织背景。

Explore CZ CELLxGENE CellGuide cell types, marker genes and tissue context from its published atlas snapshots.

CZ CELLxGENE CellGuide

工具	做什么
`search_cell_types`	在 CellGuide 快照中搜索细胞类型Search CZ CELLxGENE CellGuide cell types in the current snapshot's celltype_metadata.json.
`get_cell_type_info`	取一个细胞类型的 Cell Ontology 元数据与叙事Retrieve Cell Ontology metadata and the CellGuide narrative for one cell type.
`get_marker_genes`	列出某细胞类型的标记基因List marker genes for a CellGuide cell type from the current snapshot.
`get_source_data`	列出贡献该细胞类型的 CELLxGENE 数据集List CZ CELLxGENE Discover collections that contribute cells of this type in the CellGuide snapshot (source_collections/).
`get_cell_tissues`	列出该细胞类型出现的 UBERON 组织List UBERON tissues in which a cell type appears in the human (NCBITaxon:9606) CellGuide ontology tree: ontology_tree/NCBITaxon_9606/celltype_to_tissue_mappi…

[ 007 ] mcp_chembl · 6

ChEMBLChEMBL

搜索 ChEMBL 分子，查询化合物性质、靶点、实验、活性数据和药物作用机制。

Search ChEMBL molecules and retrieve compound properties, targets, assays, bioactivities and drug mechanisms.

ChEMBL web services

工具	做什么
`compound_search`	按名称、标识符或 SMILES 搜索 ChEMBL 分子Search ChEMBL molecules by name or synonym, molecule identifier, or SMILES.
`drug_search`	按疾病 EFO/MeSH 查找关联的 ChEMBL 药物Find ChEMBL parent drugs linked to a disease indication through EFO term or MeSH heading.
`get_admet`	取一个分子的计算性质（分子量、ALogP、QED 等）Retrieve ChEMBL calculated molecule properties for one molecule identifier: molecular weight, ALogP, polar surface area, hydrogen-bond counts, rotatable bond…
`get_bioactivity`	取分子和/或靶点的有界活性记录页Retrieve a bounded page of ChEMBL activity records for a molecule and/or target identifier.
`get_mechanism`	取分子和/或靶点的作用机制记录Retrieve curated ChEMBL mechanism-of-action records for a molecule and/or target identifier.
`target_search`	按标识符、名称、基因符号、物种或类型搜索靶点Search ChEMBL targets by identifier, preferred name, gene symbol, organism or target type.

[ 008 ] mcp_chemistry · 12

化学Chemistry

从 PubChem、ChEBI、Rhea 和 BindingDB 查询化学标识符、结构、性质、本体条目、生化反应及结合测量数据。

Retrieve chemical identifiers, structures, properties, ontology entries, biochemical reactions and binding measurements from PubChem, ChEBI, Rhea and BindingDB.

PubChem · ChEBI · Rhea · BindingDB

工具	做什么
`pubchem_search_compounds`	按名称、SMILES、InChIKey 或 CID 解析 PubChem 化合物Resolve a chemical name, SMILES, InChIKey or CID to PubChem compound IDs with PUG REST.
`pubchem_get_compounds`	取最多 50 个 CID 的计算性质Retrieve computed PubChem properties for up to 50 CIDs.
`pubchem_similarity_search`	按 SMILES 做同步 2D Tanimoto 相似搜索Synchronous 2D Tanimoto similarity search over PubChem (`fastsimilarity_2d`).
`pubchem_get_bioassay_summary`	取一个 CID 的生物测定活性摘要Bioassay activity summary for one PubChem CID: assay IDs, outcomes, targets and potency when PubChem supplies them.
`pubchem_get_safety`	取一个 CID 的 GHS 分类（信号、象形图、危害声明）GHS classification for one PubChem CID from PUG-View, aggregated across SDS sources (signals, pictograms, hazard statements, precautionary codes).
`chebi_search`	按名称、同义词、分子式或 InChIKey 搜索 ChEBIFull-text search of ChEBI entities (names, synonyms, formulae, InChIKeys) via the public backend.
`chebi_get_entity`	取完整 ChEBI 实体（结构、化学数据、角色、交叉引用）Full ChEBI entity: structure, chemical data, roles and cross-references.
`chebi_get_ontology`	取一个实体的出入本体关系Outgoing and incoming ChEBI ontology relations for one entity (is a, has role, conjugate acid/base, functional parent, tautomer, enantiomer, and others).
`rhea_search_reactions`	通过 SPARQL 搜索 Rhea 主反应Search Rhea master reactions through the public SPARQL endpoint.
`rhea_get_reaction`	取一个 Rhea 反应的方程式、EC、引用和底物One Rhea reaction: equation, status, transport/balance flags, EC numbers, PubMed citations, directional family IDs, and left/right participants with ChEBI ac…
`bindingdb_ligands_by_target`	取一个 UniProt 靶点的 BindingDB 亲和力配体Measured BindingDB affinities (Ki/Kd/IC50/EC50) for ligands of one UniProt target.
`bindingdb_targets_by_compound`	按查询 SMILES 的 2D 相似化合物找 BindingDB 靶点Protein targets with measured BindingDB affinities for compounds 2D-similar to a query SMILES.

[ 009 ] mcp_clinical_genomics · 20

临床基因组学Clinical Genomics

查询 CIViC 变异证据、ClinGen 基因与疾病及剂量敏感性评估，以及 Open Targets 靶点与疾病关联。

Retrieve CIViC variant evidence, ClinGen gene-disease and dosage assessments, and Open Targets target-disease associations.

CIViC · ClinGen · Open Targets

工具	做什么
`civic_gene_variants`	按 CIViC 基因 id 列出该基因的变异List CIViC variants for one gene by internal CIViC gene id via GraphQL variants(geneId).
`civic_get_assertion`	取一条 CIViC assertion（分级、疾病、疗法、分子谱）Retrieve one CIViC assertion by internal id: AMP/ASCO/CAP tier, significance, disease, therapies and linked molecular profile.
`civic_get_evidence_item`	取一条 CIViC 证据项（级别、类型、方向、引用）Retrieve one CIViC evidence item by internal id: evidence level A–E, type, direction, significance, disease, therapies, molecular profile and citation.
`civic_get_molecular_profile`	取一个分子谱及其组成变异 idRetrieve one CIViC molecular profile by internal id, including parsed name and component variant ids.
`civic_get_variant`	取一个 CIViC 变异（别名、类型、基因关联）Retrieve one CIViC variant by internal id, including aliases, variant types and gene/feature linkage.
`civic_search_assertions`	搜索 CIViC assertionsSearch CIViC assertions through the GraphQL assertions connection.
`civic_search_diseases`	按名称子串搜索 CIViC 疾病Search CIViC disease records by name substring through GraphQL diseases(name).
`civic_search_evidence`	搜索 CIViC 证据项Search CIViC evidence items through the GraphQL evidenceItems connection.
`civic_search_genes`	按精确 Entrez 符号查找 CIViC 基因Find CIViC gene records by exact Entrez symbol through GraphQL genes(entrezSymbols).
`civic_search_molecular_profiles`	按名称子串搜索分子谱Search CIViC molecular profiles by name substring through GraphQL molecularProfiles(name).
`civic_search_therapies`	按名称子串搜索疗法Search CIViC therapy records by name substring through GraphQL therapies(name).
`civic_search_variants`	按名称子串搜索变异（可限定基因）Search CIViC variants by name substring through GraphQL variants(name), optionally scoped to a CIViC gene id.
`clingen_actionability`	取 ClinGen 成人/儿科临床可操作性摘要ClinGen clinical actionability summaries from the Adult and Pediatric JSON APIs (flavor=flat).
`clingen_dosage_sensitivity`	取 ClinGen 剂量敏感性（单倍不足/三倍敏感）ClinGen dosage sensitivity curations (haploinsufficiency and triplosensitivity) from search.clinicalgenome.org/api/dosage.
`clingen_gene_validity`	取 ClinGen 基因–疾病有效性分级ClinGen gene-disease validity classifications from search.clinicalgenome.org/api/validity (Definitive, Strong, Moderate, Limited, Disputed, Refuted, No Known…
`clingen_variant_classifications`	取 ClinGen VCEP 变异致病性分类ClinGen Evidence Repository VCEP variant pathogenicity classifications.
`open_targets_disease_drugs`	取某疾病的已知与在研药物Known and investigational drugs for a disease from the Open Targets Platform GraphQL API (Disease.drugAndClinicalCandidates).
`open_targets_disease_targets`	按综合关联分列出疾病的顶级靶点Top associated targets for a disease ranked by Open Targets overall association score (Disease.associatedTargets, page index 0).
`open_targets_drug`	按 ChEMBL id 取药物注释与最高临床阶段Drug annotation from the Open Targets Platform by ChEMBL identifier (drug(chemblId)), including drug type, maximum clinical stage and mechanisms of action.
`open_targets_graphql`	向 Open Targets Platform 发送只读 GraphQL 查询POST a read-only GraphQL query to the Open Targets Platform API (https://api.platform.opentargets.org/api/v4/graphql).

[ 010 ] mcp_clinical_trials · 6

临床试验Clinical Trials

检索 ClinicalTrials.gov 临床研究，查看入组条件、干预措施、结局指标、申办方与研究状态。

Search ClinicalTrials.gov studies and inspect trial eligibility, interventions, outcomes, sponsors and study status.

ClinicalTrials.gov API

工具	做什么
`search_trials`	按病况、干预、申办方、地点、分期或状态检索 ClinicalTrials.govSearch ClinicalTrials.gov (API v2) for registered studies.
`get_trial_details`	按 NCT ID 取一项研究的方案、入组、终点和状态Retrieve one ClinicalTrials.gov study by NCT ID.
`search_by_eligibility`	按患者画像匹配入组条件Find ClinicalTrials.gov studies whose eligibility constraints match a patient profile.
`search_by_sponsor`	按主要申办方名称检索研究Find ClinicalTrials.gov studies by lead sponsor name (query.lead / LeadSponsorName).
`search_investigators`	列出匹配的研究者与中心联系人List investigators and site contacts from ClinicalTrials.gov studies matching an investigator name, institution, location, condition or status.
`analyze_endpoints`	汇总方案结局指标（单研究或一批 NCT）Summarize protocol outcome measures from ClinicalTrials.gov.

[ 011 ] mcp_drug_regulatory · 7

药品监管Drug Regulatory

检索 openFDA 药品申请和说明书，筛选监管记录并汇总指定申请字段。

Search openFDA drug applications and labeling, filter regulatory records, and summarize selected application fields.

openFDA Drugs@FDA · openFDA drug labels

工具	做什么
`count_drug_applications`	按申办方、剂型、给药途径、上市状态等计 Drugs@FDA 申请数Count Drugs@FDA applications by one field (sponsor, dosage form, route, marketing status, TE code, or pharmacologic class).
`get_drug_application`	按 NDA/ANDA/BLA 号取一份申请Fetch one Drugs@FDA application by NDA, ANDA, or BLA number (prefix plus six digits).
`get_drug_statistics`	Drugs@FDA 语料快照：总数、更新日期、状态与热门剂型Corpus snapshot of Drugs@FDA: application total, last_updated, marketing-status counts, and the top dosage forms, routes, and sponsors.
`get_generic_equivalents`	按品牌药活性成分集合找仿制药申请Find Drugs@FDA applications whose product active-ingredient set matches a brand-name reference.
`list_pharmacologic_classes`	列出 Drugs@FDA 中的药理学分类及申请数List pharmacologic classes attached to Drugs@FDA records, with application counts.
`search_drug_applications`	按商品名、通用名、成分、申办方等搜索 Drugs@FDASearch FDA Drugs@FDA applications (NDA/ANDA/BLA) by brand, generic name, active ingredient, sponsor, marketing status, dosage form, route, pharmacologic clas…
`search_drug_labels`	搜索 FDA 结构化产品说明书（SPL）Search FDA Structured Product Labels via openFDA /drug/label.json by substance, generic or brand name, route, or product type (HUMAN PRESCRIPTION DRUG / HUMA…

[ 012 ] mcp_expression · 15

表达Expression

查询 GTEx 组织表达和 eQTL 关联，以及 PanglaoDB 已发布快照中的细胞标记基因。

Explore GTEx tissue expression and eQTL associations, and query the published PanglaoDB marker-gene snapshot.

GTEx · PanglaoDB

工具	做什么
`gtex_calculate_eqtl`	在指定组织中计算一对基因–变异的 eQTL（含不显著结果）Calculate a gene–variant eQTL in one GTEx tissue with GET /association/dyneqtl.
`gtex_dataset_info`	列出 GTEx 数据集版本（GENCODE、基因组、dbSNP、样本数）List GTEx dataset releases.
`gtex_eqtl_genes`	列出某组织中至少有一个显著 cis-eQTL 的基因List eGenes (genes with at least one significant cis-eQTL) for a tissue.
`gtex_expression_summary`	汇总一个基因在各 GTEx 组织中的表达Profile one gene across GTEx tissues: resolve a symbol or Ensembl ID to the pinned dataset's versioned GENCODE ID (GET /reference/gene), then rank tissues by…
`gtex_gene_expression`	取样本级（非中位）标准化表达Sample-level (not median) normalized expression.
`gtex_median_expression`	取基因 × 组织的中位 TPMMedian gene expression (TPM) for genes × tissues.
`gtex_multi_tissue_eqtls`	取 METASOFT 多组织 eQTL 元分析METASOFT multi-tissue eQTL meta-analysis.
`gtex_resolve_genes`	把基因符号或 Ensembl ID 解析为带版本的 GENCODE IDResolve gene symbols or Ensembl IDs to versioned GENCODE IDs with GET /reference/gene.
`gtex_sample_info`	取 GTEx 分析样本与供体元数据GTEx analysis-sample and donor metadata.
`gtex_single_tissue_eqtls`	取预计算的显著单组织 eQTLPrecomputed significant single-tissue eQTLs.
`gtex_tissue_sites`	列出某数据集的组织位点（gtex_v8 约 54 个）List GTEx tissue site details for a pinned dataset.
`gtex_top_expressed_genes`	按中位 TPM 列出某组织表达最高的基因Top-n genes by median TPM in one tissue.
`panglaodb_cell_types_for_gene`	查某基因在 PanglaoDB 中作为标记的细胞类型Look up PanglaoDB cell types for which a gene is listed as a marker.
`panglaodb_marker_genes`	过滤 PanglaoDB 细胞类型标记表快照Filter the frozen PanglaoDB cell-type marker table.
`panglaodb_options`	枚举 PanglaoDB 标记表中可用于过滤的取值Enumerate distinct PanglaoDB marker-table values for use as panglaodb_marker_genes filters: species (verbatim, including dirty upstream tokens), organs (orga…

[ 013 ] mcp_genes_ontologies · 10

基因与本体Genes Ontologies

通过 MyGene.info、UniProt、OLS、QuickGO、Reactome 和 KEGG 解析基因与蛋白标识符，浏览生物本体、功能注释和通路。

Resolve gene and protein identifiers, browse biological ontologies and annotations, and query pathways with MyGene.info, UniProt, OLS, QuickGO, Reactome and KEGG.

MyGene.info · UniProt · OLS · QuickGO · Reactome · KEGG API and usage conditions

工具	做什么
`get_go_annotations`	按 UniProt 登录号取 QuickGO 基因本体注释（有界页）Retrieve Gene Ontology annotations for one UniProt accession from EMBL-EBI QuickGO (GET /services/annotation/search).
`get_kegg_entries`	按 KEGG 标识取基因、通路、化合物等条目（学术用途）Retrieve KEGG entries (genes, pathways, compounds and other databases).
`get_ontology_term`	按本体 id 与 CURIE/IRI 取 OLS4 术语Look up one OLS4 term by ontology id plus CURIE, short form or IRI (GET /api/ontologies/{id}/terms).
`get_uniprot_entries`	按最多 50 个登录号批量取 UniProtKB 记录Retrieve UniProtKB records for a batch of accessions through rest.uniprot.org search (one OR-query, at most 50 accessions).
`link_kegg_ids`	在 KEGG 数据库之间交叉引用或转换外部标识Cross-reference KEGG identifiers with GET /link/{target_db}/{ids} or convert outside identifiers with GET /conv/{target_db}/{ids} (https://www.kegg.jp/kegg/r…
`list_ontologies`	列出 OLS4 中的本体List ontologies in the EMBL-EBI Ontology Lookup Service (OLS4 GET /api/ontologies).
`map_reactome_pathways`	把基因符号或 UniProt 登录号映射到 Reactome 通路Map gene symbols or UniProt accessions to Reactome pathways via AnalysisService (POST /identifiers/ with a text/plain identifier list).
`query_genes`	通过 MyGene.info 批量解析基因符号或标识符Resolve gene symbols or identifiers through MyGene.info v3 batch query (POST /v3/query).
`search_kegg`	在 KEGG 标识与名称字段中做子串搜索（学术用途）Search KEGG identifier and name fields.
`search_ontology_terms`	搜索 OLS4 术语标签与同义词Search OLS4 term labels and synonyms (GET /api/search).

[ 014 ] mcp_genomes · 11

基因组Genomes

查询 Ensembl 基因组注释、同源关系、序列和变异，以及 UCSC 基因组组装和轨道。坐标规则取决于所选数据源。

Retrieve Ensembl genome annotations, homology, sequences and variants, and inspect UCSC genome assemblies and tracks. Coordinate conventions depend on the selected source.

Ensembl REST · UCSC Genome Browser API

工具	做什么
`ensembl_homology`	取一个基因的 Ensembl Compara 同源/旁系（无比对）Retrieve Ensembl Compara orthologues, paralogues or projections for one gene as condensed rows (no alignments).
`ensembl_lookup`	查找一个 Ensembl 基因、转录本或蛋白Look up one Ensembl gene, transcript or protein.
`ensembl_overlap_region`	列出与基因组区间重叠的 Ensembl 特征List Ensembl features overlapping a genomic region.
`ensembl_sequence`	从 Ensembl 取序列Fetch sequence from Ensembl.
`ensembl_vep_variant`	用 Ensembl VEP 预测变异后果Predict variant consequences with Ensembl VEP.
`ensembl_xrefs`	列出一个 Ensembl 稳定 ID 的外部交叉引用List external cross-references for one Ensembl stable ID.
`ucsc_chrom_sizes`	列出某 UCSC 组装的染色体/contig 名称与长度List chromosome and contig names with sizes for a UCSC assembly.
`ucsc_conservation`	汇总某 UCSC wiggle/bigWig 轨道的逐碱基保守性Summarise per-base conservation for a UCSC wiggle/bigWig track (default phyloP100way).
`ucsc_list_tracks`	列出某 UCSC 组装的叶轨道List leaf tracks for a UCSC assembly.
`ucsc_tfbs_clusters`	取与区间重叠的 ENCODE 转录因子结合位点簇ENCODE transcription-factor binding-site clusters overlapping a region.
`ucsc_track_data`	取任意 UCSC 轨道在某区间的原始行Fetch raw rows for any UCSC track in a region.

[ 015 ] mcp_human_genetics · 14

人类遗传学Human Genetics

查询 GWAS Catalog 关联、eQTL Catalogue 数据集及指定区域的汇总统计，以及公开 PheWeb 门户。

Find GWAS Catalog associations, inspect eQTL Catalogue datasets and bounded summary-statistic regions, and query public PheWeb portals.

GWAS Catalog · eQTL Catalogue · PheWeb

工具	做什么
`eqtl_associations`	用官方元数据与 tabix 字节范围读取 eQTL Catalogue 汇总统计Read eQTL Catalogue summary statistics using the official metadata and tabix-indexed HTTPS byte ranges; the retired REST API is not used.
`eqtl_list_datasets`	列出 eQTL Catalogue 数据集（研究 × 组织 × 定量方法）List datasets from the official eQTL Catalogue metadata (one study × tissue or cell type × quantification method), cached for the process lifetime.
`gwas_associations_for_gene`	列出映射到某 HGNC 基因的 GWAS Catalog 关联List NHGRI-EBI GWAS Catalog v2 associations whose variants map to one HGNC gene symbol (Ensembl mapping, including flanking genes for intergenic variants).
`gwas_associations_for_trait`	列出注释到某 EFO/MONDO/HP 性状的 GWAS 关联List NHGRI-EBI GWAS Catalog v2 associations annotated to one EFO/MONDO/HP trait.
`gwas_associations_for_variant`	列出某个 dbSNP rsID 的 GWAS 关联List NHGRI-EBI GWAS Catalog v2 associations for one dbSNP rsID.
`gwas_get_study`	按 GCST 登录号取一项 GWAS Catalog 研究Fetch one NHGRI-EBI GWAS Catalog v2 study by GCST accession.
`gwas_get_variant`	按 rsID 取 GWAS Catalog 变异记录（GRCh38）Fetch one NHGRI-EBI GWAS Catalog v2 variant record (GRCh38 location, mapped genes, consequence) by dbSNP rsID.
`gwas_search_studies`	按 EFO、性状标签或 PubMed id 搜索 GWAS 研究Search NHGRI-EBI GWAS Catalog v2 studies by EFO id, exact EFO trait label, and/or PubMed id (filters combine).
`gwas_search_traits`	按标签子串搜索 GWAS Catalog 性状Search NHGRI-EBI GWAS Catalog v2 EFO trait annotations by case-insensitive label substring.
`phewas_finngen_gene`	FinnGen R12 基因区 PheWAS（每个表型区内最显著变异）Gene-region PheWAS from the FinnGen R12 public PheWeb (GRCh38): for each disease endpoint, the best-associated variant in the padded gene region.
`phewas_instances`	列出本域可查询的公开 PheWeb 门户List the public PheWeb PheWAS portals this domain can query.
`phewas_list_phenotypes`	列出 PheWeb 实例发布的疾病终点（目前 FinnGen R12）List disease endpoints from a PheWeb instance that publishes /api/phenos (currently FinnGen R12).
`phewas_search_phenotypes`	按自由文本搜索 PheWeb 表型自动补全Search a PheWeb instance's phenotype autocomplete by free text (disease name, code, and on some instances gene or rsID).
`phewas_variant`	对一个变异做针对门户全部表型的 PheWASPheWAS for one variant against every phenotype in a public PheWeb portal, most-significant first.

[ 016 ] mcp_literature · 9

文献Literature

通过 OpenAlex 和 arXiv 检索学术文献，获取出版元数据和可用的访问链接。

Search scholarly works through OpenAlex and arXiv, and retrieve publication metadata and available access links.

OpenAlex · arXiv API · arXiv API usage terms

工具	做什么
`openalex_search_works`	按文本、年份、类型、期刊或开放获取状态搜索 OpenAlex 作品Search OpenAlex scholarly works by text, year, type, venue, or open-access status.
`openalex_get_work`	按 W-id、URL 或 DOI 取一篇 OpenAlex 作品Fetch one OpenAlex work by OpenAlex W-id, openalex.org URL, or DOI.
`openalex_get_author`	按 A-id、URL 或 ORCID 取作者主页（可选代表作）Fetch one OpenAlex author profile by A-id, openalex.org URL, or ORCID, optionally with a bounded sample of that author's most-cited works.
`openalex_search_authors`	按姓名搜索 OpenAlex 作者Search OpenAlex author profiles by name.
`openalex_citations`	列出引用某作品的文献（入边引用图）List works that cite a given OpenAlex work (incoming citation graph).
`openalex_references`	列出某作品引用的文献List the works a given OpenAlex work cites.
`openalex_venue_info`	按 S-id、ISSN、URL 或名称查找期刊/仓储Look up OpenAlex sources (journals, repositories, conferences) by S-id, ISSN, source URL, or name.
`arxiv_search`	通过官方 Atom API 搜索 arXiv 预印本Search arXiv preprints through the official Atom API.
`arxiv_get_papers`	按标识符批量取 arXiv 元数据与摘要Fetch arXiv paper metadata, including abstracts, for a batch of identifiers.

[ 017 ] mcp_omics_archives · 17

组学归档Omics Archives

在 GEO、ArrayExpress、MetaboLights、MGnify 和 PRIDE Archive 中查找实验、研究及数据文件引用。

Discover experiments, studies and file references in GEO, ArrayExpress, MetaboLights, MGnify and PRIDE Archive.

NCBI GEO · ArrayExpress · MetaboLights · MGnify · PRIDE

工具	做什么
`arrayexpress_get_experiment`	按登录号取一项 ArrayExpress/BioStudies 功能基因组实验Retrieve one ArrayExpress functional-genomics experiment from the EMBL-EBI BioStudies JSON API (GET /studies/{accession}).
`arrayexpress_get_experiment_files`	列出实验声明的文件及 FTP/HTTP 基址（不下载内容）List files declared on an ArrayExpress BioStudies submission (GET /studies/{accession}) together with the /info FTP and HTTP base links when present.
`arrayexpress_get_experiment_samples`	把 MAGE-TAB SDRF 解析为逐样本行Parse the MAGE-TAB SDRF of an ArrayExpress experiment into per-sample rows (characteristics, factor values, assay/data-file columns).
`arrayexpress_search_experiments`	通过 BioStudies 搜索 ArrayExpress 实验Search the ArrayExpress collection through BioStudies GET /arrayexpress/search.
`geo_get_series`	取 NCBI GEO 系列（GSE）元数据，含样本Fetch NCBI GEO series (GSE) metadata.
`geo_search_series`	搜索 GEO DataSets 并返回有界摘要页Search NCBI GEO DataSets (ESearch db=gds) and return a bounded ESummary page.
`metabolights_get_studies`	取公开 MetaboLights 研究（MTBLS）的 ISA 投影Fetch public MetaboLights studies (MTBLSnnn).
`metabolights_get_study_files`	列出公开 MetaboLights 研究的文件List files for a public MetaboLights study.
`metabolights_list_studies`	列出公开 MetaboLights 研究登录号List public MetaboLights study accessions.
`metabolights_search_data_files`	在研究的 FILES 树中搜索数据文件Search a public MetaboLights study's FILES tree.
`mgnify_get_studies`	取 MGnify 宏基因组研究（MGYS）Retrieve MGnify metagenomics studies (MGYSnnnnnnnn).
`mgnify_get_study_analyses`	列出一项 MGnify 研究的分析List analyses for one MGnify study.
`mgnify_search_studies`	搜索 MGnify 研究Search MGnify studies through API v2.
`pride_find_projects_for_protein`	按蛋白（多为 UniProt）查找 PRIDE 项目Find PRIDE Archive projects whose identifications include a protein (typically a UniProt accession).
`pride_get_projects`	按 PXD/PAD/PRD 取 PRIDE 项目元数据Fetch PRIDE Archive project metadata (PXD, PAD or PRD accessions).
`pride_search_project_proteins`	列出亲和蛋白质组项目中的蛋白证据行List protein evidence rows for one PRIDE affinity-proteomics project.
`pride_search_projects`	搜索 PRIDE Archive 蛋白质组项目Search PRIDE Archive proteomics projects.

[ 018 ] mcp_protein_annotation · 13

蛋白注释Protein Annotation

查询 InterPro/Pfam 蛋白结构域与特征、Human Protein Atlas 组织及细胞注释，以及 STRING 蛋白关联。

Inspect protein domains and signatures with InterPro/Pfam, tissue and cell annotations from the Human Protein Atlas, and STRING protein associations.

InterPro · Human Protein Atlas · STRING

工具	做什么
`get_domain_architecture`	取 UniProt 蛋白的 InterPro 结构域架构Retrieve InterPro domain architecture for UniProt proteins.
`get_interpro_entry`	取一个 InterPro 条目或 Pfam 家族Fetch one InterPro entry (IPRxxxxxx) or Pfam family (PFxxxxx).
`get_pfam_clan`	取一个 Pfam clan（InterPro set）Fetch a Pfam clan (InterPro set CLxxxx).
`get_pfam_family_proteins`	列出匹配某 Pfam 家族的 UniProt 蛋白List UniProt proteins matching a Pfam family.
`get_pfam_family_proteomes`	报告含某 Pfam 家族的 UniProt 蛋白质组Report UniProt proteomes that contain a Pfam family.
`get_protein_atlas_gene`	取 Human Protein Atlas 基因记录Retrieve a Human Protein Atlas gene record.
`get_string_best_similarity_hits`	把基因映射到 STRING 后取最佳 Smith–Waterman 命中Map gene symbols to STRING IDs then GET/POST /api/json/homology_best for the best Smith–Waterman hit of each protein in a target species.
`get_string_network`	取 STRING v12.0 互作网络Map gene symbols to STRING v12.0 identifiers then retrieve the interaction network.
`get_string_similarity_scores`	取基因之间的 Smith–Waterman bitscoreMap gene symbols then retrieve Smith–Waterman bitscores among them.
`map_string_ids`	把基因符号、同义词或 UniProt 登录号映射为 STRING IDMap gene symbols, synonyms or UniProt accessions to STRING v12.0 protein identifiers.
`search_interpro_entries`	按关键词搜索 InterPro 或成员数据库Keyword search of InterPro or a member database.
`search_pfam_clans`	按关键词搜索 Pfam clanKeyword search of Pfam clans (InterPro sets).
`search_protein_atlas`	按选定列搜索 Human Protein AtlasColumn-selected Human Protein Atlas search.

[ 019 ] mcp_pubmed · 7

PubMedPubMed

检索生物医学文献，获取 PubMed 记录和相关文章、转换文献标识符，并通过 NCBI 和 Europe PMC 查询可用的开放全文及访问元数据。

Search biomedical literature, retrieve PubMed records and related articles, convert identifiers, and access available open full text and access metadata through NCBI and Europe PMC.

PubMed · NCBI E-utilities · Europe PMC

工具	做什么
`search_articles`	用 Entrez 查询检索 PubMed，返回 PMID、总数和有界页Search PubMed with an Entrez query.
`get_article_metadata`	取最多 200 个 PMID 的题录、标识符和摘要（不是全文）Retrieve NCBI PubMed metadata for up to 200 PMIDs: citation summaries, article identifiers and abstracts when available.
`convert_article_ids`	用 PMC ID Converter 在 PMID / PMCID / DOI 之间转换Convert a same-type batch of PMID, PMCID or DOI identifiers with the NCBI PMC ID Converter.
`find_related_articles`	用 ELink 查找相关文献、PMC、基因、蛋白或核酸Find Entrez records linked to PubMed articles with NCBI ELink.
`lookup_article_by_citation`	用 ECitMatch 把书目引文匹配到 PMIDMatch bibliographic citations to PubMed IDs with NCBI ECitMatch.
`get_full_text_article`	从 Europe PMC 取开放获取全文 XML（最多 5 个 PMCID）Retrieve Open Access full-text XML from Europe PMC for PMC articles.
`get_copyright_status`	报告元数据、可访问全文和已声明许可（OA 标志不是再利用授权）Report metadata availability, accessible full text, and stated licenses for PubMed articles using Europe PMC core metadata and PMC ID Converter embargo fields.

[ 020 ] mcp_regulation · 16

调控Regulation

查找 ENCODE 实验与调控数据、JASPAR 转录因子基序，以及 UniBind 结合位点证据。

Find ENCODE experiments and regulatory data, JASPAR transcription-factor motifs, and UniBind binding-site evidence.

ENCODE · JASPAR · UniBind

工具	做什么
`encode_search_experiments`	按测定、靶点、生物样本等搜索 ENCODE 实验Search ENCODE functional-genomics experiments through the portal JSON search API.
`encode_search_biosamples`	搜索 ENCODE 生物样本（细胞系、组织、原代细胞）Search ENCODE biosamples (cell lines, tissues, primary cells) through the portal JSON search API.
`encode_list_files`	列出 ENCODE 数据文件（格式、输出类型、组装）List ENCODE data files through the portal JSON search API.
`encode_get_experiment`	按 ENCSR 登录号取一项实验Retrieve one ENCODE experiment by accession (ENCSR…).
`encode_get_file`	按 ENCFF 登录号取一个文件记录Retrieve one ENCODE file record by accession (ENCFF…).
`encode_get_biosample`	按 ENCBS 登录号取一个生物样本Retrieve one ENCODE biosample by accession (ENCBS…).
`jaspar_get_matrix`	按版本化矩阵 id 取 JASPAR 转录因子谱（含 PFM 与 logo）Retrieve one JASPAR transcription-factor profile by versioned matrix id (for example MA0002.2), including the position frequency matrix, species, collection…
`jaspar_matrix_versions`	列出某 JASPAR 基础矩阵 id 的已发布版本List released versions of a JASPAR base matrix id (for example MA0002).
`jaspar_list_matrices`	列出 JASPAR TF 结合谱（可按集合过滤）List JASPAR TF binding profiles.
`jaspar_list_species`	列出有 JASPAR 谱的物种List species that have JASPAR profiles (NCBI tax_id and scientific name).
`jaspar_list_taxa`	列出 JASPAR 分类群（脊椎、植物、昆虫等）List JASPAR taxonomic groups.
`jaspar_list_collections`	列出 JASPAR 集合（CORE 为非冗余精选集）List JASPAR collections.
`jaspar_list_releases`	列出 JASPAR 数据库发行版List JASPAR database releases.
`unibind_search_tfbs`	搜索带直接 TF–DNA 预测的 UniBind ChIP-seq 数据集Search UniBind ChIP-seq datasets with direct TF–DNA predictions.
`unibind_get_dataset`	按 tf_id 取一个 UniBind 数据集Retrieve one UniBind dataset by tf_id (identifier.cell_line.TF, as returned by unibind_search_tfbs).
`unibind_tfbs_in_region`	返回与基因组区间重叠的 UniBind 2021 结合位点Return UniBind 2021 TF binding sites overlapping a genomic interval via the UCSC Genome Browser hubApi (GET /getData/track) against UniBind's public Robust o…

[ 021 ] mcp_research_resources · 5

研究资源Research Resources

检索 Antibody Registry 的抗体记录与 RRID，并通过 Grants.gov 查找资助机会。

Search antibody records and RRIDs in the Antibody Registry, and discover funding opportunities through Grants.gov.

Antibody Registry · Grants.gov API

工具	做什么
`search_antibodies`	按名称、靶点、货号或克隆搜索 Antibody RegistrySearch the Antibody Registry (RRID:SCR_006397) by antibody name, target, catalog number or clone.
`get_antibody`	按登录号或 RRID 取抗体记录Retrieve Antibody Registry records for one accession or RRID (3643095, AB_3643095, or RRID:AB_3643095).
`find_antibodies_by_catalog`	按厂商货号精确匹配抗体记录Find Antibody Registry records whose catalogNum or listed catAlt alternatives equal a vendor catalog number (case-insensitive).
`get_antibody_registry_stats`	取 Antibody Registry 规模与更新日期Return Antibody Registry size and last-update date.
`search_grants`	搜索 Grants.gov 资助机会Search Grants.gov funding opportunities.

[ 022 ] mcp_rna · 9

RNARNA

浏览 Rfam RNA 家族、注释、序列比对与协方差模型，或提交序列检索。

Explore Rfam RNA families, annotations, alignments and covariance models, or submit a bounded sequence search.

Rfam API

工具	做什么
`accession_to_id`	把 Rfam 登录号（RF00001）转成家族 idConvert an Rfam accession (RF00001) to its family id.
`get_covariance_model`	下载 Rfam 家族的 Infernal 协方差模型Download the Infernal covariance model for an Rfam family from https://rfam.org/family/{id}/cm.
`get_family`	按登录号或家族 id 取 Rfam 家族元数据Retrieve Rfam family metadata by accession (RF00001) or family id from https://rfam.org/family/{id}?content-type=application/json.
`get_seed_alignment`	下载 Rfam SEED 比对Download the Rfam SEED alignment from https://rfam.org/family/{id}/alignment.
`get_sequence_regions`	列出家族 FULL 比对中的序列区间（有界页）List FULL-alignment sequence regions for an Rfam family from https://rfam.org/family/{id}/regions as a bounded page.
`get_structure_mapping`	取家族到 PDB 残基的映射Retrieve PDB residue mappings for an Rfam family from https://rfam.org/family/{id}/structures?content-type=application/json.
`get_tree`	下载 SEED 系统发生树（NHX/Newick）Download the Rfam seed phylogenetic tree in NHX/Newick form from https://rfam.org/family/{id}/tree.
`id_to_accession`	把 Rfam 家族 id 转成登录号Convert an Rfam family id to its accession (RF00001).
`search_sequence`	把一条 DNA/RNA 序列提交到 Rfam 协方差模型库检索Search one DNA/RNA sequence against the Rfam covariance-model library.

[ 023 ] mcp_structures_interactions · 16

结构与相互作用Structures Interactions

查询 RCSB PDB 结构、AlphaFold 预测、EMDB 密度图、Complex Portal 复合物和 IntAct 分子相互作用。

Search RCSB PDB structures, AlphaFold predictions, EMDB maps, Complex Portal complexes and IntAct molecular interactions.

RCSB PDB · AlphaFold DB · EMDB · Complex Portal · IntAct

工具	做什么
`alphafold_check_coverage`	检查最多 40 个 UniProt 登录号是否有 AlphaFold DB 覆盖Check AlphaFold DB coverage for up to 40 unique UniProt accessions.
`alphafold_get_prediction`	取一个 UniProt 登录号的 AlphaFold 预测结构元数据Retrieve AlphaFold DB predicted-structure metadata for one UniProt accession.
`complexportal_get_complexes`	按 CPX 登录号取 Complex Portal 复合物Fetch curated Complex Portal records by CPX accession from the EBI Complex Portal web service.
`complexportal_search_by_participant`	按参与者登录号（UniProt/ChEBI/RNAcentral）搜索复合物Search Complex Portal for complexes that mention a participant accession (UniProt, ChEBI or RNAcentral).
`emdb_get_entries`	取最多 25 个 EMDB 电镜条目的元数据Fetch EMDB cryo-EM entry metadata for up to 25 accessions (EMD-1234, emd-1234 or 1234).
`emdb_get_entry_section`	取 EMDB 条目的详细分区（文献、map、样品等）Fetch one detailed metadata section for EMDB entries: publications (primary and auxiliary citations), map (dimensions, voxel size, statistics, contour, symme…
`emdb_get_validation`	取 EMDB 验证指标（Q-score、FSC 分辨率等）Fetch EMDB validation-analysis metrics (Q-score, atom inclusion, contour recommendations, FSC-derived resolution, volume estimates).
`emdb_search_entries`	用 Solr/Lucene 查询搜索 EMDBSearch EMDB with a Solr/Lucene query against GET /search/{query}.
`intact_build_network`	围绕 UniProt 种子构建深度为 1 的 IntAct 二体互作网络Build a depth-1 IntAct binary-interaction network around UniProt seed accessions.
`intact_fetch_interactions`	按 UniProt、基因符号或 MIQL 搜索 IntAct 互作Search IntAct binary interactions with a UniProt accession, gene symbol or MIQL query via the Interaction Search service.
`intact_get_interaction_details`	按 EBI- 登录号取一条互作的策展细节Retrieve curated detail for one IntAct interaction accession (EBI-…) from the graph data service: type, host, detection method, publication, cross-references…
`intact_get_interactor`	把 UniProt、基因符号或 IntAct AC 解析为互作体记录Resolve a UniProt accession, gene symbol or IntAct interactor AC to IntAct interactor records.
`pdb_get_entities`	取一个 PDB 条目的聚合物实体元数据Retrieve polymer-entity metadata for one PDB entry from the RCSB Data API, including polymer type, chain IDs, source organisms, UniProt mappings and SIFTS-al…
`pdb_get_ligands`	列出 PDB 条目中结合的非聚合物配体List bound nonpolymer ligands for one PDB entry from the RCSB Data API, with chemical-component formula, InChIKey and stereo SMILES when served.
`pdb_get_structures`	取最多 25 个 PDB ID 的条目级摘要Fetch entry-level RCSB PDB summaries for up to 25 unique PDB IDs: title, experimental methods, resolution, determination methodology, dates, assembly/entity…
`pdb_search_structures`	用 Search API v2 搜索 RCSB PDB 条目Search RCSB PDB entries with the Search API v2.

[ 024 ] mcp_variants · 18

变异Variants

查询 CADD 变异评分、gnomAD 群体频率、ClinVar 解读和 dbSNP 记录。

Look up CADD variant scores, gnomAD population frequencies, ClinVar interpretations and dbSNP records.

CADD API and usage conditions · gnomAD · ClinVar · dbSNP

工具	做什么
`cadd_position_scores`	返回一个核基因组位点上所有可能 SNV 的 CADD 分数Return CADD raw and PHRED scores for every possible SNV at one nuclear position (up to three alts).
`cadd_range_scores`	返回最多 100 bp 窗口内每个 SNV 的 CADD 分数Return CADD raw and PHRED scores for every SNV in a nuclear window of at most 100 bp (1-based inclusive).
`cadd_variant_score`	返回一个核基因组 SNV 的 CADD raw 与 PHRED 分数Return the CADD raw and PHRED score for one nuclear SNV (chrom, pos, ref, alt).
`get_variant`	按 chrom-pos-ref-alt 查 gnomAD 短变异的群体等位基因计数Look up one gnomAD short variant by chrom-pos-ref-alt on the chosen dataset and return population allele counts.
`search_variants`	按 rsID、变异 ID 或前缀搜索 gnomAD 变异Search gnomAD for variant IDs matching an rsID, a chrom-pos-ref-alt ID, or a prefix.
`gene_variants`	列出一个基因中的 gnomAD 短变异List gnomAD short variants in one gene (HGNC symbol or Ensembl gene ID).
`gene_constraint`	取 gnomAD 基因约束指标（pLI、o/e、z）Fetch gnomAD gene constraint metrics (pLI, observed/expected LoF/missense/synonymous ratios with 90% CI, z-scores) for one HGNC symbol or Ensembl gene ID.
`region_variants`	列出最多 1 Mb 核基因组窗口中的 gnomAD 短变异List gnomAD short variants in a nuclear genomic window of at most 1 Mb (1-based inclusive).
`liftover_variant`	用 gnomAD liftover 表在 GRCh37 与 GRCh38 之间映射变异Map a chrom-pos-ref-alt variant ID between GRCh37 and GRCh38 using gnomAD's liftover table.
`clinvar_variants`	列出 gnomAD 镜像的基因内 ClinVar 变异List ClinVar variants in a gene as mirrored by gnomAD, including clinical significance, review status and gold stars.
`structural_variants`	列出与基因重叠的 gnomAD 结构变异List gnomAD structural variants overlapping a gene.
`get_structural_variant`	按发行版标识符取一个 gnomAD 结构变异Look up one gnomAD structural variant by its release-specific identifier (for example DEL_chr17_599b1512 in gnomad_sv_r4).
`mitochondrial_variants`	列出 MT 基因或 chrM 窗口中的 gnomAD 线粒体变异List gnomAD mitochondrial variants with heteroplasmy-aware counts (ac_het, ac_hom, max_heteroplasmy) for one MT gene or a chrM window.
`clinvar_search`	搜索 NCBI ClinVar 并返回种系/体细胞分类Search live NCBI ClinVar (ESearch+ESummary, db=clinvar) and return variation records with germline, somatic clinical-impact and oncogenicity classifications,…
`clinvar_get_records`	按最多 50 个 VCV/RCV 或变异 ID 取 ClinVar 记录Fetch live NCBI ClinVar variation records for up to 50 VCV/RCV accessions or bare variation IDs.
`clinvar_variant_by_rsid`	按 dbSNP rsID 取关联的 ClinVar 变异记录Return live NCBI ClinVar variation records that reference a dbSNP rsID (one rsID can map to several VCVs).
`dbsnp_get_rsids`	取最多 20 个 rsID 的 RefSNP 记录（坐标、等位基因、频率）Fetch NCBI Variation Services RefSNP records for up to 20 rsIDs: GRCh38/GRCh37 placements, alleles, gene context, per-study frequencies and ClinVar xrefs.
`dbsnp_search_by_region`	列出基因组窗口中的 dbSNP rsIDList dbSNP rsIDs in a genomic window via ESearch db=snp (Variation Services has no region endpoint).

[ 025 ] mcp_zinc · 5

ZINCZINC

按 ZINC 标识符查找可购买化合物，通过 SmallWorld 检索相似分子，并查看三维分区元数据与下载引用。

Find purchasable compounds by ZINC identifier, search similar molecules through SmallWorld, and inspect 3D tranche metadata and download references.

ZINC / CartBlanche22 · SmallWorld API

工具	做什么
`zinc_search_by_id`	按 ZINC 标识符查找可购买化合物Look up purchasable ZINC22/ZINC20 compounds by ZINC identifier through CartBlanche22.
`zinc_search_by_smiles`	在公开 SmallWorld ZINC20 在售索引上按 SMILES 搜索相似分子Search the active public SmallWorld ZINC20 for-sale index by SMILES.
`zinc_search_by_supplier`	把厂商货号解析为 ZINC 物质Resolve vendor catalog numbers to ZINC substances through CartBlanche22 /catitems.txt.
`zinc_get_3d`	定位对接可用的 3D 构象及 tranche 下载引用Locate docking-ready 3D conformers for ZINC compounds.
`zinc_random_sample`	抽取可购买 ZINC22 化合物的随机样本Draw a random sample of purchasable ZINC22 compounds through CartBlanche22 /substance/random.json and its dedicated /substance/random/{task}.json polling route.