Introduction

PubMed Central Open Access (PMCOA) packages bundle JATS XML articles with associated assets (figures, tables, supplementary files) as distributed by the PMC Open Access service. These packages are a primary source of machine-readable scholarly articles in the biomedical sciences.

Usage

Use the .pmcoa file extension, or the --from pmcoa option, when importing from a PMCOA package e.g.

stencila convert article.pmcoa doc.smd

Info

PMCOA is currently supported for import (decoding) only.

Implementation

PMCOA decoding is implemented in the Rust crate codec-pmc. The codec extracts the JATS XML article and associated assets from the package archive. Structuring operations are applied to normalize citations, convert table images to rows, and convert math images to TeX.

Limitations

Export (encoding) to PMCOA format is not supported.

The quality of the imported document depends on the quality of the source JATS XML, which varies between publishers.

Supplementary data files within the package are not always linked to the main article content.