Format Converter for PMC‑SM‑BioC

A robust Java tool that converts PubMed Central (PMC) supplementary materials (SM) into the interoperable BioC format for downstream text mining and analysis. Download the prebuilt JAR .

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Overview

The Format Converter ingests supplementary material files (PDF, Word, Excel, CSV/TSV, simple HTML) and emits BioC XML (optionally BioC JSON) with consistent structure, provenance, and metadata. It is designed for batch conversion and integration with biomedical NLP pipelines.

Features

• Multi‑format input: PDF, DOC/DOCX, XLS/XLSX, CSV/TSV, HTML.
• Standards‑compliant BioC output.
• Table linearization with row/column metadata.
• Batch and resumable processing.
• Container‑ready, reproducible runs.

Supported Formats

Input → Allowed Output

• PDF → BioC, PubTator
• BioC(XML) → PubTator
• PubTator → BioC
• PPT / PPTx → BioC, PubTator
• Word (.doc) / Wordx (.docx) → BioC, PubTator
• RTF → BioC
• Excel (.xls) / Excelx (.xlsx) → BioC, PubTator
• CSV / TSV → BioC
• TXT (free text) → BioC, PubTator
• IMG (OCR images) → BioC, PubTator
• XML → BioC
• tar.gz → Decompression

Installation

git clone https://github.com/<org>/pmc-sm-bioc-converter.git
cd pmc-sm-bioc-converter
mvn package

Or use the prebuilt JAR:

Usage

java -jar FormatConverter.jar [inputfile] [outputfile] [output format:BioC|PubTator] [input format:BioC|PubTator] [fold]

Positional arguments

• [inputfile] and [outputfile] can be file or folder
• BioC-XML|PubTator|FreeText|PDF|MSWord|MSExcel formats are allowed in [inputfile].
• BioC and PubTator formats are allowed in [outputfile].
• BioC-XML is the default format.

Output

• BioC collection with documents and passages.
• Metadata includes file type, page/sheet, row/col indices, and checksums.
• Tables are represented as tab‑separated rows.

Reproducibility

• Fixed dependencies (PDFBox, POI, etc.).
• Containerized execution.
• UTC timestamps and UTF‑8 encoding.

Citation

If you use PMC‑SM‑BioC or this converter, please cite our paper:

Wei C‑H, Leaman R, Lai P‑T, Comeau D, Tian S, Lu Z. PMC‑SM‑BioC enables FAIR access to supplementary materials at scale. PLOS Biology. 2025.

License

Apache License 2.0. See LICENSE for details.