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The dataset generation failed because of a cast error
Error code:   DatasetGenerationCastError
Exception:    DatasetGenerationCastError
Message:      An error occurred while generating the dataset

All the data files must have the same columns, but at some point there are 5 new columns ({'Chr1', '30427671', '61', '55', '60'}) and 1 missing columns ({'>Chr1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF'}).

This happened while the csv dataset builder was generating data using

zip://genomes/Arabidopsis_thaliana/Col-1/assembly.fa.fai::/tmp/hf-datasets-cache/medium/datasets/40931744314007-config-parquet-and-info-maize-genetics-plexbench--2d8d0b38/downloads/55cf27e20a455550e93623a4c4c94fcbf9340a60b0094eb7e0b3f6b69defab83

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2302, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Chr1: string
              30427671: int64
              55: int64
              60: int64
              61: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 783
              to
              {'>Chr1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF': Value(dtype='string', id=None)}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1321, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 935, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1882, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2013, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 5 new columns ({'Chr1', '30427671', '61', '55', '60'}) and 1 missing columns ({'>Chr1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF'}).
              
              This happened while the csv dataset builder was generating data using
              
              zip://genomes/Arabidopsis_thaliana/Col-1/assembly.fa.fai::/tmp/hf-datasets-cache/medium/datasets/40931744314007-config-parquet-and-info-maize-genetics-plexbench--2d8d0b38/downloads/55cf27e20a455550e93623a4c4c94fcbf9340a60b0094eb7e0b3f6b69defab83
              
              Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)

Need help to make the dataset viewer work? Open a discussion for direct support.

>Chr1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF
string
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAAT
CTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTT
CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA
TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT
GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA
GCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTTATTGTAACCTTAGGGTTGGTTT
ATCTCAAGAATCTTATTAATTGTTTGGACTGTTTATGTTTGGACATTTATTGTCATTCTT
ACTCCTTTGTGGAAATGTTTGTTCTATCAATTTATCTTTTGTGGGAAAATTATTTAGTTG
TAGGGATGAAGTCTTTCTTCGTTGTTGTTACGCTTGTCATCTCATCTCTCAATGATATGG
GATGGTCCTTTAGCATTTATTCTGAAGTTCTTCTGCTTGATGATTTTATCCTTAGCCAAA
AGGATTGGTGGTTTGAAGACACATCATATCAAAAAAGCTATCGCCTCGACGATGCTCTAT
TTCTATCCTTGTAGCACACATTTTGGCACTCAAAAAAGTATTTTTAGATGTTTGTTTTGC
TTCTTTGAAGTAGTTTCTCTTTGCAAAATTCCTCTTTTTTTAGAGTGATTTGGATGATTC
AAGACTTCTCGGTACTGCAAAGTTCTTCCGCCTGATTAATTATCCATTTTACCTTTGTCG
TAGATATTAGGTAATCTGTAAGTCAACTCATATACAACTCATAATTTAAAATAAAATTAT
GATCGACACACGTTTACACATAAAATCTGTAAATCAACTCATATACCCGTTATTCCCACA
ATCATATGCTTTCTAAAAGCAAAAGTATATGTCAACAATTGGTTATAAATTATTAGAAGT
TTTCCACTTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACACCCCCCACCTCCCCC
CCCCCCCCCCACCCCCCAAATTGAGAAGTCAATTTTATATAATTTAATCAAATAAATAAG
TTTATGGTTAAGAGTTTTTTACTCTCTTTATTTTTCTTTTTCTTTTTGAGACATACTGAA
AAAAGTTGTAATTATTAATGATAGTTCTGTGATTCCTCCATGAATCACATCTGCTTGATT
TTTCTTTCATAAATTTATAAGTAATACATTCTTATAAAATGGTCAGAGAAACACCAAAGA
TCCCGAGATTTCTTCTCACTTACTTTTTTTCTATCTATCTAGATTATATAAATGAGATGT
TGAATTAGAGGAACCTTTGATTCAATGATCATAGAAAAATTAGGTAAAGAGTCAGTGTCG
TTATGTTATGGAAGATGTGAATGAAGTTTGACTTCTCATTGTATATGAGTAAAATCTTTT
CTTACAAGGGAAGTCCCCAATTGGTCAACATGTGAAAGCACGTGTCATGTTCTTACTTTT
GTTTGGGTAATCTTCTAATTACTGTATATGGAAGATGTGAATGAAGTTTTGGTCCTGAAT
GTGGCCAAGGTTCCGTCATTTGGAGATACGAAATCAAATCTCCTTTAAGATTTTGTTTTT
ATAATGTGTTCTTCCATCCACATCTATCTCCATATGATATGGACCATATCATACATCATC
ATTTGTCCAAATGCATGAATGAATTTGGAAATAGGTACGAGAATGCCAACAATGACAAGA
AGGGATCAAAGACAGTTTTTAAAACAATATTTTACAGGGTTTTAATCTAATTCTAAGTTT
TGGTCACTCACTTTGTTAAAAGAATAATTCAGTGTCTGGACACTAAAATCTTCCAAAAAC
CCCATATACATATATGCTATTTCGATACTTATATTTATTTACTCAGCATAAAAAATATTA
ACCATGTATTCATAGTAAAATGTTTCATGTGATATCAAACCAGCGACAACAAAAGTATTA
TTCCCCTCATTATGTTTGACTCCTATTATATTTTTATTTTAATTTTTTTCACTATCATCT
TTCTTGCAATGAAAGTCCCATATATTGGTCAACATTTCAAACCACTTGTTCTCTTTTATG
TTTTGGTAAGAGCTATCTTCTAAATTTATAATACGCATAAATTCAAAAGTAAAAGAAAAT
TTTGGTCATGAATGTTGTTTAAGTCATTTGGAGATACGAAATCAAATCTCCTTGTAGATT
TTGTTTTTAGAATGTCGTTCCTTTTTCATCATCTTAGCTATATCTACAGCTATATATCCT
ATCTTTAAACCTATATTATTTTTTCCTCTCTTCACCAAAGCCATGTTTTTTAGTTGTGGC
GAAAAATAAGAAATCCATACATCAACATATCGCTTTCGTTACCTTAAATTTTGGCTTGTT
ATGAAGGCATGTCATAACGTTTCTAGTCACAACTCACAAGCATACCAACGACCATGATAA
ATCCAAAAAGTAGAAACAATCTATTATCTAAACCCCCAAAAGACAAAAGAAAAAAGTAGA
AAGAAAAGGTAGGCAGAGATATAATGCTGGTTTTATTTGTTTGTTAAAAGATATTGCTAT
TTCTGCCAATATTAAAACTTCACTTAGGAAGACTTGAACCTACCACACGTTAGTGACTAA
TGAGAGCCACTAGATAATTGCATGCATCCCACACTAGTACTAATTTTCTAGGGATATTAG
AGTTTTCTAATCACCTACTTCCTACTATGTGTATGTTATCTACTGGCGTGGATGCTTTTA
AAGATGTTACGTTATTATTTTGTTCGGTTTGGAAAACGGCTCAATCGTTATGAGTTCGTA
AGACACATACATTGTTCCATGATAAAATGCAACCCCACGAACCATTTGCGACAAGCAAAA
CAACATGGTCAAAATTAAAAGCTAACAATTAGCCAGCGATTCAAAAAGTCAACCTTCTAG
ATGGATTTAACAACATATCGATAGGATTCAAGATTAAAAATAAGCACACTCTTATTAATG
TTAAAAAACGAATGAGATGAAAATATTTGGCGTGTTCACACACATAATCTAGAAGACAGA
TTCGAGTTGCTCTCCTTTGTTTTGCTTTGGGAGGGACCCATTATTACCGCCCAGCAGCTT
CCCAGCCTTCCTTTATAAGGCTTAATTTATATTTATTTAAATTTTATATGTTCTTCTATT
ATAATACTAAAAGGGGAATACAAATTTCTACAGAGGATGATATTCAATCCACGGTTCACC
CAAACCGATTTTATAAAATTTATTATTAAATCTTTTTTAATTGTTAAATTGGTTTAAATC
TGAACTCTGTTTACTTACATTGATTAAAATTCTAAACCATCATAAGTAAAAAATAATATG
ATTAAGACTAATAAATCTTAATAGTTAATACTACTCGGTTTACTACATGAAATTTCATAC
CATCAATTGTTTTAATAATCTTTAAAATTGTTAGGACCGGTAAAACCATACCAATTAAAC
CGGAGATCCATATTAATTTAATTAAGAAAATAAAAATAAAAGGAATAAATTGTCTTATTT
AAACGCTGACTTCACTGTCTTCCTCCCTCCAAATTATTAGATATACCAAACCAGAGAAAA
CAAATACATAATCGGAGAAATACAGATTACAGAGAGCGAGAGAGATCGACGGCGAAGCTC
TTTACCCGGAAACCATTGAAATCGGACGGTTTAGTGAAAATGGAGGATCAAGTTGGGTTT
GGGTTCCGTCCGAACGACGAGGAGCTCGTTGGTCACTATCTCCGTAACAAAATCGAAGGA
AACACTAGCCGCGACGTTGAAGTAGCCATCAGCGAGGTCAACATCTGTAGCTACGATCCT
TGGAACTTGCGCTGTAAGTTCCGAATTTTCTGAATTTCATTTGCAAGTAATCGATTTAGG
TTTTTGATTTTAGGGTTTTTTTTTGTTTTGAACAGTCCAGTCAAAGTACAAATCGAGAGA
TGCTATGTGGTACTTCTTCTCTCGTAGAGAAAACAACAAAGGGAATCGACAGAGCAGGAC
AACGGTTTCTGGTAAATGGAAGCTTACCGGAGAATCTGTTGAGGTCAAGGACCAGTGGGG
ATTTTGTAGTGAGGGCTTTCGTGGTAAGATTGGTCATAAAAGGGTTTTGGTGTTCCTCGA
TGGAAGATACCCTGACAAAACCAAATCTGATTGGGTTATCCACGAGTTCCACTACGACCT
CTTACCAGAACATCAGGTTTTCTTCTATTCATATATATATATATATATATATGTGGATAT
ATATATATGTGGTTTCTGCTGATTCATAGTTAGAATTTGAGTTATGCAAATTAGAAACTA
TGTAATGTAACTCTATTTAGGTTCAGCAGCTATTTTAGGCTTAGCTTACTCTCACCAATG
TTTTATACTGATGAACTTATGTGCTTACCTCCGGAAATTTTACAGAGGACATATGTCATC
TGCAGACTTGAGTACAAGGGTGATGATGCGGACATTCTATCTGCTTATGCAATAGATCCC
ACTCCCGCTTTTGTCCCCAATATGACTAGTAGTGCAGGTTCTGTGGTGAGTCTTTCTCCA
TATACACTTAGCTTTGAGTAGGCAGATCAAAAAAGAGCTTGTGTCTACTGATTTGATGTT
TTCCTAAACTGTTGATTCGTTTCAGGTCAACCAATCACGTCAACGAAATTCAGGATCTTA
CAACACTTACTCTGAGTATGATTCAGCAAATCATGGCCAGCAGTTTAATGAAAACTCTAA
CATTATGCAGCAGCAACCACTTCAAGGATCATTCAACCCTCTCCTTGAGTATGATTTTGC
AAATCACGGCGGTCAGTGGCTGAGTGACTATATCGACCTGCAACAGCAAGTTCCTTACTT
GGCACCTTATGAAAATGAGTCGGAGATGATTTGGAAGCATGTGATTGAAGAAAATTTTGA
GTTTTTGGTAGATGAAAGGACATCTATGCAACAGCATTACAGTGATCACCGGCCCAAAAA
ACCTGTGTCTGGGGTTTTGCCTGATGATAGCAGTGATACTGAAACTGGATCAATGGTAAG
CTTTTTTTACTCATATATAATCACAACCTATATCGCTTCTATATCTCACACGCTGAATTT
TGGCTTTTAACAGATTTTCGAAGACACTTCGAGCTCCACTGATAGTGTTGGTAGTTCAGA
TGAACCGGGCCATACTCGTATAGATGATATTCCATCATTGAACATTATTGAGCCTTTGCA
CAATTATAAGGCACAAGAGCAACCAAAGCAGCAGAGCAAAGAAAAGGTTTAACACTCTCA
CTGAGAAACATGACTTTGATACGAAATCTGAATCAACATTTCATCAAAAAGATTTAGTCA
AATGACCTCTAAATTATGAGCTATGGGTCTGCTTTCAGGTGATAAGTTCGCAGAAAAGCG
AATGCGAGTGGAAAATGGCTGAAGACTCGATCAAGATACCTCCATCCACCAACACGGTGA
AGCAGAGCTGGATTGTTTTGGAGAATGCACAGTGGAACTATCTCAAGAACATGATCATTG
GTGTCTTGTTGTTCATCTCCGTCATTAGTTGGATCATTCTTGTTGGTTAAGAGGTCAAAT
CGGATTCTTGCTCAAAATTTGTATTTCTTAGAATGTGTGTTTTTTTTTGTTTTTTTTTCT
TTGCTCTGTTTTCTCGCTCCGGAAAAGTTTGAAGTTATATTTTATTAGTATGTAAAGAAG
AGAAAAAGGGGGAAAGAAGAGAGAAGAAAAATGCAGAAAATCATATATATGAATTGGAAA
AAAGTATATGTAATAATAATTAGTGCATCGTTTTGTGGTGTAGTTTATATAAATAAAGTG
ATATATAGTCTTGTATAAGAAAGGGATTTTACATGAGACCCAAATATGAGTAAAGGGTGT
TGGCTCAAAGATTCATTTAGCAACCAAAGTTGCATTTGCAAGGAAATGAAAAGGTGTTAA
End of preview.

Dataset Card for Maize and Arabidopsis gene expression

Plant Gene expression data used for benchmarking sequence to gene expression prediction ML models.

Dataset Description

Species included are Maize and Arabidopsis thaliana. Dataset includes gene expression values for leaf and root tissues. Within the tasks folder, datasets are broken down by species-task-tissue. Genomes in the genomes folders include the annotation and the GFF files associated with that specific genome. All tasks are split by 80% train, 10% validation, and 10% test.

Dataset Structure

dataset
  genomes/
    Arabidopsis_thaliana/
      annotation.fa
      ath.gff
    Zea_mays/
      annotation.fa
      ath.gff
  tasks/
    species-task-tissue/
      train.tsv
      validate.tsv
      test.tsv
  • Curated by: Taylor Ferebee, Travis Wrightsman, Jingjing Zhai, Aaron Gokaslan, Volodymyr Kuleshov, Edward S. Buckler
  • Repository: [https://github.com/maize-genetics/expression-survey]
  • Paper: PLExBench: A benchmarking suite for predicting gene expression in plants
  • License: MIT

Dataset Sources

sample_name species genotype library_layout library_selection reads_location organ age condition replicate batch reference
SRR505743 Arabidopsis_thaliana Col-0 single-read random sra root seedling controlled 1 1 SRP013631
SRR505744 Arabidopsis_thaliana Col-0 single-read random sra leaf seedling controlled 1 1 SRP013631
SRR953400 Arabidopsis_thaliana Col-0 single-read random sra leaf seeding controlled 1 1 PRJNA215448
SRR1005386 Arabidopsis_thaliana Col-0 single-read random sra leaf seedling controlled 1 1 PRJNA222364
SRR578947 Arabidopsis_thaliana Col-0 single-read random sra root seedling controlled 1 1 SRP013631
SRR578948 Arabidopsis_thaliana Col-0 single-read random sra root seedling controlled 1 1 SRP013631
ERR2096663 Zea_mays B73 paired-end polyA sra leaf seedling controlled 1 1 PRJEB22166
ERR2096664 Zea_mays B73 paired-end polyA sra leaf seedling controlled 1 1 PRJEB22166
ERR2096665 Zea_mays B73 paired-end polyA sra leaf seedling controlled 1 1 PRJEB22166
ERR2096666 Zea_mays B73 paired-end polyA sra leaf seedling controlled 1 1 PRJEB22166
ERR2096667 Zea_mays B73 paired-end polyA sra leaf seedling controlled 1 1 PRJEB22166
ERR3773807 Zea_mays B73 paired-end polyA sra root seedling controlled 1 1 PRJEB35943
ERR3773808 Zea_mays B73 paired-end polyA sra root seedling controlled 1 1 PRJEB35943
ERR986091 Zea_mays B73 paired-end random sra root seedling controlled 1 1 PRJEB10406

Curation Rationale

To choose experiments for leaf and root tissues, we focused on datasets that have been used in a recent study and can be found in multiple databases.

Data Collection and Processing

In the max gene expression datasets, for each gene, we take the maximum transcript per million TPM value over experiments. Similarly, for the absolute expression datasets, we take the mean TPM value over experiments. Finally, for the on-off ex- pression, we assign 1 to a gene if it has a TPM value in one of the tissues. To create train-test-validation splits, we use orthogroup guided splitting as introduced by Washburn et al. 2019. Then, we split the training test sets so that we train on 80% of the orthogroups and test on 10%. Note that for each of the task-based datasets, we keep the same train-test-validate split.

BibTeX:

Dataset Card Authors

Taylor Ferebee (tf259@cornell.edu)

Dataset Card Contact

Taylor Ferebee (tf259@cornell.edu), Cinta Romay, Edward S. Buckler

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