BioSample dataset for ontology mapping evaluation

Datasets for the evaluation of automatic curation of BioSample using Large Language Models (LLMs). Files biosample_cellosaurus_mapping_gold_standard.tsvThe gold-standard dataset for the cell line ontology mapping task. This was manually created by the authors. biosample_cellosaurus_mapping_testset.jsonThe BioSample dataset used for the cell line ontology mapping task. This was collected using the EBI BioSamples API. biosample_cellosaurus_mapping_result_llm_assisted.tsvThe result of the cell line ontology mapping of the test dataset by the LLM-assisted pipeline. biosample_cellosaurus_mapping_result_metasra.tsvThe result of the cell line ontology mapping of the test dataset by directly using the MetaSRA pipeline. biosample_gene_extraction_testset.jsonThe BioSample dataset used for the gene name extraction task. This was collected using the EBI BioSamples API. biosample_gene_extraction_result.tsv The result of the gene name extraction from the test dataset by the LLM-assisted pipeline. Licenses biosample_cellosaurus_mapping_gold_standard.tsv is licensed under CC BY 4.0. All other files are licensed under CC0.