Supporting Workflow Reproducibility by Linking Bioinformatics Tools across Papers and Executable Code

TL;DR

This paper introduces CoPaLink, an automated method that links bioinformatics tools mentioned in scientific texts and workflow code to enhance reproducibility and understanding of biological data analysis workflows.

Contribution

The paper presents a novel integrated approach combining NER and entity linking to connect workflow descriptions with executable code in bioinformatics.

Findings

High individual F1-measure (84-89) for NER components

Joint accuracy of 66% on Nextflow workflows

Effective bridging of narrative descriptions and code implementations

Abstract

Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description in a paper would improve workflow understanding, support reproducibility, and facilitate reuse. This task requires the linking of Bioinformatics tools in workflow code with their mentions in a published workflow description. Results: We present CoPaLink, an automated approach that integrates three components: Named Entity Recognition (NER) for identifying tool mentions in scientific text, NER for tool mentions in workflow code, and entity linking grounded on Bioinformatics knowledge bases. We propose approaches for all three steps achieving a high individual F1-measure (84 - 89) and a joint accuracy of 66 when evaluated on Nextflow workflows using Bioconda and Bioweb Knowledge bases. CoPaLink leverages corpora of scientific articles and workflow executable code with curated tool annotations to bridge the gap between narrative descriptions and workflow implementations. Availability: The code is available at https://gitlab.liris.cnrs.fr/sharefair/copalink-experiments and https://gitlab.liris.cnrs.fr/sharefair/copalink. The corpora are also available at https://doi.org/10.5281/zenodo.18526700, https://doi.org/10.5281/zenodo.18526760 and https://doi.org/10.5281/zenodo.18543814.