xlink

name	xlink
description	Use when following local EDirect link relations such as PubMed `CITED`, `CITES`, or `PMCID` from an incoming UID stream or `ENTREZ_DIRECT` message.
disable-model-invocation	true
user-invocable	true

xlink

Local link resolver built on xcommon.sh, xlink.ini, and rchive -link. It reads UIDs from stdin, -id, -input, or an upstream ENTREZ_DIRECT message, follows a named link target, and emits either raw linked UIDs or a wrapped local result set for the destination database.

Quick Start

• Command: xlink -target <link-name>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xlink
• Critical environment: EDIRECT_LOCAL_ARCHIVE

When To Use This Tool

• Traversing record-to-record links inside a prepared local EDirect archive
• Moving from one UID set to another after xsearch, xfilter, or manual ID input
• Translating link targets into the destination database defined in xlink.ini
• Working with PubMed citation or PubMed Central link-outs in the x* local stack

Common Patterns

# Follow PubMed citation links in the local archive
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xsearch -db pubmed -query 'Havran W* [AUTH]' | xlink -target CITED

# Jump from PubMed IDs to linked PMC IDs
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
printf '2539356\n' | xlink -db pubmed -target PMCID -raw

# Feed linked IDs into the next local step
export EDIRECT_LOCAL_ARCHIVE=/path/to/local/archive
xsearch -query 'dna repair' | xlink -target CITED | xfetch

Recommended Workflow

1. Set EDIRECT_LOCAL_ARCHIVE and make sure the upstream step is producing valid local UIDs or an ENTREZ_DIRECT message.
2. Supply the source database with -db when it is not already encoded in the incoming message; otherwise the script falls back to pubmed.
3. Choose a link target such as CITED, CITES, or PMCID.
4. Keep wrapped output for downstream x* stages, or add -raw if the next command wants plain UIDs.

Guardrails

• This is a local link-following tool, not a remote Entrez elink client.
• -target is mandatory; the script exits with ERROR: Insufficient arguments given to xlink if you do not supply it.
• Source inspection shows xlink.ini currently maps [pubmed] CITED=pubmed, CITES=pubmed, and PMCID=pmc.
• Without -raw, linked UIDs are wrapped in ENTREZ_DIRECT XML using the destination database from xlink.ini; with -raw, plain linked UIDs are sent to stdout.
• The script accepts input from -id, -input, stdin, or an upstream ENTREZ_DIRECT message parsed by shared xcommon.sh helpers.
• A configured local postings/archive installation is still required before link traversal works.