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BI
bio-entrez-fetch
Maintainer FreedomIntelligence · Last updated April 1, 2026
Fetch records from NCBI Entrez by accession or UID.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-entrez-fetch
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Retrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities).
- handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='gb', retmode='text') genbank_text = handle.read() handle.close().
Source Doc
Excerpt From SKILL.md
Entrez.efetch() - Retrieve Full Records
Fetch complete records in various formats from any NCBI database.
## 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 | 'text', 'xml' |
retstart | Start index | 0 |
retmax | Max records | 20 |
WebEnv | History server session | From esearch |
query_key | History server query | From esearch |
Use cases
- Use bio-entrez-fetch for genomics and bioinformatics workflows.
- Apply bio-entrez-fetch to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- entrez-search - Find record IDs before fetching
- entrez-link - Find related records in other databases
- batch-downloads - Download large numbers of records efficiently
- sequence-io/read-sequences - Parse downloaded sequences with SeqIO
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