NCBI Database Skill

Quick reference guide for querying NCBI databases via E-utilities API.

Quick Start

1. Search for a Gene

Find human BRCA1 gene:

Database: gene
Term: BRCA1[Gene Name] AND Homo sapiens[Organism]

2. Get Gene Summary

Database: gene
ID: 672

3. Fetch DNA Sequence

Database: nucleotide
ID: NM_001385642
Format: fasta

4. Get Taxonomy

Database: taxonomy
ID: 9606

5. Search PubMed

Database: pubmed
Term: CRISPR[Title/Abstract] AND 2023[PDAT]

Common Database IDs

Database	ID Parameter Value
Nucleotide	nuccore
Protein	protein
Gene	gene
Taxonomy	taxonomy
PubMed	pubmed
dbSNP	snp
ClinVar	clinvar
Assembly	assembly
Structure (MMDB)	structure
GEO	gds
SRA	sra

Common Return Formats

Format	retmode	rettype	Use Case
JSON	json	-	Programmatic parsing
XML	xml	-	Structured data
FASTA	text	fasta	Sequence data
GenBank	text	gb	Full record
Summary	json	summary	Quick overview
Abstract	text	abstract	PubMed abstract

Essential Workflows

Find Gene → Get Sequence

1. Search gene: esearch -db gene -query "GENE_NAME[Gene Name] AND SPECIES[Organism]"
2. Get ID: Extract ID from result
3. Find sequences: elink -dbfrom gene -linkname gene_nucleotide -id GENE_ID
4. Fetch: efetch -db nuccore -id SEQ_ID -rettype fasta

Find Gene → Find Literature

1. Search gene: Get Gene ID
2. Link to PubMed: elink -dbfrom gene -linkname gene_pubmed -id GENE_ID
3. Fetch abstracts: efetch -db pubmed -id PUBMED_IDS -rettype abstract

API Endpoint

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Examples (Full URLs)

Search Gene

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=BRCA1[Gene+Name]+AND+Homo+sapiens[Organism]&retmax=5&retmode=json

Gene Summary

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=672&retmode=json

Fetch Sequence (FASTA)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_001385642&rettype=fasta&retmode=text

Fetch Sequence (GenBank)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_001385642&rettype=gb&retmode=text

Taxonomy

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=9606&rettype=xml&retmode=text

PubMed Search

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR[Title/Abstract]+AND+2023[PDAT]&retmax=20&retmode=json

Field Tags (for searching)

Tag	Description	Example
[Gene Name]	Gene symbol	BRCA1[Gene Name]
[Organism]	Species name	Homo sapiens[Organism]
[Title]	Paper title	CRISPR[Title]
[Title/Abstract]	Title or abstract	cancer[Title/Abstract]
[Author]	Author name	Smith[Author]
[Journal]	Journal name	Nature[Journal]
[PDAT]	Publication date	2023[PDAT]
[DP]	Date of publication	2022[DP]
[All Fields]	Search all fields	mutation[All Fields]

Field Operators

Operator	Description	Example
AND	Both terms	BRCA1 AND TP53
OR	Either term	cancer OR tumor
NOT	Exclude term	human NOT mouse
[Title]	Field search	CRISPR[Title]
*	Truncation	bacter*
" "	Phrase search	"breast cancer"

Search Modifiers

Modifier	Description	Example
[Organism]	Species filter	Homo sapiens[Organism]
[filter]	Results filter	latest[filter]
[pt]	Publication type	review[pt]
[dp]	Date range	2020:2023[dp]

Rate Limits

• Without API key: 3 requests/second
• With API key: 10 requests/second

Get API key: https://www.ncbi.nlm.nih.gov/account/

Tips

1. Always include your email: email=user@example.com
2. Use JSON for parsing: retmode=json
3. For large queries: use usehistory=y + webenv
4. Check retmax for pagination
5. Use esummary for quick checks before efetch

Documentation

• Full documentation: https://www.ncbi.nlm.nih.gov/books/NBK25497/
• API Reference: https://www.ncbi.nlm.nih.gov/books/NBK25501/
• EDirect: https://www.ncbi.nlm.nih.gov/books/NBK25500/