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Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about".
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.
SEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates. Triggers on "SEC", "size exclusion", "chromatography", "oligomer analysis", "protein assembly", "SEC report".
Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more skills", "install skill", "community skills", "find a skill for".
Audit or refresh a curated pack of eight high-signal omics runtime skills in a BioClaw installation. Use when the user wants stronger built-in guidance for common omics analyses inside agent containers without changing BioClaw source code. Ensures the eight runtime skill folders exist under `container/skills/` with the expected flat file layout.
ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
| name | pubmed-search |
| description | Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about". |
Search NCBI PubMed for scientific literature using BioPython's Entrez module.
from Bio import Entrez
Entrez.email = "bioclaw@example.com"
# Search
handle = Entrez.esearch(db="pubmed", term="CRISPR delivery methods", retmax=20, sort="date")
record = Entrez.read(handle)
handle.close()
id_list = record["IdList"]
print(f"Found {record['Count']} results, showing top {len(id_list)}")
# Fetch details
handle = Entrez.efetch(db="pubmed", id=id_list, rettype="xml")
records = Entrez.read(handle)
handle.close()
for article in records['PubmedArticle']:
medline = article['MedlineCitation']
pmid = str(medline['PMID'])
title = medline['Article']['ArticleTitle']
# Get authors
authors = medline['Article'].get('AuthorList', [])
first_author = f"{authors[0].get('LastName', '')} {authors[0].get('Initials', '')}" if authors else "Unknown"
# Get journal and year
journal = medline['Article']['Journal']['Title']
pub_date = medline['Article']['Journal']['JournalIssue'].get('PubDate', {})
year = pub_date.get('Year', 'N/A')
# Get abstract
abstract_parts = medline['Article'].get('Abstract', {}).get('AbstractText', [])
abstract = ' '.join(str(a) for a in abstract_parts)[:300]
print(f"PMID: {pmid}")
print(f"Title: {title}")
print(f"Authors: {first_author} et al.")
print(f"Journal: {journal} ({year})")
print(f"Abstract: {abstract}...")
print(f"Link: https://pubmed.ncbi.nlm.nih.gov/{pmid}/")
print()
*PubMed Search: "CRISPR delivery methods"*
_Found 1,234 results. Top 5:_
*1.* Lipid nanoparticle-mediated CRISPR delivery...
_Smith J et al. — Nature (2026)_
PMID: 12345678
pubmed.ncbi.nlm.nih.gov/12345678
*2.* AAV-based CRISPR therapeutics: advances and challenges
_Chen L et al. — Cell (2026)_
PMID: 12345679
pubmed.ncbi.nlm.nih.gov/12345679
Support these query patterns:
"CRISPR"[Title] AND "delivery"[Title] — title-specific"2026"[Date - Publication] — date filter"Nature"[Journal] — journal filterreview[Publication Type] — type filterAfter showing results, suggest: