ncbi-bioproject

name	ncbi-bioproject
description	Skills for enriching study entries with NCBI BioProject metadata. Use this when you see studies with bioproject_ids (PRJNA...) that could be enriched with sample counts, publication DOIs, or organism information.

NCBI BioProject Enrichment

This skill helps enrich study entries in db/sfas-brcs.yaml with metadata from NCBI BioProject.

When to Use

Use this skill when:

• A study has bioproject_ids but is missing sample_count, primary_reference, or organism
• You need to verify or supplement study metadata
• The user asks to enrich studies from NCBI

Command Line Tool

The script scripts/enrich_from_ncbi.py fetches metadata from NCBI.

Fetch full metadata

uv run scripts/enrich_from_ncbi.py PRJNA561781

Output (YAML):

bioproject_id: PRJNA561781
title: Native Miscanthus rhizosphere and endophytic microbiome
description: Survey of the native Miscanthus rhizosphere...
organism: soil metagenome
sample_count: 466
submitter_organization: University of Illinois at Urbana-Champaign
project_data_type: Targeted loci environmental
inferred_data_modality: AMPLICON_16S

Get enrichment suggestions

uv run scripts/enrich_from_ncbi.py suggest PRJNA561781

This outputs only fields that would add new information to a study entry.

Multiple BioProjects

uv run scripts/enrich_from_ncbi.py PRJNA561781 PRJNA733109 --format json

Available Metadata

Field	Description	Maps to Schema
sample_count	Number of SRA runs	Study.sample_count
primary_reference	First linked publication DOI	Study.primary_reference
organism	Target organism	Study.organism
inferred_data_modality	Data type (AMPLICON, METAGENOMICS, etc.)	Study.data_modalities
description	Project description	Study.description

Data Modality Mapping

The script maps NCBI project data types to schema DataModalityType:

NCBI Data Type	Schema Modality
Metagenome	METAGENOMICS
Targeted loci / Targeted loci environmental	AMPLICON_16S
Genome sequencing	GENOMICS
Transcriptome	TRANSCRIPTOMICS
Metatranscriptome	METATRANSCRIPTOMICS

Example Workflow

1. Find a study with bioproject_ids but missing metadata:

   - name: Native Miscanthus Rhizosphere Microbiome
     bioproject_ids:
     - PRJNA561781
     nmdc_ingest_priority: HIGH
   

2. Run enrichment:

   uv run scripts/enrich_from_ncbi.py suggest PRJNA561781
   

3. Update the study entry with suggested fields:

   - name: Native Miscanthus Rhizosphere Microbiome
     bioproject_ids:
     - PRJNA561781
     sample_count: 466
     data_modalities:
     - AMPLICON_16S
     nmdc_ingest_priority: HIGH
   

Rate Limits

NCBI E-utilities has rate limits:

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

The script includes appropriate delays. For bulk operations, consider adding an API key.

Direct API Access (Alternative)

If you need quick lookups without the script:

# BioProject summary
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=bioproject&id=561781&retmode=json" | jq .

# SRA run count
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=PRJNA561781&retmode=json" | jq '.esearchresult.count'

# Linked PubMed articles
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=bioproject&db=pubmed&id=561781&retmode=json" | jq .