Pubmed Database

# Advanced Biological Database Linking (ELink)

## 1. Core Concepts: Database vs. Linkname

A query requires both a `target_database` and a `linkname`:

*   Target Database: The destination repository (e.g., `gene`, `nuccore`,
    `pccompound`).
*   Linkname: The specific "semantic bridge" defined by NCBI. Linknames follow
    the naming convention: `dbfrom_db_subset`. One database pair can have
    multiple linknames representing different relationships.

### Common Database and Linkname Pairs

*   **pubmed**, `pubmed_pubmed_citedin`: **Forward Citations** — Find papers
    that cite the source paper.
*   **pubmed**, `pubmed_pubmed_refs`: **Backward Citations** — Extract the
    source paper's bibliography.
*   **pubmed**, `pubmed_pubmed`: **Similar Articles** — Papers sharing MeSH
    terms or keywords.
*   **pmc**, `pubmed_pmc`: **Full Text** — Resolve a PMID to a PMCID (required
    for BioC API).
*   **pccompound**, `pubmed_pccompound`: **Chemicals** — Find specific chemicals
    or drugs mentioned (CIDs).
*   **pcassay**, `pubmed_pcassay`: **PubChem BioAssays** — Link to experimental
    results and screening data.
*   **gene**, `pubmed_gene`: **Genetics** — Identify specific NCBI Gene records
    discussed.
*   **nuccore**, `pubmed_nuccore`: **Sequence Data** — Link to
    GenBank/nucleotide sequences.
*   **protein**, `pubmed_protein`: **Proteins** — Link to RefSeq or GenPept
    protein records.
*   **clinvar**, `pubmed_clinvar`: **Clinical Variants** — Find links to the
    ClinVar database (mutations).
*   **snp**, `pubmed_snp`: **SNPs** — Find specific Single Nucleotide
    Polymorphisms.
*   **sra**, `pubmed_sra`: **Raw Data** — Find raw datasets in the Sequence Read
    Archive.
*   **structure**, `pubmed_structure`: **3D Structures** — Find molecular
    structures (PDB) for proteins/ligands.

This list covers the most common `pubmed → X` links. For the full list of all
ELink linknames across all NCBI databases, see the
[NCBI Entrez Links catalog](https://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html).

--------------------------------------------------------------------------------

## 2. Procedural Wisdom: Handling Failure Modes

### The "Indexing Lag" Problem (Recent Papers)

NCBI links are not created instantly. There is a human-in-the-loop and automated
indexing process that results in a **4-8 week delay** for cross-database links.

**Symptom**: `find_linked_biological_data` returns `[]` for a paper published 2
weeks ago.

**Strategy**: If the paper is very recent, **pivot immediately** to semantic
search or full-text extraction. Use `get_full_text_pmc` and search for primary
identifiers in the prose (e.g., by searching for specific identifiers or
nomenclature manually).

### The "High-Citation" Timeout

For foundational papers with >10,000 citations, `pubmed_pubmed_citedin` may fail
or timeout.

**Strategy**: Instead of linking, use `search_pubmed` with the title of the
paper in quotes or a specific query like `"citations for PMID [SOURCE_PMID]"`

### Verifying Open Access Availability

Before calling `get_full_text_pmc`, it is more reliable to check the link first

**Workflow**: Call `find_linked_biological_data` with `target_database="pmc"`
and `linkname="pubmed_pmc"`. If it returns a result, the paper is definitely in
the PMC BioC database. If not, don't waste time on a full-text fetch; use
`fetch_article_abstracts` instead.

--------------------------------------------------------------------------------

## 3. Category-Specific Tips

### Chemical Entities (`pccompound`, `pcassay`)

Links to chemical databases typically return **internal identifiers** (e.g.,
PubChem CIDs) rather than common names.

**Example**: A link to a drug study might return `["4091"]`.

**Note**: To resolve these to names, you must use a separate metadata lookup or
search strategy, as the linking tool only provides the relationship, not the
entity details.

### Sequence and Genomic Data (`nuccore`, `protein`, `gene