bioRxiv-MCP-Server

import requests from bs4 import BeautifulSoup from urllib.parse import quote def generate_biorxiv_search_url(term=None, title=None, author1=None, author2=None, abstract_title=None, text_abstract_title=None, journal_code="biorxiv", section=None, start_date=None, end_date=None, num_results=10, sort="relevance-rank"): """根据用户输入的字段生成 bioRxiv 搜索 URL""" base_url = "https://www.biorxiv.org/search/" query_parts = [] if term: query_parts.append(f"{quote(term)}") if title: query_parts.append(f"title%3A{quote(title)} title_flags%3Amatch-all") if author1: query_parts.append(f"author1%3A{quote(author1)}") if author2: query_parts.append(f"author2%3A{quote(author2)}") if abstract_title: query_parts.append(f"abstract_title%3A{quote(abstract_title)} abstract_title_flags%3Amatch-all") if text_abstract_title: query_parts.append(f"text_abstract_title%3A{quote(text_abstract_title)} text_abstract_title_flags%3Amatch-all") if journal_code: query_parts.append(f"jcode%3A{quote(journal_code)}") if section: query_parts.append(f"toc_section%3A{quote(section)}") if start_date and end_date: query_parts.append(f"limit_from%3A{start_date} limit_to%3A{end_date}") query_parts.append(f"numresults%3A{num_results}") query_parts.append(f"sort%3A{quote(sort)} format_result%3Astandard") return base_url + "%20".join(query_parts) def scrape_biorxiv_results(search_url): """从 bioRxiv 搜索结果页面解析文章信息，包括 DOI""" headers = { 'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/110.0.0.0 Safari/537.36' } response = requests.get(search_url, headers=headers) if response.status_code == 200: soup = BeautifulSoup(response.text, 'html.parser') articles = soup.find_all('li', class_='search-result') results = [] for article in articles: title_tag = article.find('span', class_='highwire-cite-title') title = title_tag.text.strip() if title_tag else "No title" authors_tag = article.find('span', class_='highwire-citation-authors') authors = authors_tag.text.strip() if authors_tag else "No authors" abstract_tag = article.find('div', class_='highwire-cite-snippet') abstract = abstract_tag.text.strip() if abstract_tag else "No abstract" link_tag = article.find('a', class_='highwire-cite-linked-title') link = "https://www.biorxiv.org" + link_tag['href'] if link_tag else "No link" doi_tag = article.find('span', class_='highwire-cite-metadata-doi') doi_link = doi_tag.text.strip().replace("doi:", "").strip() if doi_tag else "No DOI" metadata = {} result = { "Title": title, "Authors": authors, "DOI_link": doi_link, "Link": link } if doi_link != "No DOI": metadata = doi_get_biorxiv_metadata(doi_link.replace("https://doi.org/", "")) if metadata: result.update(metadata) results.append(result) return results else: print(f"Error: Unable to fetch data (status code: {response.status_code})") return None def doi_get_biorxiv_metadata(doi, server="biorxiv"): """使用 bioRxiv API 通过 DOI 获取文章的详细元数据""" url = f"https://api.biorxiv.org/details/{server}/{doi}/na/json" headers = { 'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/110.0.0.0 Safari/537.36' } response = requests.get(url, headers=headers) if response.status_code == 200: data = response.json() if 'collection' in data and len(data['collection']) > 0: article = data['collection'][0] return { "DOI": article.get("doi", "No DOI"), "Title": article.get("title", "No title"), "Authors": article.get("authors", "No authors"), "Corresponding Author": article.get("author_corresponding", "No corresponding author"), "Corresponding Institution": article.get("author_corresponding_institution", "No institution"), "Date": article.get("date", "No date"), "Version": article.get("version", "No version"), "Category": article.get("category", "No category"), "JATS XML Path": article.get("jats xml path", "No XML path"), "Abstract": article.get("abstract", "No abstract") } else: print("No data found for DOI:", doi) return None else: print(f"Error: Unable to fetch metadata (status code: {response.status_code})") return None def search_key_words(key_words, num_results=10): # 生成搜索 URL search_url = generate_biorxiv_search_url(term=key_words, num_results=num_results) print("Generated URL:", search_url) # 获取并解析搜索结果 articles = scrape_biorxiv_results(search_url) return articles def search_advanced(term, title, author1, author2, abstract_title, text_abstract_title, section, start_date, end_date, num_results): # 生成搜索 URL search_url = generate_biorxiv_search_url(term, title=title, author1=author1, author2=author2, abstract_title=abstract_title, text_abstract_title=text_abstract_title, section=section, start_date=start_date, end_date=end_date, num_results=num_results) print("Generated URL:", search_url) # 获取并解析搜索结果 articles = scrape_biorxiv_results(search_url) return articles if __name__ == "__main__": # 1. search_key_words key_words = "COVID-19" articles = search_key_words(key_words, num_results=5) print(articles) # 2. search_advanced # 示例：用户输入搜索参数 term = "CRISPR" title = "CRISPR" author1 = "Doudna" author2 = None abstract_title = "genome" text_abstract_title = None section = "New Results" start_date = "2025-02-27" end_date = "2025-03-18" num_results = 5 articles = search_advanced(term, title, author1, author2, abstract_title, text_abstract_title, section, start_date, end_date, num_results) print(articles) # 3. doi get biorxiv metadata doi = "10.1101/2024.06.25.600517" metadata = doi_get_biorxiv_metadata(doi) print(metadata)