bio-entrez-fetch
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into Biopython objects.
npx skills add majiayu000/claude-skill-registry --skill entrez-fetch --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Entrez Fetch Retrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities). ## Required Setup ```python from Bio import Entrez Entrez.email = 'your.email@example.com' # Required by NCBI Entrez.api_key = 'your_api_key' # Optional, raises rate limit 3->10 req/sec ``` ## Core Functions ### Entrez.efetch() - Retrieve Full Records Fetch complete records in various formats from any NCBI database. ```python # Fetch GenBank record by ID handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='gb', retmode='text') genbank_text = handle.read() handle.close() # Fetch FASTA sequence handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='fasta', retmode='text') fasta_text = handle.read() handle.close() # Fetch multiple records handle = Entrez.efetch(db='nucleotide', id='NM_007294,NM_000059', rettype='fasta', retmode='text') ``` **Key Parameters:** | Parameter | Description | Example | |-----------|-------------|---------| | `db` | Database name | `'nucleotide'`, `'protein'`, `'pubmed'` | | `id` | Record ID(s) | `'NM_007294'` or `'123,456,789'` | | `rettype` | Return type | `'fasta'`, `'gb'`, `'abstract'` | | `retmode` | Return mode | `'tex
- Required Setup
- Core Functions
- Entrez.efetch() - Retrieve Full Records
- Common Return Types by Database
- Entrez.esummary() - Document Summaries
- Parsing with Biopython
- Parse into SeqRecord Objects
- Parse Multiple Records
- Parse XML with Entrez.read()
- Code Patterns
- Fetch Sequence by Accession
- Fetch GenBank with Features
- Fetch PubMed Abstract
- Get Record Summaries
What does the bio-entrez-fetch skill do?
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into Biopython objects.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill entrez-fetch --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.