Delete OmniGenBench_metadata.json
Browse files- OmniGenBench_metadata.json +0 -2246
OmniGenBench_metadata.json
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{
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"collection": "OmniGenBench",
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"collection_doi": "https://doi.org/10.48550/arXiv.2505.14402",
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"datasets": [
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{
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"dataset_name": "mRNA",
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"task_description": "mRNA Degradation Rate Prediction: measures in-line hydrolysis of 102-130 nt constructs under different conditions",
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"dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
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"species": null,
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"task_type": "Token Regression",
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"seq_col": [
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"sequence"
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],
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"label_col": [
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"deg_Mg_pH10",
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"deg_pH10",
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"deg_Mg_50C",
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"deg_50C"
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],
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"label_categories": null,
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"splits": null,
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"excluded": "Token regression data format is not supported by our framework.",
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"task_category": "RNA Stability Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "snmd",
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"task_description": "Single Nucleotide Mutation Detection: flags mutated positions in synthetic plant RNAs (up to ten random SNVs per sequence)",
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"dataset_doi": "collection_doi",
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"species": "Plant",
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"task_type": "Token Classification",
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"seq_col": [
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"seq",
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"mut"
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],
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"label_col": "ratio",
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"label_categories": null,
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"splits": null,
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"excluded": "Token classification data format is not supported by our framework.",
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"task_category": "Variant Effect Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "snmr",
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"task_description": "Single Nucleotide Mutation Repair: proposes the corrected base at each mutated position",
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"dataset_doi": "collection_doi",
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"species": null,
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"task_type": "Token Classification",
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"seq_col": [
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"seq",
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"mut"
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],
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"label_col": "ratio",
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"label_categories": null,
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"splits": null,
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"excluded": "Token classification data format is not supported by our framework.",
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"task_category": "Variant Effect Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "ssp_archive2",
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"task_description": "RNA Secondary Structure Prediction",
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"dataset_doi": "collection_doi",
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"species": null,
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"task_type": "Multi-label Classification",
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"seq_col": [
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"seq"
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],
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"label_col": "label",
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"splits": null,
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"excluded": "Multi-label classification data format is not supported by our framework.",
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"task_category": "RNA Structure Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "ssp_bprna",
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"task_description": "RNA Secondary Structure Prediction",
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"dataset_doi": "collection_doi",
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"species": null,
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"task_type": "Multi-label Classification",
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"seq_col": [
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"seq"
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],
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"label_col": "label",
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"excluded": "Multi-label classification data format is not supported by our framework.",
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"task_category": "RNA Structure Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "ssp_rnastralign",
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"task_description": "RNA Secondary Structure Prediction",
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"dataset_doi": "collection_doi",
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"species": null,
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"task_type": "Multi-label Classification",
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"seq"
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],
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"excluded": "Multi-label classification data format is not supported by our framework.",
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"task_category": "RNA Structure Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "ssp_strand2",
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"task_description": "RNA Secondary Structure Prediction",
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"dataset_doi": "collection_doi",
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"species": null,
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"task_type": "Multi-label Classification",
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"seq"
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],
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"label_col": "label",
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"excluded": "Multi-label classification data format is not supported by our framework.",
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"task_category": "RNA Structure Prediction",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "region_classification_arabidopsis",
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"task_description": "Token-level 3-way classification of 5'UTR, CDS, and 3'UTR regions in Arabidopsis transcripts.",
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"dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
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"species": "Arabidopsis thaliana",
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"task_type": "Token Classification",
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"seq_col": [
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"5utr",
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"cds",
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"3utr"
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],
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"excluded": "Token classification data format is not supported by our framework.",
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"task_category": "Sequence Annotation",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "region_classification_rice",
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"task_description": "Token-level 3-way classification of 5'UTR, CDS, and 3'UTR regions in Rice transcripts.",
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"dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
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"species": "Oryza sativa L. ssp. japonica",
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"task_type": "Token Classification",
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"seq_col": [
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"5utr",
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"task_category": "Sequence Annotation",
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"molecular_level": "RNA"
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},
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{
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"dataset_name": "te_prediction_arabidopsis",
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"task_description": "Prediction of high vs low translational efficiency on 5' UTRs in Arabidopsis",
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"dataset_doi": "https://doi.org/10.1038/s42256-024-00946-z",
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"species": "Arabidopsis thaliana",
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}
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},
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"task_category": "Translation Efficiency Prediction",
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{
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"dataset_path": "./OmniGenBench/te_prediction_rice_test.csv.gz"
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}
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},
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"task_category": "Translation Efficiency Prediction",
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"molecular_level": "RNA"
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},
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| 398 |
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{
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"dataset_name": "chromatin_access_arabidopis_thaliana",
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| 400 |
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"task_description": "Prediction of chromatin accessibility in Arabidopsis thaliana (plant)",
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| 401 |
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"dataset_doi": "https://doi.org/10.1126/science.ado9336",
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"species": "Arabidopsis thaliana",
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"task_type": "Multi-label Classification",
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"excluded": "Multi-label classification data format is not supported by our framework.",
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"task_category": "Sequence Annotation",
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| 412 |
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"molecular_level": "DNA"
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| 413 |
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},
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| 414 |
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{
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"dataset_name": "chromatin_access_oryza_sativa_MH63_RS2",
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"task_description": "Prediction of chromatin accessibility in Oryza sativa MH63 RS2 (plant)",
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"dataset_doi": "https://doi.org/10.1126/science.ado9336",
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"species": "Oryza sativa",
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