菜单
Search PubMed for scientific papers matching a query. Retrieves ranked results with abstracts, journals, citation counts (via Europe PMC), and author information. Filters by date range, journal type, publication type, and study type. Saves a structured TSV and a formatted report.
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基于 SOC 职业分类
Pan-cancer analysis for a gene across all 33 TCGA cancer types plus DepMap and CPTAC. Use this skill when the user asks for pan-cancer analysis, cross-cancer comparison, multi-cancer gene report, or wants to analyze a gene across ALL cancer types at once. Generates a comprehensive PDF report with expression, survival (KM curves + log-rank), mutation, copy-number, DepMap cell-line data, and CPTAC protein data. Covers TCGA expression + survival, TCGA mutation/CNA survival, DepMap 26Q1 expression/copy-number/mutations, and CPTAC proteomics.
DepMap analysis for a gene across CANCER CELL LINES (NOT patient samples). Modules: expression, mutation, copy number, essentiality. Data is streamed directly from the DepMap API — no full dataset download needed. Also includes standalone co-expression (depmap_coexpression.py) and co-essentiality (depmap_coessentiality.py) scripts for cell-line correlations. For patient/tumor co-expression use coexpression-for-gene (TCGA/GTEx) instead.
Co-expression in PATIENT SAMPLES (TCGA tumors / GTEx normal tissues). NOT for cell lines — use depmap_coexpression.py for DepMap cell-line co-expression. Fetches real TCGA expression from cBioPortal API (PanCancer Atlas). GTEx requires user-provided expression file.
Run Cox proportional hazards regression on clinical and molecular data. Fits univariate and multivariate Cox models, computes hazard ratios with confidence intervals, tests the proportional hazards assumption, and generates forest plots and Schoenfeld residual plots.
Correlate gene expression or dependency scores with drug sensitivity data from PRISM (DepMap). Identifies drugs whose sensitivity correlates with the gene's expression or essentiality, and generates correlation plots.
Analyze TCGA somatic mutations in a gene via cBioPortal API (PanCancer Atlas). Supports local TCGA MAF file as fallback. Computes mutation frequencies, identifies hotspot residues, classifies mutation types, and generates lollipop plots and summaries.
| name | pubmed-search |
| description | Search PubMed for scientific papers matching a query. Retrieves ranked results with abstracts, journals, citation counts (via Europe PMC), and author information. Filters by date range, journal type, publication type, and study type. Saves a structured TSV and a formatted report. |
Execute targeted searches of the PubMed database to find relevant papers on any biomedical topic. Returns ranked results with rich metadata (abstracts, citations, MeSH terms, authors) and generates formatted reports plus visualizations of publication trends.
Use when:
Do NOT use when:
paper-digest-single)preprint-tracker for recent preprints)Inputs:
--query STRING — PubMed query string (required; supports MeSH, Author, Journal filters)--max-results INT — Maximum papers to retrieve (default: 50)--date-from — Start date (YYYY or YYYY/MM/DD; default: 2020/01/01)--date-to — End date (YYYY or YYYY/MM/DD; default: today)--pub-type — Filter by publication type: review, clinical_trial, meta_analysis, original--journal-filter — Comma-separated journal names to include--sort-by — Sort results: relevance (default), date, citations--fetch-citations — Flag: fetch citation counts from Europe PMC (slower, richer)--abstract-words INT — Max abstract preview length (default: 100)Outputs (in --outdir):
search_results.tsv — Tabular results: pmid, title, authors, journal, year, doi, abstract_preview, pub_type, citationssearch_report.md — Formatted markdown list of papers with full citationskeyword_cloud.png — Bar chart of top 20 keywords across all abstractspublication_timeline.png — Papers per year bar chartjournal_distribution.png — Pie chart of papers by journalsearch_log.txt — Query parameters and processing notesExecute PubMed eSearch
Batch Fetch Metadata (eFetch)
Extract Abstract Keywords
Fetch Citation Counts (optional)
Sort Results
Generate Outputs
Simple search, last 2 years:
python pubmed_search.py --query "CRISPR gene therapy" --max-results 50 --outdir ./results
Filter by publication type (reviews only):
python pubmed_search.py --query "cancer immunotherapy" --pub-type review --max-results 100 --outdir ./reviews
Clinical trials from top journals:
python pubmed_search.py --query "CAR-T therapy" --pub-type clinical_trial \
--journal-filter "Nature,Science,Lancet" --outdir ./trials
Sort by citation count (most cited first):
python pubmed_search.py --query "GWAS risk factors" --sort-by citations \
--fetch-citations --max-results 100 --outdir ./cited
Custom date range with MeSH filtering:
python pubmed_search.py --query "Alzheimer's Disease[MeSH]" \
--date-from 2022/01/01 --date-to 2024/12/31 --max-results 200 --outdir ./results
Export as JSON for programmatic use:
python pubmed_search.py --query "transcriptomics single cell" --output-format json --outdir ./data
| Parameter | When to Use | Example |
|---|---|---|
--query | Always required; use MeSH terms for precision | --query "Diabetes Mellitus[MeSH]" |
--max-results | Start with 50-100, increase if comprehensive review needed | --max-results 200 |
--date-from | Restrict to recent papers (e.g., last 2-3 years for fast-moving fields) | --date-from 2022/01/01 |
--pub-type | Filter to review articles for quick synthesis | --pub-type review |
--journal-filter | When you trust only high-impact journals | --journal-filter "Nature,Science,Cell" |
--sort-by citations | Find most influential papers in the field | --sort-by citations --fetch-citations |
--sort-by date | Track recent developments in a fast-moving area | --sort-by date |
--fetch-citations | When citation impact matters (adds 30-60 sec per search) | --fetch-citations |
| Error | Cause | Solution |
|---|---|---|
| "No results found" | Query is too specific or uses incorrect MeSH | Try simpler keywords, remove MeSH filters |
| "Query syntax error" | Malformed PubMed query string | Test query on pubmed.gov first, then copy exact syntax |
| ">10,000 results found" | Query too broad; will retrieve only first N results | Add year filter, specific MeSH terms, or author names |
| "Empty abstracts" | Some papers lack abstracts (older, review types) | Expected; filters still work on title and metadata |
| "Citation counts unavailable" | Europe PMC API timeout or down | Retry with --fetch-citations, or skip citations |
| "Memory error on large results" | Fetching too many papers at once (>500) | Reduce --max-results or split query into smaller searches |
| "Duplicate papers in TSV" | Different PMID versions of same paper | Expected; manually deduplicate if needed |
See requirements.txt for exact versions. Core dependencies:
requests — HTTP API calls to PubMed and Europe PMCpandas — Data organization and TSV exportmatplotlib — Visualization of trends and distributionsxml.etree.ElementTree — PubMed XML parsing (stdlib)json — Metadata serialization (stdlib)re — Regular expressions for text processing (stdlib)