pmc2info

EDirect shell pipeline that converts PMC <article> XML into a normalized PMCInfo XML record set. It extracts citation metadata, title, abstract, authors, license text, and section passages, then normalizes common section titles such as introduction, results, and methods.

Quick Start

• Command: pmc2info
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/pmc2info
• Environment prerequisite: add /home/vimalinx/miniforge3/envs/bio/bin to PATH so xtract, transmute, and related EDirect helpers are available

When To Use This Tool

• Convert PMC full-text XML into PMCInfo XML for archive or indexing workflows.
• Extract normalized article metadata and sectioned text from PMC articles.
• Process PMC XML fetched by efetch -db pmc -format xml or extracted from open-access tar archives.
• Use this when you need PMC full text; do not use it for PubMed PubmedArticle XML.

Common Patterns

# 1) Convert one PMC article fetched live from NCBI
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

efetch -db pmc -id 6260607 -format xml | pmc2info > article.pmcinfo.xml

# 2) Convert PMC article XML streamed from an OA archive tarball
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

tar -xOzf oa_bundle.tar.gz --to-stdout | pmc2info > batch.pmcinfo.xml

# 3) Inspect the first part of the normalized PMCInfo output
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

efetch -db pmc -id 6260607 -format xml | pmc2info | sed -n '1,40p'

Recommended Workflow

1. Start from PMC article XML, either via efetch -db pmc -format xml or an extracted OA archive payload.
2. Activate the bio environment or export the EDirect bin directory into PATH before invoking the wrapper.
3. Inspect one converted article first to verify the expected PMCInfo structure, citation block, and normalized passage labels.
4. Scale to bulk conversion only after confirming the section mapping and output schema meet your downstream parser's expectations.

Guardrails

• There is no real help mode. With dependencies available, pmc2info -help still runs the pipeline and errors only because no XML input was supplied.
• Without the bio bin directory on PATH, the live failure is a series of xtract: command not found and transmute: command not found messages.
• With dependencies available but no XML input, the live failure is No data supplied to xtract from stdin or file.
• This script expects PMC <article> XML, not PubMed PubmedArticle or DocumentSummary XML.
• Section normalization is driven by an internal title map for common headings such as introduction, results, discussion, materials and methods, and statistical analysis. Unmapped headings pass through less cleanly.