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ncbi-database-skill

v1.0.6

Published

Comprehensive NCBI Database CLI tool for querying E-utilities API - Gene, PubMed, ClinVar, SRA, BLAST, and more

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Links

Git

Maintainers

yanmengliyanmengli

Keywords

ncbibioinformaticse-utilitiespubmedgenbankgeneproteinnucleotidecliclinvardbsnpsrablastvariantgenomics

Readme

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 protected]
  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/