肿瘤变异与治疗证据查询：参数与补充说明¶

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

查询 CIViC 分子特征组合详情¶

dnakit.databases.civic_get_molecular_profile(*, molecular_profile_id, evidence_limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`molecular_profile_id`	integer	必填	CIViC molecular profile ID (e.g., 12 for BRAF V600E)
`evidence_limit`	integer	None	Maximum number of evidence items to return (default: 10)
`verbose`	bool	True	运行提示开关。

查询 CIViC 肿瘤变异详情¶

dnakit.databases.civic_get_variant(*, variant_id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`variant_id`	integer	必填	CIViC variant ID (e.g., 4170)
`verbose`	bool	True	运行提示开关。

按基因查询 CIViC 肿瘤变异¶

dnakit.databases.civic_get_variants_by_gene(*, gene_id=None, gene_name=None, gene_symbol=None, gene=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`gene_id`	integer	None	CIViC gene ID (e.g., 19 for EGFR, 12 for BRAF). Find gene IDs using civic_search_genes.
`gene_name`	string	None	Gene symbol (e.g., 'EGFR', 'BRAF', 'TP53'). Will be looked up automatically. Aliases: gene, gene_symbol, query.
`gene_symbol`	string	None	Alias for gene_name. Standard gene symbol (e.g., 'KRAS', 'BRCA1', 'EGFR').
`gene`	string	None	Alias for gene_name. Gene symbol (e.g., 'EGFR', 'KRAS').
`limit`	integer	None	Maximum number of variants to return (default: 500, uses cursor pagination to bypass CIViC's 100/page server cap)
`verbose`	bool	True	运行提示开关。

检索 CIViC 临床解释结论¶

dnakit.databases.civic_search_assertions(*, limit=None, therapy=None, therapy_name=None, disease=None, disease_name=None, variant_name=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`limit`	integer	None	Maximum number of assertions to return (default: 20, recommended max: 100)
`therapy`	string	None	Filter by therapy/drug name (e.g., 'imatinib', 'ponatinib'). Alias: therapy_name.
`therapy_name`	string	None	Alias for therapy. Filter by therapy/drug name.
`disease`	string	None	Filter by disease name (e.g., 'leukemia', 'melanoma'). Alias: disease_name.
`disease_name`	string	None	Alias for disease. Filter by disease name.
`variant_name`	string	None	Filter by variant name (e.g., 'V600E', 'T315I').
`verbose`	bool	True	运行提示开关。

检索 CIViC 变异临床证据¶

dnakit.databases.civic_search_evidence_items(*, limit=None, status=None, therapy=None, therapy_name=None, disease=None, disease_name=None, molecular_profile=None, evidence_type=None, significance=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`limit`	integer	None	Maximum number of evidence items to return (default: 20, recommended max: 100)
`status`	string \| null	None	Filter by curation status. Default: ACCEPTED (peer-reviewed). Options: ACCEPTED, SUBMITTED, REJECTED, ALL (returns all statuses combined).
`therapy`	string	None	Filter by therapy/drug name (e.g., 'imatinib', 'pembrolizumab'). Alias: therapy_name. Note: matches any evidence item where the therapy appears, including combination regimens — results may include multi-drug combinations.
`therapy_name`	string	None	Alias for therapy. Filter by therapy/drug name.
`disease`	string	None	Filter by disease name (e.g., 'leukemia', 'melanoma', 'lung cancer'). Alias: disease_name. Note: CIViC uses specific disease names (e.g., 'Lung Non-small Cell Carcinoma', not 'NSCLC'); try partial names or multiple searches if results are empty.
`disease_name`	string	None	Alias for disease. Filter by disease name.
`molecular_profile`	string	None	Filter by molecular profile name (e.g., 'BRAF V600E', 'EGFR T790M', 'KRAS G12C'). Uses substring matching — 'FLT3 ITD' will also match 'FLT3 ITD AND FLT3 D835Y'. For gene fusions, CIViC uses double-colon notation: 'GENE::PARTNER Fusion' (e.g., 'FGFR2::BICC1 Fusion', 'ALK::EML4 Fusion'). Use civic_search_molecular_profiles to discover exact profile names. Gene-prefixed clinical spellings ('EGFRvIII', 'BRAFV600E') are also handled: CIViC names the profile '<gene> <designation>' ('EGFR VIII'), so that separated form is queried too and both result sets are merged, reported in normalization_note.
`evidence_type`	string \| null	None	Filter by evidence type. Values: PREDICTIVE (drug response), DIAGNOSTIC (disease diagnosis), PROGNOSTIC (patient outcomes), PREDISPOSING (disease risk), ONCOGENIC (variant pathogenicity), FUNCTIONAL (molecular function).
`significance`	string \| null	None	Filter by clinical significance. Values depend on evidence_type, e.g. SENSITIVITYRESPONSE, RESISTANCE (predictive); BETTER_OUTCOME, POOR_OUTCOME (prognostic); POSITIVE, NEGATIVE (diagnostic); ONCOGENIC, PROTECTIVE. Use to separate, e.g., resistance from sensitivity evidence for a variant.
`verbose`	bool	True	运行提示开关。

检索 CIViC 收录的肿瘤相关基因¶

dnakit.databases.civic_search_genes(*, limit=None, name=None, query=None, gene_name=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`limit`	integer	None	Maximum number of genes to return (default: 10, recommended max: 100)
`name`	string	None	Gene symbol to search for (e.g., "EGFR", "BRAF", "BRCA1"). Alias: use 'query' or 'gene_name' instead.
`query`	string	None	Gene symbol to search for (e.g., "FLT3", "KRAS", "TP53"). Alias for 'name'.
`gene_name`	string	None	Gene symbol to search for. Alias for 'name'.
`verbose`	bool	True	运行提示开关。

检索 CIViC 收录的药物与治疗方案¶

dnakit.databases.civic_search_therapies(*, limit=None, name=None, query=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`limit`	integer	None	Maximum number of therapies to return (default: 20, recommended max: 100)
`name`	string	None	Filter by therapy/drug name (e.g., 'imatinib', 'ponatinib', 'pembrolizumab'). Alias: query.
`query`	string	None	Alias for name. Filter by therapy/drug name.
`verbose`	bool	True	运行提示开关。

按基因查询 COSMIC 体细胞突变¶

dnakit.databases.cosmic_get_mutations_by_gene(*, operation=None, gene=None, gene_name=None, max_results=None, genome_build=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	string	None	Operation type (fixed: get_by_gene)
`gene`	string	None	Gene symbol (e.g., BRAF, TP53, EGFR, KRAS, PIK3CA). Alias: gene_name also accepted.
`gene_name`	string	None	Alias for gene parameter. Gene symbol (e.g., FLT3, BRAF, TP53).
`max_results`	integer	None	Maximum number of mutations to return (default: 100, max: 500)
`genome_build`	integer	None	Genome build version: 37 (GRCh37/hg19) or 38 (GRCh38/hg38). Default: 37
`verbose`	bool	True	运行提示开关。

检索 COSMIC 肿瘤体细胞突变¶

dnakit.databases.cosmic_search_mutations(*, operation=None, terms=None, query=None, max_results=None, genome_build=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	string	None	Operation type (fixed: search)
`terms`	string	None	Search query - gene name (e.g., BRAF), mutation (e.g., V600E), or mutation ID (e.g., COSM476). Aliases: query or gene also accepted.
`query`	string	None	Alias for terms. Search query - gene name, mutation, or COSMIC ID.
`max_results`	integer	None	Maximum number of results to return (default: 20, max: 500)
`genome_build`	integer	None	Genome build version: 37 (GRCh37/hg19) or 38 (GRCh38/hg38). Default: 37
`verbose`	bool	True	运行提示开关。

查询 OncoKB 肿瘤变异作用与治疗证据¶

dnakit.databases.onco_kb_annotate_variant(*, operation=None, gene=None, gene_symbol=None, variant=None, tumor_type=None, alteration=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	string	None	Operation type (fixed: annotate_variant)
`gene`	string	None	Gene symbol (e.g., BRAF, EGFR, TP53, KRAS)
`gene_symbol`	string	None	Alias for gene. Gene symbol (e.g., BRAF, EGFR, TP53, KRAS).
`variant`	string	None	Variant notation - protein change (e.g., V600E, T790M, G12D)
`tumor_type`	string	None	Optional OncoTree tumor type code (e.g., MEL for melanoma, LUAD for lung adenocarcinoma)
`alteration`	string	None	Alias for variant. Protein change notation (e.g., "V600E", "T790M", "G12D").
`verbose`	bool	True	运行提示开关。

按区间检索肿瘤拷贝数变异样本¶

dnakit.databases.progenetix_cnv_search(*, reference_name, start, end, variant_type=None, filters=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`reference_name`	string	必填	RefSeq chromosome accession. Examples: 'refseq:NC_000007.14' (chr7/GRCh38), 'refseq:NC_000017.11' (chr17/GRCh38), 'refseq:NC_000001.11' (chr1/GRCh38).
`start`	integer	必填	Start position (1-based, GRCh38). Example: 55019017 for EGFR start.
`end`	integer	必填	End position (1-based, GRCh38). Example: 55211628 for EGFR end.
`variant_type`	string	None	CNV type: 'DUP' for amplification/duplication, 'DEL' for deletion. Leave empty for any CNV type.
`filters`	string	None	Optional NCIt ontology code to filter by cancer type. Example: 'NCIT:C4017' for breast cancer.
`limit`	integer	None	Maximum number of biosamples to return (default: 10).
`verbose`	bool	True	运行提示开关。

列出 Progenetix 肿瘤拷贝数变异队列¶

dnakit.databases.progenetix_list_cohorts(*, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`limit`	integer	None	Maximum number of cohorts to return (default: 10).
`verbose`	bool	True	运行提示开关。

列出 Progenetix 可用筛选术语¶

dnakit.databases.progenetix_list_filtering_terms(*, prefixes=None, limit=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`prefixes`	string	None	Ontology prefix to filter terms by. Use 'NCIT' for NCI Thesaurus cancer types (default), 'EDAM' for operation types, 'HP' for HPO phenotypes.
`limit`	integer	None	Maximum number of terms to return (default: 25).
`verbose`	bool	True	运行提示开关。

按疾病本体检索肿瘤生物样本¶

dnakit.databases.progenetix_search_biosamples(*, filters, limit=None, skip=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`filters`	string	必填	NCIt ontology code to filter biosamples by cancer type. Examples: 'NCIT:C3058' (Glioblastoma), 'NCIT:C4017' (Breast Carcinoma), 'NCIT:C9145' (Acute Myeloid Leukemia), 'NCIT:C3224' (Melanoma), 'NCIT:C4872' (Lung Adenocarcinoma), 'NCIT:C3167' (Neuroblastoma).
`limit`	integer	None	Maximum number of biosamples to return (default: 10).
`skip`	integer	None	Number of results to skip for pagination (default: 0).
`verbose`	bool	True	运行提示开关。