BioSample dataset for ontology mapping evaluation

Description

Datasets for the evaluation of automatic curation of BioSample using Large Language Models (LLMs). Files biosample cellosaurus mapping gold standard.tsv The gold-standard dataset for the cell line ontology mapping task. This was manually created by the authors. biosample cellosaurus mapping testset.json The BioSample dataset used for the cell line ontology mapping task. This was collected using the EBI BioSamples API . biosample cellosaurus mapping result llm assisted.tsv The result of the cell line ontology mapping of the test dataset by the LLM-assisted pipeline . biosample cellosaurus mapping result metasra.tsv The result of the cell line ontology mapping of the test dataset by directly using the MetaSRA pipeline . biosample gene extraction testset.json The 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.

Description from Zenodo, shortened.

Files (6)

• TSVbiosample_cellosaurus_mapping_result_metasra.tsv47 kB
• JSONbiosample_cellosaurus_mapping_testset.json1.7 MB
• TSVbiosample_gene_extraction_result.tsv3.4 MB
• TSVbiosample_cellosaurus_mapping_gold_standard.tsv22 kB
• TSVbiosample_cellosaurus_mapping_result_llm_assisted.tsv564 kB
• JSONbiosample_gene_extraction_testset.json11 MB

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