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Datasets:
chumphati
/
1M_RNAseq_SRA_samples_annotations

Tasks:
Tabular Classification
Text Classification
Languages:
English
Tags:
biology
rnaseq
sra
metadata
annotations
bioinformatics
License:
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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 3 new columns ({'uberon_name', 'value', 'cosine_similarity'}) and 1 missing columns ({'run_accession,study_accession,instrument_platform,library_selection,library_strategy,base_count,sequencing_source,biopsy_site,bs_uberon_code,biopsy_type,cell_line,cell_type,organ,organ_uberon_code,disease,do_code,is_cancer,treatment,treatment_time,response,age,sex,ethnicity'}).

This happened while the csv dataset builder was generating data using

hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations/manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv (at revision 0f6bd478dc328525e082108eed62e85df74cc5ba), [/tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/800k_completed_metadata.csv.gz (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/800k_completed_metadata.csv.gz), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_disease_values_mapped_to_dot_with_cosine.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_disease_values_mapped_to_dot_with_cosine.tsv), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_organ_values_mapped_to_uberon_with_cosine.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_organ_values_mapped_to_uberon_with_cosine.tsv), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv)]

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 "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1800, in _prepare_split_single
                  writer.write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 765, in write_table
                  self._write_table(pa_table, writer_batch_size=writer_batch_size)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 773, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
                  return cast_table_to_schema(table, schema)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              value: string
              uberon_name: string
              cosine_similarity: double
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 628
              to
              {'run_accession,study_accession,instrument_platform,library_selection,library_strategy,base_count,sequencing_source,biopsy_site,bs_uberon_code,biopsy_type,cell_line,cell_type,organ,organ_uberon_code,disease,do_code,is_cancer,treatment,treatment_time,response,age,sex,ethnicity': Value('string')}
              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 1347, 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 980, in convert_to_parquet
                  builder.download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 882, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 943, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1646, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1802, 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 3 new columns ({'uberon_name', 'value', 'cosine_similarity'}) and 1 missing columns ({'run_accession,study_accession,instrument_platform,library_selection,library_strategy,base_count,sequencing_source,biopsy_site,bs_uberon_code,biopsy_type,cell_line,cell_type,organ,organ_uberon_code,disease,do_code,is_cancer,treatment,treatment_time,response,age,sex,ethnicity'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations/manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv (at revision 0f6bd478dc328525e082108eed62e85df74cc5ba), [/tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/800k_completed_metadata.csv.gz (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/800k_completed_metadata.csv.gz), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_disease_values_mapped_to_dot_with_cosine.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_disease_values_mapped_to_dot_with_cosine.tsv), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_organ_values_mapped_to_uberon_with_cosine.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/FINAL_pass_unique_organ_values_mapped_to_uberon_with_cosine.tsv), /tmp/hf-datasets-cache/medium/datasets/76358883644537-config-parquet-and-info-chumphati-1M_RNAseq_SRA_s-fdc3f12d/hub/datasets--chumphati--1M_RNAseq_SRA_samples_annotations/snapshots/0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv (origin=hf://datasets/chumphati/1M_RNAseq_SRA_samples_annotations@0f6bd478dc328525e082108eed62e85df74cc5ba/manual_dics/global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv)]
              
              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? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

run_accession,study_accession,instrument_platform,library_selection,library_strategy,base_count,sequencing_source,biopsy_site,bs_uberon_code,biopsy_type,cell_line,cell_type,organ,organ_uberon_code,disease,do_code,is_cancer,treatment,treatment_time,response,age,sex,ethnicity
string
DRR006379,PRJDB2573,ILLUMINA,other,RNA-Seq,1155551472,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,RNA-PCR,not applicable,unknown,unknown,unknown,indonesia
DRR006411,PRJDB2573,ILLUMINA,other,RNA-Seq,892184688,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR001636,PRJDA74549,ILLUMINA,other,RNA-Seq,10748726512,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006443,PRJDB2573,ILLUMINA,other,RNA-Seq,1785032604,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR000897,PRJDA63201,ILLUMINA,other,RNA-Seq,837507136,bulk,uterus,UBERON:0000995,primary,HeLa,cells,uterine cervix,UBERON:0000002,adenocarcinoma,DOID:299,true,unknown,not applicable,not applicable,30Y6M,female,African American
DRR006395,PRJDB2573,ILLUMINA,other,RNA-Seq,3401654148,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR001173,PRJDA69989,ILLUMINA,other,RNA-Seq,942609312,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,25 mM,not applicable,unknown,82Y,female,Caucasian
DRR006444,PRJDB2573,ILLUMINA,other,RNA-Seq,1411286688,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006396,PRJDB2573,ILLUMINA,other,RNA-Seq,1168000200,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR001174,PRJDA69989,ILLUMINA,other,RNA-Seq,1683594408,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,25 mM,not applicable,unknown,82Y,female,Caucasian
DRR006412,PRJDB2573,ILLUMINA,other,RNA-Seq,1114844544,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia:manado
DRR001637,PRJDA74549,ILLUMINA,other,RNA-Seq,9256447208,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006413,PRJDB2573,ILLUMINA,other,RNA-Seq,1384376904,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR006414,PRJDB2573,ILLUMINA,other,RNA-Seq,1168161768,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR006415,PRJDB2573,ILLUMINA,other,RNA-Seq,1171413360,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia:manado
DRR001175,PRJDA69989,ILLUMINA,other,RNA-Seq,1274794436,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,unknown,not applicable,not applicable,82Y,female,Caucasian
DRR006397,PRJDB2573,ILLUMINA,other,RNA-Seq,1390483548,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR002593,PRJDB2198,ILLUMINA,other,RNA-Seq,1501885400,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,3h,unknown,82Y,female,Caucasian
DRR006380,PRJDB2573,ILLUMINA,other,RNA-Seq,1095352704,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,RNA,not applicable,unknown,unknown,male,indonesia:manado
DRR001638,PRJDA74549,ILLUMINA,other,RNA-Seq,7664614440,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR002594,PRJDB2198,ILLUMINA,other,RNA-Seq,1294879374,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,3h,unknown,82Y,female,Caucasian
DRR006381,PRJDB2573,ILLUMINA,other,RNA-Seq,1405230264,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR006416,PRJDB2573,ILLUMINA,other,RNA-Seq,1092049884,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia:manado
DRR001639,PRJDA74549,ILLUMINA,other,RNA-Seq,9034120608,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR002595,PRJDB2198,ILLUMINA,other,RNA-Seq,1738426052,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,6h,unknown,82Y,female,Caucasian
DRR006445,PRJDB2573,ILLUMINA,other,RNA-Seq,910075860,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006446,PRJDB2573,ILLUMINA,other,RNA-Seq,1051295724,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR001176,PRJDA69989,ILLUMINA,other,RNA-Seq,1068884424,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,unknown,not applicable,not applicable,82Y,female,Caucasian
DRR006447,PRJDB2573,ILLUMINA,other,RNA-Seq,1099023876,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR001622,PRJDA74549,ILLUMINA,other,RNA-Seq,2198179768,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR001624,PRJDA74549,ILLUMINA,other,RNA-Seq,2233820728,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006417,PRJDB2573,ILLUMINA,other,RNA-Seq,1293147648,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR001627,PRJDA74549,ILLUMINA,other,RNA-Seq,1997235160,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR001628,PRJDA74549,ILLUMINA,other,RNA-Seq,14192528648,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR001629,PRJDA74549,ILLUMINA,other,RNA-Seq,9786770344,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR001640,PRJDA74549,ILLUMINA,other,RNA-Seq,6413906608,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR002596,PRJDB2198,ILLUMINA,other,RNA-Seq,1155046632,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,6h,unknown,82Y,female,Caucasian
DRR002597,PRJDB2198,ILLUMINA,other,RNA-Seq,1464629288,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,9h,unknown,82Y,female,Caucasian
DRR006398,PRJDB2573,ILLUMINA,other,RNA-Seq,1438045920,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR002598,PRJDB2198,ILLUMINA,other,RNA-Seq,2157903378,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,9h,unknown,82Y,female,Caucasian
DRR001630,PRJDA74549,ILLUMINA,other,RNA-Seq,8876218904,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR001631,PRJDA74549,ILLUMINA,other,RNA-Seq,7762199960,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006418,PRJDB2573,ILLUMINA,other,RNA-Seq,1307210040,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006382,PRJDB2573,ILLUMINA,other,RNA-Seq,1310010768,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,RNA,not applicable,unknown,unknown,female,indonesia:manado
DRR006383,PRJDB2573,ILLUMINA,other,RNA-Seq,1362454956,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia:manado
DRR006384,PRJDB2573,ILLUMINA,other,RNA-Seq,1161191808,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR001641,PRJDA74549,ILLUMINA,other,RNA-Seq,5890259464,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006419,PRJDB2573,ILLUMINA,other,RNA-Seq,1275646032,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006420,PRJDB2573,ILLUMINA,other,RNA-Seq,1395470664,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006399,PRJDB2573,ILLUMINA,other,RNA-Seq,1425104892,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR002599,PRJDB2198,ILLUMINA,other,RNA-Seq,2377391530,bulk,urinary bladder,UBERON:0001255,primary,T24,neoplastic cell,urinary bladder,UBERON:0001255,cancer,DOID:162,true,glucose deprivation,24h,unknown,82Y,female,Caucasian
DRR003595,PRJDB2065,ILLUMINA,other,RNA-Seq,1661020003,bulk,eye; retina; pigmented layer of retina,UBERON:0000970;UBERON:0000966;UBERON:0001782,primary,hTERT-RPE1,epithelial cell,eye,UBERON:0000970,unknown,unknown,false,control siRNA,not applicable,unknown,1Y,female,unknown
DRR001632,PRJDA74549,ILLUMINA,other,RNA-Seq,12043796912,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR003596,PRJDB2065,ILLUMINA,other,RNA-Seq,1693351824,bulk,eye; retina; pigmented layer of retina,UBERON:0000970;UBERON:0000966;UBERON:0001782,primary,hTERT-RPE1,epithelial cell,eye,UBERON:0000970,unknown,unknown,false,HBiX1 siRNA,not applicable,unknown,1Y,female,unknown
DRR006421,PRJDB2573,ILLUMINA,other,RNA-Seq,1330920828,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006422,PRJDB2573,ILLUMINA,other,RNA-Seq,1378854936,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006423,PRJDB2573,ILLUMINA,other,RNA-Seq,1447009704,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006385,PRJDB2573,ILLUMINA,other,RNA-Seq,1205176140,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006424,PRJDB2573,ILLUMINA,other,RNA-Seq,1235755368,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006425,PRJDB2573,ILLUMINA,other,RNA-Seq,1225777680,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006400,PRJDB2573,ILLUMINA,other,RNA-Seq,1352658060,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006426,PRJDB2573,ILLUMINA,other,RNA-Seq,1551120876,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR003597,PRJDB2065,ILLUMINA,other,RNA-Seq,1575019797,bulk,eye; retina; pigmented layer of retina,UBERON:0000970;UBERON:0000966;UBERON:0001782,primary,hTERT-RPE1,epithelial cell,eye,UBERON:0000970,unknown,unknown,false,siRNA,not applicable,unknown,1Y,female,unknown
DRR001633,PRJDA74549,ILLUMINA,other,RNA-Seq,6548106344,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006459,PRJDB2573,ILLUMINA,other,RNA-Seq,1274219820,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR001634,PRJDA74549,ILLUMINA,other,RNA-Seq,7532415936,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006460,PRJDB2573,ILLUMINA,other,RNA-Seq,1460853324,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR001635,PRJDA74549,ILLUMINA,other,RNA-Seq,7681848200,bulk,adrenal gland,UBERON:0002369,primary,PC12 HTT-SW2-Q73-TagRFP clone 17,unknown,brain,UBERON:0000955,adrenal gland pheochromocytoma,DOID:0050892,false,unknown,not applicable,not applicable,unknown,male,unknown
DRR006386,PRJDB2573,ILLUMINA,other,RNA-Seq,1263890880,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia
DRR006387,PRJDB2573,ILLUMINA,other,RNA-Seq,1343810808,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006388,PRJDB2573,ILLUMINA,other,RNA-Seq,1260349812,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006461,PRJDB2573,ILLUMINA,other,RNA-Seq,1360320156,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006389,PRJDB2573,ILLUMINA,other,RNA-Seq,3995018712,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006390,PRJDB2573,ILLUMINA,other,RNA-Seq,4152753036,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR003598,PRJDB2065,ILLUMINA,other,RNA-Seq,917636211,bulk,eye; retina; pigmented layer of retina,UBERON:0000970;UBERON:0000966;UBERON:0001782,primary,hTERT-RPE1,epithelial cell,eye,UBERON:0000970,unknown,unknown,false,XIST siRNA,not applicable,unknown,1Y,female,unknown
DRR006391,PRJDB2573,ILLUMINA,other,RNA-Seq,1354060728,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006462,PRJDB2573,ILLUMINA,other,RNA-Seq,1267312968,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006475,PRJDB2573,ILLUMINA,other,RNA-Seq,1643335092,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006463,PRJDB2573,ILLUMINA,other,RNA-Seq,1145820060,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006476,PRJDB2573,ILLUMINA,other,RNA-Seq,1094570928,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006392,PRJDB2573,ILLUMINA,other,RNA-Seq,1396152720,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006477,PRJDB2573,ILLUMINA,other,RNA-Seq,968795892,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006393,PRJDB2573,ILLUMINA,other,RNA-Seq,1352147904,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006401,PRJDB2573,ILLUMINA,other,RNA-Seq,3685741344,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006464,PRJDB2573,ILLUMINA,other,RNA-Seq,1388988468,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006402,PRJDB2573,ILLUMINA,other,RNA-Seq,670000536,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006374,PRJDB2573,ILLUMINA,other,RNA-Seq,904787892,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,RNA-PCR,not applicable,unknown,unknown,unknown,indonesia
DRR006478,PRJDB2573,ILLUMINA,other,RNA-Seq,1145428488,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006375,PRJDB2573,ILLUMINA,other,RNA-Seq,969379956,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,RNA,not applicable,unknown,unknown,unknown,indonesia
DRR006427,PRJDB2573,ILLUMINA,other,RNA-Seq,3247644768,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR006465,PRJDB2573,ILLUMINA,other,RNA-Seq,1464608052,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006403,PRJDB2573,ILLUMINA,other,RNA-Seq,1756793412,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006376,PRJDB2573,ILLUMINA,other,RNA-Seq,1018550772,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,RNA,not applicable,unknown,unknown,unknown,indonesia
DRR006394,PRJDB2573,ILLUMINA,other,RNA-Seq,1219565088,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006428,PRJDB2573,ILLUMINA,other,RNA-Seq,1333974348,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006429,PRJDB2573,ILLUMINA,other,RNA-Seq,1365948612,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia: bitung
DRR006430,PRJDB2573,ILLUMINA,other,RNA-Seq,1501837488,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006479,PRJDB2573,ILLUMINA,other,RNA-Seq,1125806508,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia: bitung
DRR006492,PRJDB2573,ILLUMINA,other,RNA-Seq,1321828776,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,male,indonesia:manado
DRR006493,PRJDB2573,ILLUMINA,other,RNA-Seq,1316200608,bulk,blood,UBERON:0000178,blood,primary tissue,unknown,unknown,unknown,malaria,DOID:12365,false,unknown,not applicable,not applicable,unknown,female,indonesia:manado
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1M RNAseq SRA samples annotations

  • 800k_completed_metadata.csv: main metadata table for approximately 800k annotated RNA-seq/SRA samples.
  • 800k_rnaseq_metappuccino_labels.db: SQLite database containing Metappuccino labels and associated structured metadata.
  • manual_dics/: folder containing manual normalization and cross-column remapping dictionaries.
    • FINAL_pass_unique_biopsy_site_values_mapped_to_uberon_with_cosine.tsv: maps raw biopsy_site values to normalized UBERON anatomical terms.
    • FINAL_pass_unique_organ_values_mapped_to_uberon_with_cosine.tsv: maps raw organ values to normalized UBERON anatomical terms.
    • FINAL_pass_unique_disease_values_mapped_to_dot_with_cosine.tsv: maps raw disease values to normalized DOT/DOID disease terms.
    • global_all_column_remaps_WITH_ONTOLOGY_MAPPING_VALUE_ONLY.tsv: defines cross-column remapping rules for values found in the wrong metadata field.
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