CPL-Article: a corpus annotated with bioinformatics tool names in publications describing workflows

CPL-Article is a corpus describing bioinformatics tool names in English publications describing bioinformatics workflows. These annotations are available in the BRAT Rapid Annotation Tool (BRAT) standoff format (https://brat.nlplab.org/standoff.html). This corpus is composed of 50 articles related to Nextflow workflows randomly selected from PubMed Central with a total of 76,002 tokens and 1,523 annotated tokens corresponding to 1,455 tool occurrences (425 unique tools). Repository organisation The articles are separated into seven different directories: Five folders (iteration_{i}) are provided, each corresponding to a different split of the training data. This allows experiments to be run on different splits. An another folder contains the 36 articles used for training. The last folder contains 14 articles used for testing. Contact Clémence Sebe, clemence.sebe@universite-paris-saclay.fr Funding This work received support from the National Research Agency under the France 2030 program, with reference to ANR-22-PESN-0007.