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Datasets:
Kimchikilla
/
gaia-corpus

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Size:
10K<n<100K
Tags:
soil
microbiome
metagenomics
agriculture
environmental-science
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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 1308 new columns ({'Microvirga', 'Caedimonadaceae', 'Caldilineaceae', 'Leptospiraceae', 'Candidatus_Udaeobacter', 'Nocardiopsaceae', 'Caldalkalibacillus', 'Prosthecomicrobium', 'Stella', 'Rhodoligotrophos', 'Raineyella', 'Singulisphaera', 'Thermogutta', 'Roseburia', 'Alteromonadaceae', 'Bdellovibrio', 'Desulfobacteraceae', 'Sphingoaurantiacus', 'Polycyclovorans', 'Parviterribacter', 'Chthonomonadaceae', 'Nubsella', 'Vulgatibacter', 'Pseudomonas', 'Massarinaceae', 'Ambisporaceae', 'Shewanellaceae', 'Helvella', 'Clostridiales_Family_XII._Incertae_Sedis', 'Marinifilaceae', 'Patulibacter', 'Knoellia', 'Akkermansia', 'Cytophagaceae', 'Lutispora', 'Riemerella', 'Candidatus_Alysiosphaera', 'Hahella', 'Rothia', 'Heliimonas', 'Planctomyces', 'Cyanobacteriaceae', 'Frankia', 'Asticcacaulis', 'Desulfotomaculum', 'Desulfuromonas', 'Amorphus', 'Syntrophomonadaceae', 'Spirochaetaceae', 'Streptomyces', 'Candidatus_Berkiella', 'Massilia', 'Algoriphagus', 'Chujaibacter', 'Anabaena', 'Cryobacterium', 'Clostridiales_Family_XIII._Incertae_Sedis', 'Oerskovia', 'Leptospira', 'Zavarzinella', 'Niveispirillum', 'Bacteriovorax', 'Legionella', 'Sphingobacterium', 'Bosea', 'Niameybacter', 'Ancylobacter', 'Magnetococcus', 'Caenimonas', 'Methylophilaceae', 'Asanoa', 'Lutibaculum', 'Piskurozymaceae', 'Arthrobacter', 'Lessoniaceae', 'Acidisphaera', 'Egibacteraceae', 'Moraxellaceae', 'Aridibacter', 'Bicosoeca', 'Geothermomicrobium', 'Deinococcus', 'Acidiphilium', 'Rheinheimera', 'Ruminococcaceae', 'Micrococcaceae', 'Thiohaloba
...
acter', 'Polyangium', 'Constrictibacter', 'Burkholderia', 'Cellvibrionaceae', 'Actinomycetospora', 'Erythrobacteraceae', 'Actinocorallia', 'Crossiella', 'Verrucomicrobia_subdivision_3', 'Oscillospiraceae', 'Synechococcus', 'Salpingoecidae', 'Jiangella', 'Edaphobacter', 'Papillibacter', 'Glycomyces', 'Roseiflexaceae', 'Nitriliruptoraceae', 'Rhodanobacteraceae', 'Hodophilus', 'Dehalococcoidaceae', 'Magnetospira', 'Deinococcaceae', 'Luteimonas', 'Truepera', 'Coriobacteriaceae', 'Friedmanniella', 'Psychroglaciecola', 'Cutibacterium', 'Lautropia', 'Pedobacter', 'Syntrophaceae', 'Nitrosospira', 'Nordella', 'Caldicoprobacter', 'Intestinimonas', 'Xylariaceae', 'Pelomonas', 'Enterorhabdus', 'Methylobacillus', 'Rhodobiaceae', 'Oceanicaulis', 'Domibacillus', 'Nakamurellaceae', 'Succinivibrionaceae', 'Roseiflexus', 'Geminicoccus', 'Halobacteriovoraceae', 'Brachybacterium', 'Angustibacter', 'Alcanivoracaceae', 'Rhodanobacter', 'Thioalkalispiraceae', 'Gaiellaceae', 'Oceanirhabdus', 'Gardnerella', 'Anaerostipes', 'Arcticibacter', 'Ruania', 'Camisiidae', 'Gelidibacter', 'Occallatibacter', 'Desnuesiella', 'Erysipelothrix', 'Criblamydiaceae', 'Rhizocola', 'Sporacetigenium', 'Ralstonia', 'Limnothrix', 'Sphaerobacteraceae', 'Kofleria', 'Ktedonobacter', 'Actinospicaceae', 'Brevundimonas', 'Burkholderiaceae', 'Flavisolibacter', 'Limnochordaceae', 'Candidatus_Promineofilum', 'Propionimicrobium', 'Nakamurella', 'Methanosarcina', 'Tetracladium', 'Bryobacter', 'Candidatus_Chloroploca', 'Alterococcus'}) and 6 missing columns ({'source_group', 'redistribution_decision', 'notes', 'sha256', 'bytes', 'path'}).

This happened while the csv dataset builder was generating data using

hf://datasets/Kimchikilla/gaia-corpus/processed_real/gaia-abundance-v1.csv (at revision 0e8db43d392c8a4b3aee4574c029d026dfa678b0), ['hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/manifest.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-abundance-v1.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-abundance-v2.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v1.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v2.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v3.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v7.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/public_soil_baseline_summary.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/public_soil_dataset_inventory.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/public_soil_prescription_candidate_index.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/soil_state_neon_ph.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/soil_state_westerfeld.csv']

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/python3.14/site-packages/datasets/builder.py", line 1837, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/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/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2369, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2297, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              sample_id: string
              analysis_id: string
              Acantholichen: double
              Acaulospora: double
              Acaulosporaceae: double
              Acetatifactor: double
              Acetitomaculum: double
              Acetivibrio: double
              Acetobacter: double
              Acetobacteraceae: double
              Acidaminobacter: double
              Acidaminococcaceae: double
              Acidibacter: double
              Acidicaldus: double
              Acidicapsa: double
              Acidiferrobacteraceae: double
              Acidimicrobiaceae: double
              Acidiphilium: double
              Acidipila: double
              Acidisoma: double
              Acidisphaera: double
              Aciditerrimonas: double
              Acidithiobacillaceae: double
              Acidithiobacillus: double
              Acidithrix: double
              Acidobacteriaceae: double
              Acidobacterium: double
              Acidocella: double
              Acidothermaceae: double
              Acidothermus: double
              Acidovorax: double
              Acinetobacter: double
              Actaea: double
              Actinoallomurus: double
              Actinocatenispora: double
              Actinocorallia: double
              Actinokineospora: double
              Actinomadura: double
              Actinomyces: double
              Actinomycetaceae: double
              Actinomycetospora: double
              Actinophytocola: double
              Actinoplanes: double
              Actinopolymorpha: double
              Actinospica: double
              Actinospicaceae: double
              Actinotalea: double
              Acuticoccus: double
              Adhaeribacter: double
              Adinetidae: double
              Aeromicrobium: double
              Aeromonadaceae: double
              Aeromonas: double
              Aestuariimicrobium: double
              Aestuariispira: double
              Aetherobacter: double
              Afifella: double
              Afipia: double
              Agaricicola: double
              Agathobacter: double
              Agrococcus: double
              Agromyces: double
              Ahrensia: double
              Akkermansia: double
              Albidovulum: double
              Alcaligenaceae: double
              Alcanivoracaceae: double
              Alcanivorax: double
              Algoriphagus: double
              ...
              etrobacter: double
              Thermosporothrix: double
              Thermotunica: double
              Thioalkalispira: double
              Thioalkalispiraceae: double
              Thiobacillus: double
              Thiohalobacter: double
              Thiohalophilus: double
              Thiomonas: double
              Thiothrix: double
              Thiotrichaceae: double
              Timonella: double
              Tissierella: double
              Tissierellaceae: double
              Tistlia: double
              Tistrella: double
              Tomitella: double
              Trichocomaceae: double
              Trichomonascaceae: double
              Tropheryma: double
              Truepera: double
              Trueperaceae: double
              Tsukamurella: double
              Tsukamurellaceae: double
              Tumebacillus: double
              Tunicatimonas: double
              Turicibacter: double
              Turneriella: double
              Tylenchidae: double
              Tyzzerella: double
              Uliginosibacterium: double
              Umbelopsidaceae: double
              Umbelopsis: double
              Undibacterium: double
              Ureibacillus: double
              Vampirovibrio: double
              Variibacter: double
              Variovorax: double
              Veillonella: double
              Veillonellaceae: double
              Verrucomicrobia_subdivision_3: double
              Verrucomicrobiaceae: double
              Verrucomicrobium: double
              Vibrio: double
              Vicinamibacter: double
              Vicinamibacteraceae: double
              Virgisporangium: double
              Vogesella: double
              Vulgatibacter: double
              Vulgatibacteraceae: double
              Williamsia: double
              Woeseia: double
              Woeseiaceae: double
              Wolbachia: double
              Woodsholea: double
              Xanthobacteraceae: double
              Xanthomonadaceae: double
              Xanthomonas: double
              Xylaria: double
              Xylariaceae: double
              Yersiniaceae: double
              Zavarzinella: double
              Zoogloea: double
              Zoogloeaceae: double
              Zymomonas: double
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 167876
              to
              {'path': Value('string'), 'bytes': Value('int64'), 'sha256': Value('string'), 'source_group': Value('string'), 'redistribution_decision': Value('string'), 'notes': 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 1369, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1683, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1839, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
                  ...<4 lines>...
                  )
              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 1308 new columns ({'Microvirga', 'Caedimonadaceae', 'Caldilineaceae', 'Leptospiraceae', 'Candidatus_Udaeobacter', 'Nocardiopsaceae', 'Caldalkalibacillus', 'Prosthecomicrobium', 'Stella', 'Rhodoligotrophos', 'Raineyella', 'Singulisphaera', 'Thermogutta', 'Roseburia', 'Alteromonadaceae', 'Bdellovibrio', 'Desulfobacteraceae', 'Sphingoaurantiacus', 'Polycyclovorans', 'Parviterribacter', 'Chthonomonadaceae', 'Nubsella', 'Vulgatibacter', 'Pseudomonas', 'Massarinaceae', 'Ambisporaceae', 'Shewanellaceae', 'Helvella', 'Clostridiales_Family_XII._Incertae_Sedis', 'Marinifilaceae', 'Patulibacter', 'Knoellia', 'Akkermansia', 'Cytophagaceae', 'Lutispora', 'Riemerella', 'Candidatus_Alysiosphaera', 'Hahella', 'Rothia', 'Heliimonas', 'Planctomyces', 'Cyanobacteriaceae', 'Frankia', 'Asticcacaulis', 'Desulfotomaculum', 'Desulfuromonas', 'Amorphus', 'Syntrophomonadaceae', 'Spirochaetaceae', 'Streptomyces', 'Candidatus_Berkiella', 'Massilia', 'Algoriphagus', 'Chujaibacter', 'Anabaena', 'Cryobacterium', 'Clostridiales_Family_XIII._Incertae_Sedis', 'Oerskovia', 'Leptospira', 'Zavarzinella', 'Niveispirillum', 'Bacteriovorax', 'Legionella', 'Sphingobacterium', 'Bosea', 'Niameybacter', 'Ancylobacter', 'Magnetococcus', 'Caenimonas', 'Methylophilaceae', 'Asanoa', 'Lutibaculum', 'Piskurozymaceae', 'Arthrobacter', 'Lessoniaceae', 'Acidisphaera', 'Egibacteraceae', 'Moraxellaceae', 'Aridibacter', 'Bicosoeca', 'Geothermomicrobium', 'Deinococcus', 'Acidiphilium', 'Rheinheimera', 'Ruminococcaceae', 'Micrococcaceae', 'Thiohaloba
              ...
              acter', 'Polyangium', 'Constrictibacter', 'Burkholderia', 'Cellvibrionaceae', 'Actinomycetospora', 'Erythrobacteraceae', 'Actinocorallia', 'Crossiella', 'Verrucomicrobia_subdivision_3', 'Oscillospiraceae', 'Synechococcus', 'Salpingoecidae', 'Jiangella', 'Edaphobacter', 'Papillibacter', 'Glycomyces', 'Roseiflexaceae', 'Nitriliruptoraceae', 'Rhodanobacteraceae', 'Hodophilus', 'Dehalococcoidaceae', 'Magnetospira', 'Deinococcaceae', 'Luteimonas', 'Truepera', 'Coriobacteriaceae', 'Friedmanniella', 'Psychroglaciecola', 'Cutibacterium', 'Lautropia', 'Pedobacter', 'Syntrophaceae', 'Nitrosospira', 'Nordella', 'Caldicoprobacter', 'Intestinimonas', 'Xylariaceae', 'Pelomonas', 'Enterorhabdus', 'Methylobacillus', 'Rhodobiaceae', 'Oceanicaulis', 'Domibacillus', 'Nakamurellaceae', 'Succinivibrionaceae', 'Roseiflexus', 'Geminicoccus', 'Halobacteriovoraceae', 'Brachybacterium', 'Angustibacter', 'Alcanivoracaceae', 'Rhodanobacter', 'Thioalkalispiraceae', 'Gaiellaceae', 'Oceanirhabdus', 'Gardnerella', 'Anaerostipes', 'Arcticibacter', 'Ruania', 'Camisiidae', 'Gelidibacter', 'Occallatibacter', 'Desnuesiella', 'Erysipelothrix', 'Criblamydiaceae', 'Rhizocola', 'Sporacetigenium', 'Ralstonia', 'Limnothrix', 'Sphaerobacteraceae', 'Kofleria', 'Ktedonobacter', 'Actinospicaceae', 'Brevundimonas', 'Burkholderiaceae', 'Flavisolibacter', 'Limnochordaceae', 'Candidatus_Promineofilum', 'Propionimicrobium', 'Nakamurella', 'Methanosarcina', 'Tetracladium', 'Bryobacter', 'Candidatus_Chloroploca', 'Alterococcus'}) and 6 missing columns ({'source_group', 'redistribution_decision', 'notes', 'sha256', 'bytes', 'path'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/Kimchikilla/gaia-corpus/processed_real/gaia-abundance-v1.csv (at revision 0e8db43d392c8a4b3aee4574c029d026dfa678b0), ['hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/manifest.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-abundance-v1.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-abundance-v2.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v1.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v2.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v3.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/gaia-metadata-v7.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/public_soil_baseline_summary.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/public_soil_dataset_inventory.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/public_soil_prescription_candidate_index.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/soil_state_neon_ph.csv', 'hf://datasets/Kimchikilla/gaia-corpus@0e8db43d392c8a4b3aee4574c029d026dfa678b0/processed_real/soil_state_westerfeld.csv']
              
              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.

path
string
bytes
int64
sha256
string
source_group
string
redistribution_decision
string
notes
string
configs/emp.yaml
517
667f1a3f6567f08ffd6592502200716a58774c038e4d3bcf977affd91a6ac981
config
include
Gaia source configuration
configs/mgnify.yaml
768
3ca13103b98c6aab1d6f34e86269a909503760802f96641f3ef8ce3d95bfbbf1
config
include
Gaia source configuration
configs/neon.yaml
865
c6435936e06ecafb1c2473ad50d1938e3a2d0ca79487786a5338d5e9b2090929
config
include
Gaia source configuration
processed_real/gaia-abundance-v1.csv
21,816,452
9572ef51b6c05e229a85a714d92127d76aa724f6967224287375e744e147f158
mixed_public_processed
include
MGnify-derived abundance matrix
processed_real/gaia-abundance-v2.csv
81,216,632
53f9d1f9022db96bab519d6d6d6f1146f03e3be42d97007cbd49230cfeb7d4eb
mixed_public_processed
include
Expanded public abundance matrix
processed_real/gaia-corpus-v1.pkl
11,858,403
1b4256b42a98bf7cb90681bad50070ec277222f34853ef3edf8680e4a6cc71fa
mixed_public_processed
include
Serialized training corpus; pickle, use in trusted environments only
processed_real/gaia-corpus-v2.pkl
14,684,400
eefc648b08b594edf4317939e6c6c4703ee9cf4d08be559a2297a3063d97c763
mixed_public_processed
include
Serialized training corpus; pickle, use in trusted environments only
processed_real/gaia-corpus-v3.pkl
20,797,709
4ca570a7714b28474e31e014ed329f7e0bc27068c5badd905a547df81e83f6ae
mixed_public_processed
include
Serialized training corpus; pickle, use in trusted environments only
processed_real/gaia-corpus-v7-clr.pkl
21,533,145
258a3eb0de84c1d747e36a65f278ad8e14248f3f9c819fb5256c6547496e71d1
mixed_public_processed
include
CLR-normalized serialized training corpus; pickle, use in trusted environments only
processed_real/gaia-metadata-v1.csv
177,713
e032952d60ed95caeb1331254a7eeb12bb5c48dd43c214487178ed88c9114932
mixed_public_processed
include
MGnify-derived metadata
processed_real/gaia-metadata-v2.csv
209,648
bccd54baddc29bacdc493e615aa4f2b56b109391ad5b9cb8baf374d4ad146566
mixed_public_processed
include
EMP + v1 metadata
processed_real/gaia-metadata-v3.csv
312,258
683919c3478b4eb8c7f48a767b404744c3a1343a4004c5c446eb416553f71547
mixed_public_processed
include
EMP + MGnify + NEON metadata
processed_real/gaia-metadata-v7.csv
312,258
683919c3478b4eb8c7f48a767b404744c3a1343a4004c5c446eb416553f71547
mixed_public_processed
include
Metadata aligned with gaia-corpus-v7-clr
processed_real/honest_soil_state_benchmark.json
7,636
458875052287f22753ade6c6e46912f9d217f3ad6698f7a8ab262ffe481bec4d
derived_benchmark_public
include
Bernburg benchmark section removed
processed_real/public_soil_baseline_results.json
116,726
6398b879ec3f9a71c679554c2d27ebcba962e9f87da8dccc5084b6349b676d6e
derived_benchmark_public
include
Bernburg rows removed
processed_real/public_soil_baseline_summary.csv
5,919
5fe28b164df65c4c3be35eb68ff7e0440759b5fedfb5bddba50a19b5ff9282e1
derived_benchmark_public
include
Bernburg rows removed
processed_real/public_soil_dataset_inventory.csv
2,821
069116c6eba0e8f0811df4ffcfb1a76780c1e1b5e08096a221b2b4cebc1e96a1
release_inventory
include
Bernburg row removed from public release inventory
processed_real/public_soil_dataset_inventory.json
5,334
39eea5915a81cfa317fd4069e33be5ccf5e4dc311b84772aa7f7de8fff5c05b7
release_inventory
include
Bernburg row removed from public release inventory
processed_real/public_soil_prescription_candidate_index.csv
264,745
25caf0a7f1c93de8b880b10d0c81bb71205800e437d66a9605f945393cacc34f
westerfeld_cc_by_4_0
include
Westerfeld prescription-candidate index; Bernburg rows removed
processed_real/soil_state_data_manifest.json
1,933
3a9e9e7a5764a79066674f53adde3192b358d3123a8b9fb4d025a7469a9ba505
release_manifest
include
Sanitized soil-state manifest; Bernburg removed
processed_real/soil_state_neon_ph.csv
5,741,165
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NEON soil microbiome plus site-level pH diagnostic table
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westerfeld_cc_by_4_0
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BonaRes Westerfeld paired microbiome, soil chemistry, management, yield table
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Token vocabulary generated from public processed corpus
README.md
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Hugging Face dataset card, Korean primary
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Source license decision log, Korean primary
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End of preview.

Gaia Hugging Face 공개 데이터셋 배포 보고서

배포일: 2026-06-29
Hugging Face: https://huggingface.co/datasets/Kimchikilla/gaia-corpus

결론

이번 배포본은 원본 데이터 전체 미러가 아니라, 라이선스 리스크를 줄인 공개 가공 데이터셋이다. Gaia 코드의 Apache-2.0 라이선스를 원천 데이터에 덮어씌우지 않고, 출처별 라이선스와 이용 조건을 별도로 명시했다.

핵심 정책은 다음과 같다.

구분 처리
공개 허용 가공본 Hugging Face에 업로드
원본 대형 raw mirror Hugging Face에서 삭제
Bernburg 원본/가공 테이블 라이선스 부재로 삭제 및 제외
JGI 수동 다운로드 원본/v10 파생 파일 계정/약관 기반 다운로드라 제외
Dryad placeholder DOI는 CC0지만 로컬 파일이 0바이트라 제외
benchmark 파일 Bernburg 행/섹션 제거 후 public release 버전만 업로드

업로드된 파일

Hugging Face 공개본에는 총 25개 payload 파일과 매니페스트가 올라갔다. 저장소 검증 기준으로 raw/ 폴더는 삭제되었고, bernburg가 들어간 파일명은 남아 있지 않다.

경로 내용
processed_real/gaia-abundance-v1.csv MGnify 기반 abundance matrix
processed_real/gaia-abundance-v2.csv 확장 public abundance matrix
processed_real/gaia-corpus-v1.pkl 학습 재현용 serialized corpus
processed_real/gaia-corpus-v2.pkl 학습 재현용 serialized corpus
processed_real/gaia-corpus-v3.pkl 학습 재현용 serialized corpus
processed_real/gaia-corpus-v7-clr.pkl CLR 정규화 corpus
processed_real/gaia-metadata-v1.csv MGnify 기반 metadata
processed_real/gaia-metadata-v2.csv EMP + v1 metadata
processed_real/gaia-metadata-v3.csv EMP + MGnify + NEON metadata
processed_real/gaia-metadata-v7.csv v7 corpus metadata
processed_real/soil_state_neon_ph.csv NEON site-level pH 진단 테이블
processed_real/soil_state_westerfeld.csv BonaRes Westerfeld paired soil state 테이블
processed_real/public_soil_* Bernburg 행을 제거한 public benchmark/inventory/index
processed_real/tokenizer.json public corpus 기반 tokenizer
configs/*.yaml 데이터 소스 설정
README.md HF 데이터셋 카드
SOURCE_LICENSES.md 출처별 라이선스 판정
manifest.csv, manifest.json 파일별 크기, SHA-256, 출처 그룹

*.pkl 파일은 pickle 직렬화 파일이므로 신뢰 가능한 환경에서만 로드해야 한다.

삭제한 항목

Hugging Face에서 기존에 올라가 있던 raw/** 전체를 삭제했다. 특히 아래 항목은 공개 재배포 기준에서 제거했다.

항목 이유
raw/bernburg/** 원본 GitHub 저장소와 fork 모두 명시 라이선스 없음
processed_real/bernburg_abundance.csv Bernburg 파생 데이터라 제외
processed_real/bernburg_metadata.csv Bernburg 파생 데이터라 제외
raw/dryad_amendments/** 로컬/HF 파일이 실제 데이터가 아닌 placeholder
raw/dryad_vanadium/** 로컬/HF 파일이 실제 데이터가 아닌 0바이트 placeholder
대형 raw FASTQ/BIOM/zip mirror 공개 corpus 재현에 필수 아님, 출처별 조건 혼재

라이선스 판정

Source 공개본 처리 라이선스/근거 주의
Gaia 작성 코드/설정 포함 Apache-2.0 Gaia 작성물에만 적용
NEON 포함 NEON 공개 데이터 정책. 기존 CC0 안내와 2026-06-30 전후 CC BY 4.0 전환을 보수적으로 반영 attribution 권장
BonaRes Westerfeld 포함 DataCite DOI 10.20387/bonares-w669-gdsd 기준 CC BY 4.0 attribution 필수
Dryad amendments 실제 데이터 제외 DOI 10.5061/dryad.4qrfj6q9n는 CC0 로컬 파일이 placeholder라 미포함
Dryad vanadium 실제 데이터 제외 DOI 10.5061/dryad.6wwpzgn52는 CC0 로컬 파일이 0바이트라 미포함
Bernburg GitHub repo 제외 GitHub API 기준 fork/upstream 모두 license 없음 공개 재배포 가정 금지
JGI manual download 제외 계정/약관 기반 다운로드 재배포 조건 확인 전 제외
MGnify / EMP / Naylor 기반 corpus 가공본 포함 공개 연구 DB/데이터 기반. 원 출처 citation과 이용 조건 준수 필요 Gaia가 원천 데이터를 소유하지 않음

모델 관점에서의 의미

이번 HF 배포본으로 가능한 것은 “공개 데이터 기반 진단 baseline, corpus 학습, benchmark 재현”이다. 자동 처방 추천을 제품 수준으로 주장하기에는 아직 부족하다. 처방 모델을 위해서는 같은 농지에서 반복 측정된 미생물, 토양 화학성, 시비·관수·기상, 처방 실행, 수확량/병해/토양 개선 결과가 묶인 paired time-series 데이터가 필요하다.

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