pubmed-api-integration

PubMed API集成规范

API端点配置

const PUBMED_BASE_URL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils';
const RATE_LIMIT_DELAY = 334; // PubMed限制：3请求/秒
const REQUEST_TIMEOUT = 30000; // 30秒超时

搜索查询构建

// 搜索URL构建模式
const searchUrl = new URL(`${PUBMED_BASE_URL}/esearch.fcgi`);
searchUrl.searchParams.append('db', 'pubmed');
searchUrl.searchParams.append('term', searchQuery);
searchUrl.searchParams.append('retmax', maxResults.toString());
searchUrl.searchParams.append('retmode', 'json');
searchUrl.searchParams.append('sort', sortMap[sortBy] || 'relevance');
searchUrl.searchParams.append('tool', 'mcp-pubmed-server');
searchUrl.searchParams.append('email', process.env.PUBMED_EMAIL);

数据获取模式

1. 搜索文献ID

// 使用 esearch.fcgi 获取PMID列表
const response = await fetch(searchUrl.toString(), { timeout: REQUEST_TIMEOUT });
const data = await response.json();
const ids = data.esearchresult?.idlist || [];

2. 获取文献详情

// 使用 esummary.fcgi 获取文献详情
const summaryUrl = new URL(`${PUBMED_BASE_URL}/esummary.fcgi`);
summaryUrl.searchParams.append('db', 'pubmed');
summaryUrl.searchParams.append('id', ids.join(','));
summaryUrl.searchParams.append('retmode', 'json');

3. 获取完整摘要

// 使用 efetch.fcgi 获取完整摘要
const abstractUrl = new URL(`${PUBMED_BASE_URL}/efetch.fcgi`);
abstractUrl.searchParams.append('db', 'pubmed');
abstractUrl.searchParams.append('id', pmid);
abstractUrl.searchParams.append('rettype', 'abstract');
abstractUrl.searchParams.append('retmode', 'text');

数据格式化

文献对象结构

const article = {
    pmid: id,
    title: article.title || 'No title',
    authors: article.authors?.map(author => author.name) || [],
    journal: article.source || 'No journal',
    publicationDate: article.pubdate || 'No date',
    volume: article.volume || '',
    issue: article.issue || '',
    pages: article.pages || '',
    abstract: article.abstract || null,
    doi: article.elocationid || '',
    url: `https://pubmed.ncbi.nlm.nih.gov/${id}/`,
    publicationTypes: article.pubtype || [],
    meshTerms: article.meshterms || [],
    keywords: article.keywords || []
};