/bio-entrez-search

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--- name: bio-entrez-search description: Search NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query counts across databases. tool_type: python primary_tool: Bio.Entrez measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

Entrez Search

Search NCBI databases using Biopython's Entrez module (ESearch, EInfo, EGQuery utilities).

Required Setup

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.esearch() - Search a Database

Search any NCBI database and get matching record IDs.

handle = Entrez.esearch(db='nucleotide', term='human[orgn] AND BRCA1[gene]')
record = Entrez.read(handle)
handle.close()

print(f"Found {record['Count']} records")
print(f"IDs: {record['IdList']}")  # First 20 IDs by default

**Key Parameters:** | Parameter | Description | Default | |-----------|-------------|---------| | `db` | Database to search | Required | | `term` | Search query | Required | | `retmax` | Max IDs to return | 20 | | `retstart` | Starting index (pagination) | 0 | | `usehistory` | Store results on server | 'n' | | `sort` | Sort order | database-specific | | `datetype` | Date field to search | 'pdat' | | `reldate` | Records from last N days | None | | `mindate` | Start date (YYYY/MM/DD) | None | | `maxdate` | End date (YYYY/MM/DD) | None |

**ESearch Result Fields:**

record['Count']        # Total matching records (string)
record['IdList']       # List of record IDs
record['RetMax']       # Number of IDs returned
record['RetStart']     # Starting index
record['QueryKey']     # For history server (if usehistory='y')
record['WebEnv']       # For history server (if usehistory='y')
record['TranslationSet']  # Query translations applied
record['QueryTranslation']  # Final translated query

Entrez.einfo() - Database Information

Get information about available databases or specific database fields.

# List all available databases
handle = Entrez.einfo()
record = Entrez.read(handle)
handle.close()
print(record['DbList'])  # ['pubmed', 'protein', 'nucleotide', ...]

# Get info about specific database
handle = Entrez.einfo(db='nucleotide')
record = Entrez.read(handle)
handle.close()

print(f"Description: {record['DbInfo']['Description']}")
print(f"Record count: {record['DbInfo']['Count']}")

# List searchable fields
for field in record['DbInfo']['FieldList']:
    print(f"{field['Name']}: {field['Description']}")

**Database Info Fields:**

record['DbInfo']['DbName']       # Database name
record['DbInfo']['Description']  # Database description
record['DbInfo']['Count']        # Total records in database
record['DbInfo']['LastUpdate']   # Last update date
record['DbInfo']['FieldList']    # Searchable fields
record['DbInfo']['LinkList']     # Available links to other databases

Entrez.egquery() - Global Query

Search across all NCBI databases simultaneously.

handle = Entrez.egquery(term='CRISPR')
record = Entrez.read(handle)
handle.close()

for result in record['eGQueryResult']:
    if int(result['Count']) > 0:
        print(f"{result['DbName']}: {result['Count']} records")

Search Query Syntax

NCBI uses a specific query syntax:

Field Tags

# Search specific fields using [field_name]
term = 'BRCA1[gene]'                    # Gene name field
term = 'human[orgn]'                    # Organism field
term = 'Homo sapiens[ORGN]'             # Full organism name
term = 'NM_007294[accn]'                # Accession number
term = 'Smith J[auth]'                  # Author (PubMed)
term = 'Nature[jour]'                   # Journal (PubMed)
term = '1000:5000[slen]'                # Sequence length range
term = 'mRNA[fkey]'                     # Feature key

Boolean Operators

term = 'BRCA1 AND human'                # Both terms
term = 'cancer OR tumor'                # Either term
term = 'human NOT mouse'                # Exclude term
term = '(BRCA1 OR BRCA2) AND human'     # Grouping

Date Ranges

# Using date parameters
handle = Entrez.esearch(
    db='pubmed',
    term='CRISPR',
    datetype='pdat',     # Publication date
    mindate='2023/01/01',
    maxdate='2024/12/31'
)

# Or in query string
term = 'CRISPR AND 2024[pdat]'
term = 'CRISPR AND 2023:2024[pdat]'

Wildcards and Phrases

term = 'immun*'                         # Wildcard
term = '"breast cancer"[title]'         # Exact phrase

Common Databases

| Database | `db` value | Common Fields | |----------|------------|---------------| | PubMed | `pubmed` | `[auth]`, `[title]`, `[jour]`, `[pdat]` | | Nucleotide | `nucleotide` | `[orgn]`, `[gene]`, `[accn]`, `[slen]` | | Protein | `protein` | `[orgn]`, `[gene]`, `[accn]`, `[molwt]` | | Gene | `gene` | `[orgn]`, `[sym]`, `[chr]` | | SRA | `sra` | `[orgn]`, `[platform]`, `[strategy]` | | Taxonomy | `taxonomy` | `[scin]`, `[comn]`, `[rank]` | | Assembly | `assembly` | `[orgn]`, `[level]`, `[refseq]` |

Code Patterns

Basic Search with Pagination

from Bio import Entrez

Entrez.email = 'your.email@example.com'

def search_ncbi(db, term, max_results=100):
    handle = Entrez.esearch(db=db, term=term, retmax=max_results)
    record = Entrez.read(handle)
    handle.close()
    return record['IdList'], int(record['Count'])

ids, total = searc