Elsvier Coordinate Extraction

This package provides tools to search, download, and extract coordinates from Elseivier articles.

Installation

pip install elsvier-coordinate-extraction

or a local install:

git clone https://github.com/yourusername/elsevier-coordinate-extraction.git
cd elsevier-coordinate-extraction
pip install -e .

Usage

from elsvier_coordinate_extraction import search_articles, download_articles, extract_coordinates

# Search for articles
articles = search_articles(query="fmri", max_results=5)

# Download full-text XML for the first article using its DOI/PMID
records = [{"doi": articles[0]["doi"], "pmid": articles[0].get("pmid")}]  # type: ignore[index]
downloaded = download_articles(records)

# Extract coordinates
coordinates = extract_coordinates(downloaded)
print(coordinates)

Command-Line Interface

After installing the package, the elsevier-extract script becomes available via pip install . (or from PyPI). It accepts three mutually exclusive identifier inputs:

• --pmids for comma-separated PMIDs or a text file containing one PMID per line
• --dois for comma-separated DOIs or a text file containing one DOI per line
• --jsonl for a JSON Lines file where each line is {"doi": "...", "pmid": "..."}

Additional flags allow users to skip writing specific outputs (--skip-xml, --skip-text, --skip-tables, --skip-coordinates), continue past failures (--continue-on-error), disable caching (--no-cache), or adjust verbosity (-v/--verbose, -q/--quiet). --output-dir controls the base directory for results, and the CLI honors ELSEVIER_EXTRACTION_WORKERS when no --max-workers override is provided.

Output layout

Each article is saved under output-dir/{identifier} where {identifier} is the filesystem-friendly DOI (slashes replaced with _) or PMID. Inside that directory you will find:

• article.xml – the raw XML payload
• metadata.json – download metadata, rate-limit snapshot, and supplementary attachments
• text.txt – formatted article text (title/abstract/body)
• coordinates.json – NIMADS-style evaluation of extracted coordinates
• tables/*.csv – extracted tables named after their labels/captions

The CLI also appends every run to manifest.jsonl (with status, timing, and file list) and records failures in errors.jsonl, enabling audit and resumable processing.