Skill: hollyya/biomedical-literature-search (version 1.0.0)

--- name: biomedical-literature-search description: > Search biomedical literature from PubMed and bioRxiv for research papers. Use this skill when: (1) Finding research papers on a specific topic or disease, (2) Retrieving recent preprints from bioRxiv, (3) Getting paper titles, abstracts, and metadata, (4) Literature review for drug discovery or biomedical research. license: MIT category: knowledge-retrieval tags: [literature-search, pubmed, biorxiv, preprints, research-papers] --- # Biomedical Literature Search Search PubMed and bioRxiv for biomedical research papers with titles and abstracts. ## When to Use - Find research papers on a specific biomedical topic - Retrieve recent preprints from bioRxiv - Get paper titles, abstracts, authors, and links - Literature review for drug discovery or biomedical research ## Workflow ### PubMed Search (Keyword-based) ```python import requests import xml.etree.ElementTree as ET # Step 1: Search for PMIDs search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" params = {"db": "pubmed", "term": "PD-1 inhibitor cancer", "retmax": 10, "retmode": "json"} response = requests.get(search_url, params=params) pmids = response.json()["esearchresult"]["idlist"] # Step 2: Fetch paper details fetch_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" response = requests.get(fetch_url, params={"db": "pubmed", "id": ",".join(pmids), "rettype": "abstract", "retmode": "xml"}) ``` ### bioRxiv Fetch (Date-range based) ```python import requests # Fetch papers by date range url = "https://api.biorxiv.org/details/biorxiv/2026-02-01/2026-03-01" response = requests.get(url) papers = response.json()["collection"] for paper in papers[:5]: print(f"Title: {paper['title']}") print(f"Abstract: {paper['abstract'][:200]}...") ``` ## Expected Outputs ### PubMed Results Returns list of papers with: | Field | Description | |-------|-------------| | `title` | Paper title | | `authors` | Author list | | `abstract` | Full abstract | | `doi` | DOI identifier | | `pmid` | PubMed ID | | `date` | Publication date | | `link` | PubMed URL | ### bioRxiv Results Returns list of papers with: | Field | Description | |-------|-------------| | `title` | Paper title | | `authors` | Author list | | `abstract` | Full abstract | | `doi` | DOI identifier | | `date` | Publication date | | `category` | Subject category | | `link` | bioRxiv URL | ## Category Filters for bioRxiv | Category | Description | |----------|-------------| | `cancer_biology` | Cancer research | | `immunology` | Immune system studies | | `cell_biology` | Cellular processes | | `bioinformatics` | Computational biology | | `neuroscience` | Nervous system research | | `microbiology` | Microbial studies | | `genomics` | Genome analysis | ## Error Handling | Error | Solution | |-------|----------| | No PubMed results | Broaden search terms, check spelling | | bioRxiv timeout | Reduce date range, retry | | Empty abstract | Paper may not have abstract available | | Rate limiting | Add delay between requests (NCBI: 3 req/sec) | ## API References - **PubMed E-utilities**: https://www.ncbi.nlm.nih.gov/books/NBK25500/ - **bioRxiv API**: https://api.biorxiv.org/ ## Notes - **PubMed**: Keyword search via NCBI E-utilities API - **bioRxiv**: Date-range or category-based fetch via bioRxiv API - bioRxiv does not support direct keyword search - For comprehensive search, use both sources together See `examples/basic_example.py` for complete runnable examples.


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: suspicious (MEDIUM)