Claude-skill-registry bio-entrez-link

Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships.

install

source · Clone the upstream repo

git clone https://github.com/majiayu000/claude-skill-registry

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/entrez-link" ~/.claude/skills/majiayu000-claude-skill-registry-bio-entrez-link && rm -rf "$T"

manifest: skills/data/entrez-link/SKILL.md

source content

Entrez Link

Navigate between NCBI databases using Biopython's Entrez module (ELink utility).

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

Core Function

Entrez.elink() - Cross-Database Links

Find related records in the same or different databases.

# Find proteins linked to a gene
handle = Entrez.elink(dbfrom='gene', db='protein', id='672')
record = Entrez.read(handle)
handle.close()

# Extract linked IDs
linkset = record[0]
if linkset['LinkSetDb']:
    links = linkset['LinkSetDb'][0]['Link']
    protein_ids = [link['Id'] for link in links]
    print(f"Found {len(protein_ids)} linked proteins")

Key Parameters:

Parameter	Description	Example
`dbfrom`	Source database	`'gene'`
`db`	Target database	`'protein'`
`id`	Source record ID(s)	`'672'` or `'672,675'`
`linkname`	Specific link type	`'gene_protein_refseq'`
`cmd`	Link command	`'neighbor'` , `'neighbor_score'`

ELink Result Structure

record[0]                          # First linkset
record[0]['DbFrom']                # Source database
record[0]['IdList']                # Input IDs
record[0]['LinkSetDb']             # List of link results
record[0]['LinkSetDb'][0]['DbTo']  # Target database
record[0]['LinkSetDb'][0]['LinkName']  # Link name
record[0]['LinkSetDb'][0]['Link']  # List of linked records
record[0]['LinkSetDb'][0]['Link'][0]['Id']  # Linked ID

Common Link Paths

Gene to Other Databases

From	To	Link Name	Description
gene	protein	`gene_protein`	All proteins
gene	protein	`gene_protein_refseq`	RefSeq proteins only
gene	nucleotide	`gene_nuccore`	Nucleotide sequences
gene	nucleotide	`gene_nuccore_refseqrna`	RefSeq mRNA
gene	pubmed	`gene_pubmed`	Related publications
gene	homologene	`gene_homologene`	Homologs
gene	snp	`gene_snp`	SNPs in gene
gene	clinvar	`gene_clinvar`	Clinical variants

Nucleotide to Other Databases

From	To	Link Name	Description
nucleotide	protein	`nuccore_protein`	Encoded proteins
nucleotide	gene	`nuccore_gene`	Gene records
nucleotide	pubmed	`nuccore_pubmed`	Publications
nucleotide	taxonomy	`nuccore_taxonomy`	Organism taxonomy
nucleotide	biosample	`nuccore_biosample`	Sample info
nucleotide	sra	`nuccore_sra`	Related SRA data

Protein to Other Databases

From	To	Link Name	Description
protein	nucleotide	`protein_nuccore`	Coding sequences
protein	gene	`protein_gene`	Gene records
protein	pubmed	`protein_pubmed`	Publications
protein	structure	`protein_structure`	3D structures
protein	cdd	`protein_cdd`	Conserved domains

PubMed Links

From	To	Link Name	Description
pubmed	pubmed	`pubmed_pubmed`	Related articles
pubmed	gene	`pubmed_gene`	Mentioned genes
pubmed	protein	`pubmed_protein`	Mentioned proteins
pubmed	nucleotide	`pubmed_nuccore`	Mentioned sequences

Code Patterns

Gene to Protein

from Bio import Entrez

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

def get_proteins_for_gene(gene_id):
    handle = Entrez.elink(dbfrom='gene', db='protein', id=gene_id, linkname='gene_protein_refseq')
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return []
    return [link['Id'] for link in record[0]['LinkSetDb'][0]['Link']]

protein_ids = get_proteins_for_gene('672')  # BRCA1
print(f"RefSeq proteins: {protein_ids[:5]}")

Nucleotide to Gene

def get_gene_for_nucleotide(nuc_id):
    handle = Entrez.elink(dbfrom='nucleotide', db='gene', id=nuc_id)
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return None
    return record[0]['LinkSetDb'][0]['Link'][0]['Id']

gene_id = get_gene_for_nucleotide('NM_007294')
print(f"Gene ID: {gene_id}")

Find Related PubMed Articles

def get_related_articles(pmid, max_results=10):
    handle = Entrez.elink(dbfrom='pubmed', db='pubmed', id=pmid, linkname='pubmed_pubmed')
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return []
    links = record[0]['LinkSetDb'][0]['Link']
    return [link['Id'] for link in links[:max_results]]

related = get_related_articles('35412348')
print(f"Related articles: {related}")

Get All Available Links

def discover_links(db, record_id):
    handle = Entrez.elink(dbfrom=db, id=record_id, cmd='acheck')
    record = Entrez.read(handle)
    handle.close()

    links = {}
    for linkset in record[0].get('LinkSetDb', []):
        links[linkset['LinkName']] = linkset['DbTo']
    return links

available = discover_links('gene', '672')
for name, target in available.items():
    print(f"{name} -> {target}")

Navigate Gene -> Protein -> Structure

def gene_to_structures(gene_id):
    # Gene to protein
    handle = Entrez.elink(dbfrom='gene', db='protein', id=gene_id, linkname='gene_protein_refseq')
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return []
    protein_ids = [link['Id'] for link in record[0]['LinkSetDb'][0]['Link'][:5]]

    # Protein to structure
    handle = Entrez.elink(dbfrom='protein', db='structure', id=','.join(protein_ids))
    record = Entrez.read(handle)
    handle.close()

    structure_ids = []
    for linkset in record:
        if linkset['LinkSetDb']:
            structure_ids.extend([link['Id'] for link in linkset['LinkSetDb'][0]['Link']])
    return structure_ids

structures = gene_to_structures('672')
print(f"Structure IDs: {structures[:5]}")

Link Multiple IDs at Once

def batch_link(dbfrom, db, ids):
    if isinstance(ids, list):
        ids = ','.join(ids)

    handle = Entrez.elink(dbfrom=dbfrom, db=db, id=ids)
    record = Entrez.read(handle)
    handle.close()

    # Returns one linkset per input ID
    results = {}
    for linkset in record:
        source_id = linkset['IdList'][0]
        linked_ids = []
        if linkset['LinkSetDb']:
            linked_ids = [link['Id'] for link in linkset['LinkSetDb'][0]['Link']]
        results[source_id] = linked_ids
    return results

results = batch_link('gene', 'protein', ['672', '675', '7157'])
for gene, proteins in results.items():
    print(f"Gene {gene}: {len(proteins)} proteins")

Get Publications for a Sequence

def get_sequence_publications(accession):
    # First get the GI/UID
    handle = Entrez.esearch(db='nucleotide', term=f'{accession}[accn]')
    search = Entrez.read(handle)
    handle.close()

    if not search['IdList']:
        return []
    uid = search['IdList'][0]

    # Link to PubMed
    handle = Entrez.elink(dbfrom='nucleotide', db='pubmed', id=uid)
    record = Entrez.read(handle)
    handle.close()

    if not record[0]['LinkSetDb']:
        return []
    return [link['Id'] for link in record[0]['LinkSetDb'][0]['Link']]

pmids = get_sequence_publications('NM_007294')
print(f"PubMed IDs: {pmids[:5]}")

Link Commands

Command	Description
`neighbor`	Default - get linked records
`neighbor_score`	Include relevance scores
`neighbor_history`	Store results in history
`acheck`	List all available links
`ncheck`	Check if any links exist
`lcheck`	Check specific link exists
`llinks`	Get URLs to Entrez links
`prlinks`	Get provider links (external)

Common Errors

Error	Cause	Solution
Empty `LinkSetDb`	No links exist	Check if record has linked data
`HTTPError 400`	Invalid ID or database	Verify ID exists in source database
`KeyError`	Missing expected field	Check if `LinkSetDb` is empty first
Single linkset expected, got list	Multiple input IDs	Iterate through record list

Decision Tree

Need to find related records?
├── Know what link you want?
│   └── Use elink with specific linkname
├── Discover what links exist?
│   └── Use elink with cmd='acheck'
├── Navigate to target database?
│   └── Use elink(dbfrom=X, db=Y, id=Z)
├── Find related records in same database?
│   └── Use elink(dbfrom=X, db=X) with neighbor
├── Chain multiple databases?
│   └── Call elink multiple times
└── Need the actual records?
    └── Use elink first, then efetch with IDs

Related Skills

entrez-search - Search databases before linking
entrez-fetch - Retrieve records after finding linked IDs
batch-downloads - Download many linked records efficiently