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

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.

Extracting Information in a Low-resource Setting: Case Study on Bioinformatics Workflows

Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve accessibility and reusability but is hindered by limited annotated corpora. To address this, we framed the problem as a low-resource extraction task and tested four strategies: 1) creating a tailored annotated corpus, 2) few-shot named-entity recognition (NER) with an autoregressive language model, 3) NER using masked language models with existing and new corpora, and 4) integrating workflow knowledge into NER models. Using BioToFlow, a new corpus of 52 articles annotated with 16 entities, a SciBERT-based NER model achieved a 70.4 F-measure, comparable to inter-annotator agreement. While knowledge integration improved performance for specific entities, it was less effective across the entire information schema. Our results demonstrate that high-performance information extraction for bioinformatics workflows is achievable.