文档核对版本: 1.0.14 · 2026-09-23
massdatabase 用于获取、解析和转换化合物、谱图及通路资源，本身不是一个包罗所有化合物的数据库。先确定后续分析需要的数据来源和 ID 系统。
典型谱库流程为：下载来源文件 → 按 MSP/XML/SDF 等格式读取 → 转为 metid 数据库。通路流程为：获取物种对应的 KEGG 或其他支持资源 → 读取 → 转为 metpath 对象。保存原始资源、获取日期、物种、转换参数和来源版本。
导出 API 覆盖 KEGG、HMDB、MassBank、MoNA、GNPS、PubChem、ChEBI、LipidMaps、FooDB、BiGG、SMPDB、Reactome、WikiPathways 等相关操作，各来源支持的下载/读取/查询/转换组合不同。在线服务和文件结构可能变化；请求失败不代表化合物不存在。共享衍生数据库前检查来源使用条件和覆盖范围。
功能范围
来源特定的在线查询下载、谱图/化合物/通路解析、metid/metpath 格式转换及 ID/来源辅助工具。
使用示例
# Use the source-specific reader matching your downloaded data.
help("read_msp_data", package = "massdatabase")
help("convert_mona2metid", package = "massdatabase")
help("download_kegg_pathway", package = "massdatabase")
help("convert_kegg2metpath", package = "massdatabase")
函数查询
下面列出已核对源码中导出的 API，包括兼容接口与辅助函数。具体参数以安装版本的 R 帮助为准；例如运行 help("函数名", package = "massdatabase")。
展开导出函数列表
convert2metid, convert_bigg_universal2metid, convert_chebi2metid, convert_foodb2metid, convert_gnps2metid, convert_hmdb2metid, convert_kegg2metid, convert_kegg2metpath, convert_lipidbank2metid, convert_lipidmaps2metid, convert_massbank2metid, convert_massbank2metid_nist, convert_massbank2metid_riken, convert_mona2metid, convert_nist2metid, convert_smpdb2metpath, convert_species2source, download_bigg_model, download_bigg_universal_metabolite, download_chebi_compound, download_foodb_compound, download_gnps_spectral_library, download_kegg_compound, download_kegg_drug, download_kegg_pathway, download_kegg_rclass, download_kegg_reaction, download_lipidbank_lipid_class, download_lipidmaps_lipid, download_massbank_compound, download_pubchem_compound, download_smpdb_pathway, get_words_similarity, massdatabase_logo, massdatabase_packages, parse_pubchem_compound, parse_reactome_pathway, parse_reactome_reaction, read_bigg_model, read_bigg_universal_metabolite, read_chebi_compound, read_foodb_compound, read_gpml, read_kegg_compound, read_kegg_drug, read_kegg_pathway, read_msp_data, read_msp_data_gnps, read_msp_data_massbank, read_msp_data_mona, read_msp_data_nist, read_sdf_data_lipidmaps, read_smpdb_pathway, read_xml_data, read_xml_data_hmdb, request_bigg_model_info, request_bigg_reaction_info, request_bigg_universal_metabolite, request_bigg_universal_metabolite_info, request_bigg_universal_reaction, request_bigg_universal_reaction_info, request_bigg_version, request_chebi_compound, request_foodb_compound, request_foodb_compound_info, request_foodb_compound_info_crawler, request_foodb_compound_ms2, request_hmdb_metabolite, request_hmdb_reaction, request_kegg_compound, request_kegg_compound_info, request_kegg_drug, request_kegg_drug_info, request_kegg_pathway, request_kegg_pathway_info, request_kegg_rclass, request_kegg_rclass_info, request_kegg_reaction, request_kegg_reaction_info, request_lipidbank_lipid_class, request_lipidmaps_lipid, request_pubchem_compound, request_reactome_organisms_info, request_reactome_pathway, request_reactome_pathway_info, request_reactome_reaction, request_reactome_reaction_info, request_wikidata_metabolite, request_wikipathway, request_wikipathway_info, request_wikipathway_organisms_info, request_wikipedia_compound, request_wikipedia_scientific_classification, search_hmdb_database, show_progresser