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ImagineG2P
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imagine-ai-data-package

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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 49 new columns ({'pseudogenes', 'nitrogenase_carrier_hmm', 'ncbi_strain', 'median_protein_len', 'genes_per_mb_asm', 'q_l50', 'bacdive_id', 'n_contigs', 'nif_genes_hmm', 'annotation_qc', 'n_vnfK', 'species_name_as_published', 'genome_size_qc', 'assembly_status', 'n_anfD', 'q_ambiguous_frac', 'species_taxid', 'n_anfK', 'nitrogenase_carrier', 'has_protein_fasta', 'coding_density', 'taxid_route', 'total_residues', 'genes_per_mb', 'strain_taxid', 'total_genes', 'q_n50', 'q_n_contigs', 'mean_protein_len', 'representative_for_species', 'nitrogenase_carrier_names', 'q_nonstandard_bases', 'genome_size_bp', 'gene_density_qc', 'ncbi_gc_percent', 'gc_content', 'nitrogenase_methods_agree', 'n_vnfD', 'q_largest_contig', 'ncbi_checkm_completeness', 'ncbi_checkm_contamination', 'representative_for_strain', 'n_proteins', 'accession', 'protein_coding_genes', 'n_nifD', 'q_ambiguous_bases', 'n_nifH', 'n_nifK'}) and 10 missing columns ({'gtdb_family', 'gtdb_species_cluster', 'gtdb_is_cluster_representative', 'gtdb_phylum', 'gtdb_order', 'gtdb_species', 'gtdb_release', 'gtdb_domain', 'gtdb_class', 'gtdb_genus'}).

This happened while the csv dataset builder was generating data using

hf://datasets/ImagineG2P/imagine-ai-data-package/genomes.csv (at revision 3eebbb534521f8488e09ca3a0729c27c21457721), ['hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/genome_taxonomy_gtdb.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/genomes.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/growth_rates.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/metabolic_profiles_long.csv.gz', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/modelling_view.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/nfix_evidence_long.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/nfix_genome_labels.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/nfix_labels.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/strain_traits_long.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/strains.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/taxa.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/traits_long.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 1856, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 811, 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 822, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2381, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2309, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              species_name_as_published: string
              accession: string
              accession_core: int64
              genome_size_bp: double
              n_contigs: double
              ncbi_gc_percent: double
              protein_coding_genes: double
              total_genes: double
              pseudogenes: double
              genes_per_mb: double
              genome_size_qc: bool
              gene_density_qc: bool
              gc_content: double
              coding_density: double
              genes_per_mb_asm: double
              annotation_qc: bool
              n_proteins: double
              total_residues: double
              mean_protein_len: double
              median_protein_len: double
              q_n_contigs: double
              q_n50: double
              q_l50: double
              q_largest_contig: double
              q_ambiguous_bases: double
              q_ambiguous_frac: double
              q_nonstandard_bases: double
              bacdive_id: double
              species_taxid: double
              strain_taxid: double
              taxid_route: string
              ncbi_strain: string
              ncbi_checkm_completeness: double
              ncbi_checkm_contamination: double
              assembly_status: string
              has_protein_fasta: bool
              n_nifH: double
              n_nifD: double
              n_nifK: double
              n_vnfD: double
              n_vnfK: double
              n_anfD: double
              n_anfK: double
              nitrogenase_carrier_names: bool
              nitrogenase_carrier_hmm: bool
              nif_genes_hmm: string
              nitrogenase_carrier: bool
              nitrogenase_methods_agree: bool
              checkm2_completeness: double
              checkm2_contamination: double
              representative_for_strain: bool
              representative_for_species: bool
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 6965
              to
              {'accession_core': Value('int64'), 'gtdb_domain': Value('string'), 'gtdb_phylum': Value('string'), 'gtdb_class': Value('string'), 'gtdb_order': Value('string'), 'gtdb_family': Value('string'), 'gtdb_genus': Value('string'), 'gtdb_species': Value('string'), 'gtdb_species_cluster': Value('int64'), 'gtdb_is_cluster_representative': Value('bool'), 'checkm2_completeness': Value('float64'), 'checkm2_contamination': Value('float64'), 'gtdb_release': 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 1379, 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 956, 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 1702, 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 1858, 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 49 new columns ({'pseudogenes', 'nitrogenase_carrier_hmm', 'ncbi_strain', 'median_protein_len', 'genes_per_mb_asm', 'q_l50', 'bacdive_id', 'n_contigs', 'nif_genes_hmm', 'annotation_qc', 'n_vnfK', 'species_name_as_published', 'genome_size_qc', 'assembly_status', 'n_anfD', 'q_ambiguous_frac', 'species_taxid', 'n_anfK', 'nitrogenase_carrier', 'has_protein_fasta', 'coding_density', 'taxid_route', 'total_residues', 'genes_per_mb', 'strain_taxid', 'total_genes', 'q_n50', 'q_n_contigs', 'mean_protein_len', 'representative_for_species', 'nitrogenase_carrier_names', 'q_nonstandard_bases', 'genome_size_bp', 'gene_density_qc', 'ncbi_gc_percent', 'gc_content', 'nitrogenase_methods_agree', 'n_vnfD', 'q_largest_contig', 'ncbi_checkm_completeness', 'ncbi_checkm_contamination', 'representative_for_strain', 'n_proteins', 'accession', 'protein_coding_genes', 'n_nifD', 'q_ambiguous_bases', 'n_nifH', 'n_nifK'}) and 10 missing columns ({'gtdb_family', 'gtdb_species_cluster', 'gtdb_is_cluster_representative', 'gtdb_phylum', 'gtdb_order', 'gtdb_species', 'gtdb_release', 'gtdb_domain', 'gtdb_class', 'gtdb_genus'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/ImagineG2P/imagine-ai-data-package/genomes.csv (at revision 3eebbb534521f8488e09ca3a0729c27c21457721), ['hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/genome_taxonomy_gtdb.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/genomes.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/growth_rates.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/metabolic_profiles_long.csv.gz', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/modelling_view.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/nfix_evidence_long.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/nfix_genome_labels.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/nfix_labels.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/strain_traits_long.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/strains.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/taxa.csv', 'hf://datasets/ImagineG2P/imagine-ai-data-package@3eebbb534521f8488e09ca3a0729c27c21457721/traits_long.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)

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accession_core int64	gtdb_domain string	gtdb_phylum string	gtdb_class string	gtdb_order string	gtdb_family string	gtdb_genus string	gtdb_species string	gtdb_species_cluster int64	gtdb_is_cluster_representative bool	checkm2_completeness float64	checkm2_contamination float64	gtdb_release string
227,705	Bacteria	Bacillota	Bacilli	Paenibacillales	Paenibacillaceae	Thermobacillus	Thermobacillus xylanilyticus	907,165,215	false	99.98	0.87	v232
964,511,145	Bacteria	Bacteroidota	Bacteroidia	Flavobacteriales	Flavobacteriaceae	Polaribacter	Polaribacter amylolyticum	964,511,145	true	100	0.18	v232
20,099,375	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter	Acinetobacter variabilis	369,625	false	99.98	0.26	v232
657,795	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Burkholderiaceae_B	Bordetella	Bordetella pseudohinzii	657,795	true	100	0.14	v232
34,554,815	Bacteria	Pseudomonadota	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	Rhizobium	Rhizobium leguminosarum	2,008,365	false	100	1.67	v232
9,856,625	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Chromobacteriaceae	Aquitalea	Aquitalea denitrificans	9,856,625	true	100	0.08	v232
2,245,655	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Rhodocyclaceae	Thauera	Thauera propionica	2,245,655	true	100	0.68	v232
19,185	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Shewanellaceae	Shewanella	Shewanella halifaxensis	19,185	true	100	0.62	v232
16,863,255	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Micromonosporaceae	Planosporangium	Planosporangium mesophilum	16,863,255	true	98.55	0.14	v232
18,324,685	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Micromonosporaceae	Actinocatenispora	Actinocatenispora sera	18,324,685	true	96.79	1.49	v232
30,161,575	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Microbacteriaceae	Arenivirga	Arenivirga flava	30,161,575	true	92.98	3.28	v232
3,946,505	Bacteria	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Companilactobacillus	Companilactobacillus mishanensis	3,946,505	true	99.85	0.32	v232
17,656,525	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Mycobacteriaceae	Rhodococcus_F	Rhodococcus_F erythropolis	1,552,595	false	100	0.19	v232
23,065	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Aeromonadaceae	Tolumonas	Tolumonas auensis	23,065	true	100	1.12	v232
385,175	Bacteria	Bacillota	Bacilli	Staphylococcales	Salinicoccaceae	Salinicoccus	Salinicoccus albus	385,175	true	99.67	0.15	v232
1,183,985	Bacteria	Bacillota	Bacilli	Bacillales	DSM-1321	Peribacillus	Peribacillus loiseleuriae	1,183,985	true	100	1.54	v232
429,405	Bacteria	Bacteroidota	Bacteroidia	Cytophagales	Cyclobacteriaceae	Algoriphagus	Algoriphagus marincola	429,405	true	100	0.18	v232
2,802,875	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Bifidobacteriaceae	Galliscardovia	Galliscardovia primatium	2,802,875	true	97.55	1.05	v232
1,438,705	Bacteria	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Weissella	Weissella kandleri	1,438,705	true	99.96	0.05	v232
900,187,215	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Mycobacteriaceae	Corynebacterium	Corynebacterium imitans	739,455	false	99.99	0.13	v232
13,359,755	Bacteria	Pseudomonadota	Alphaproteobacteria	Rhizobiales	Xanthobacteraceae	Tardiphaga	Tardiphaga robiniae	13,359,755	true	100	0	v232
4,337,705	Bacteria	Actinomycetota	Rubrobacteria	Rubrobacterales	Rubrobacteraceae	Rubrobacter_C	Rubrobacter_C taiwanensis	4,337,705	true	99.69	0.4	v232
2,874,535	Bacteria	Bacillota	Bacilli	Bacillales	Cytobacillaceae	Mesobacillus	Mesobacillus jeotgali	2,874,535	true	100	0	v232
900,106,755	Bacteria	Bacteroidota	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides faecis	900,106,755	true	100	0.38	v232
23,634,845	Bacteria	Bacteroidota	Bacteroidia	Flavobacteriales	Flavobacteriaceae	Flavobacterium	Flavobacterium amniphilum	23,634,845	true	99.99	5.2	v232
820,185	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Aeromonadaceae	Aeromonas	Aeromonas tecta	820,185	true	100	0.53	v232
1,936,575	Bacteria	Bacteroidota	Bacteroidia	Flavobacteriales	Flavobacteriaceae	Polaribacter	Polaribacter agarivorans	1,936,575	true	100	0.05	v232
746,875	Bacteria	Bacillota	Bacilli	Paenibacillales	Paenibacillaceae	Fontibacillus	Fontibacillus macerans	900,454,495	false	99.99	1.06	v232
12,845	Bacteria	Bacteroidota	Bacteroidia	Bacteroidales	Tannerellaceae	Parabacteroides	Parabacteroides distasonis	12,845	true	99.97	1.28	v232
429,725	Bacteria	Bacillota	Bacilli	Bacillales	Salisediminibacteriaceae	Alkalicoccus	Alkalicoccus chagannorensis	429,725	true	99.92	0.08	v232
39,529,395	Bacteria	Actinomycetota	Actinomycetes	Streptomycetales	Streptomycetaceae	Streptomyces	Streptomyces albidochromogenes	39,529,395	true	100	0.01	v232
770,795	Bacteria	Pseudomonadota	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Noviluteimonas	Noviluteimonas dokdonensis	770,795	true	99.99	0.17	v232
426,505	Bacteria	Pseudomonadota	Alphaproteobacteria	Thalassobaculales	Thalassobaculaceae	Nisaea	Nisaea denitrificans	426,505	true	98.62	0	v232
4,295,525	Bacteria	Campylobacterota	Campylobacteria	Campylobacterales	Helicobacteraceae	Helicobacter	Helicobacter pylori	900,478,295	false	99.99	0.02	v232
9,688,945	Bacteria	Desulfobacterota	Desulfobacteria	Desulfobacterales	Desulfosarcinaceae	Desulfosarcina	Desulfosarcina alkanivorans	9,688,945	true	97.05	7.54	v232
10,634,845	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Aquipseudomonas	Aquipseudomonas antarctica	900,624,995	false	100	0.2	v232
16,862,375	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Micromonosporaceae	Actinoplanes	Actinoplanes rishiriensis	16,862,375	true	100	5.56	v232
301,055	Bacteria	Bacillota	Bacilli	Lactobacillales	Aerococcaceae	Falseniella	Falseniella ignava	301,055	true	97.94	0.12	v232
2,259,585	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Bifidobacteriaceae	Bombiscardovia	Bombiscardovia coagulans	2,259,585	true	99.5	0.1	v232
14,445	Bacteria	Bacillota	Bacilli	Lactobacillales	Lactobacillaceae	Leuconostoc	Leuconostoc mesenteroides	14,445	true	99.99	1.23	v232
285,535	Bacteria	Bacillota	Bacilli	Bacillales	Bacillaceae_L	Ferdinandcohnia	Ferdinandcohnia timonensis	285,535	true	100	1.99	v232
24,347,275	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Balneatricaceae	Amphritea	Amphritea japonica	16,592,435	false	100	0.69	v232
900,100,305	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Burkholderiaceae_C	Paracidovorax	Paracidovorax citrulli	900,100,305	true	100	0	v232
4,354,085	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Halieaceae	Halioglobus	Halioglobus unicus	4,354,085	true	99.99	0.17	v232
947,036,595	Bacteria	Bacillota	Bacilli	Staphylococcales	Staphylococcaceae	Mammaliicoccus	Mammaliicoccus lentus	2,902,755	false	100	0.42	v232
5,885,605	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Alteromonadaceae	Colwellia	Colwellia ponticola	5,885,605	true	100	0.78	v232
30,160,755	Bacteria	Pseudomonadota	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Brevundimonas	Brevundimonas denitrificans	30,160,755	true	99.99	0.94	v232
2,157,205	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Halomonadaceae	Kushneria	Kushneria marisflavi	2,157,205	true	99.99	0	v232
16,863,575	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Micromonosporaceae	Micromonospora	Micromonospora sediminimaris	16,863,575	true	100	0.13	v232
2,355,475	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Metapseudomonas	Metapseudomonas furukawaii	2,355,475	true	100	0.23	v232
382,345	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Burkholderiaceae_D	Telluria	Telluria niastensis	382,345	true	100	2.31	v232
1,570,825	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Cellulomonadaceae	Cellulosimicrobium	Cellulosimicrobium funkei	4,519,295	false	100	0.45	v232
819,445	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Mycobacteriaceae	Corynebacterium	Corynebacterium humireducens	819,445	true	100	0.12	v232
1,612,985	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Mycobacteriaceae	Nocardia	Nocardia gamkensis	1,612,985	true	100	0.17	v232
422,505	Bacteria	Bacillota	Bacilli	Paenibacillales	Paenibacillaceae	Paenibacillus_D	Paenibacillus_D pinihumi	422,505	true	100	1.25	v232
14,650,755	Bacteria	Actinomycetota	Actinomycetes	Streptomycetales	Streptomycetaceae	Streptomyces	Streptomyces chryseus	14,650,755	true	99.43	0.41	v232
42,428,765	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Pseudonocardiaceae	Kutzneria	Kutzneria kofuensis	14,203,355	false	100	3.58	v232
2,356,335	Bacteria	Actinomycetota	Actinomycetes	Mycobacteriales	Mycobacteriaceae	Mycobacterium	Mycobacterium stephanolepidis	2,356,335	true	100	0.2	v232
1,047,675	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Yersinia	Yersinia aleksiciae	1,047,675	true	94.37	0.01	v232
42,684,825	Bacteria	Bacteroidota	Bacteroidia	Sphingobacteriales	Sphingobacteriaceae	Sphingobacterium	Sphingobacterium populi	42,684,825	true	99.68	0.09	v232
900,185,595	Bacteria	Cyanobacteriota	Cyanobacteriia	Cyanobacteriales	Nostocaceae	Calothrix_A	Calothrix_A rhizosoleniae	900,185,595	true	99.89	0.14	v232
900,187,985	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Methylophilaceae	Methylobacillus	Methylobacillus rhizosphaerae	900,187,985	true	99.99	0.02	v232
525,795	Bacteria	Bacillota	Bacilli	Lactobacillales	Listeriaceae	Listeria	Listeria aquatica	525,795	true	89.95	3.06	v232
934,605	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Burkholderiaceae	Pandoraea	Pandoraea vervacti	934,605	true	100	0.15	v232
186,245	Bacteria	Campylobacterota	Campylobacteria	Campylobacterales	Sulfurovaceae	Nitratifractor	Nitratifractor salsuginis	186,245	true	100	0.02	v232
25,506,355	Bacteria	Actinomycetota	Actinomycetes	Streptosporangiales	Streptosporangiaceae	Sphaerisporangium	Sphaerisporangium corydalis	25,506,355	true	99.37	1.81	v232
16,908,875	Bacteria	Bacillota	Bacilli	Bacillales	Domibacillaceae	Bacillus_BX	Bacillus_BX ectoiniformans	16,908,875	true	100	0	v232
900,109,575	Bacteria	Bacteroidota	Bacteroidia	Sphingobacteriales	Sphingobacteriaceae	Olivibacter	Olivibacter domesticus	900,109,575	true	100	4.17	v232
3,116,835	Bacteria	Bacillota	Bacilli	Lactobacillales	Streptococcaceae	Lactococcus	Lactococcus termiticola	3,116,835	true	100	1.92	v232
701,425	Bacteria	Deinococcota	Deinococci	Deinococcales	Deinococcaceae	Deinococcus	Deinococcus frigens	701,425	true	99.99	0.15	v232
2,843,355	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Alteromonadaceae	Colwellia	Colwellia echini	2,843,355	true	100	0	v232
3,399,445	Bacteria	Pseudomonadota	Alphaproteobacteria	Caulobacterales	Parvularculaceae	Parvularcula	Parvularcula marina	3,399,445	true	99.54	0.04	v232
27,924,165	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Burkholderiaceae	Polynucleobacter	Polynucleobacter yangtzensis	1,595,965	false	99.98	0	v232
2,870,965	Bacteria	Pseudomonadota	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Tsuneonella	Tsuneonella flava	2,870,965	true	100	0.09	v232
423,845	Bacteria	Desulfobacterota	Thermodesulfobacteria	Thermodesulfobacteriales	Thermodesulfobacteriaceae	Thermodesulfobacterium	Thermodesulfobacterium hveragerdense	423,845	true	100	0.93	v232
30,268,225	Bacteria	Actinomycetota	Actinomycetes	Streptosporangiales	Streptosporangiaceae	Nocardiopsis_D	Nocardiopsis_D ansamitocini	30,268,225	true	100	0.93	v232
14,202,475	Bacteria	Actinomycetota	Actinomycetes	Streptomycetales	Streptomycetaceae	Streptomyces	Streptomyces paradoxus	14,202,475	true	100	0.05	v232
2,807,055	Bacteria	Bacteroidota	Bacteroidia	Flavobacteriales	Flavobacteriaceae	Confluentibacter	Confluentibacter citreus	2,807,055	true	99.99	0.66	v232
1,660,705	Bacteria	Bacteroidota	Bacteroidia	Bacteroidales	Marinilabiliaceae	Saccharicrinis	Saccharicrinis aurantiacus	1,660,705	true	100	0.59	v232
17,876,535	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Micrococcaceae	Paeniglutamicibacter	Paeniglutamicibacter kerguelensis	17,876,535	true	99.82	0.78	v232
1,730,285	Bacteria	Bacillota	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus_L	Enterococcus_L ureasiticus	1,730,285	true	99.99	0.13	v232
14,196,125	Bacteria	Pseudomonadota	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Brevundimonas	Brevundimonas mediterranea	14,196,125	true	99.74	0.01	v232
442,595	Bacteria	Pseudomonadota	Gammaproteobacteria	Methylococcales	Cycloclasticaceae	Cycloclasticus	Cycloclasticus pugetii	384,415	false	99.99	0.21	v232
9,299,475	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Bifidobacteriaceae	Bifidobacterium	Bifidobacterium avesanii	9,299,475	true	99.62	0.49	v232
1,676,655	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Perlucidibaca	Perlucidibaca aquatica	1,676,655	true	100	0.14	v232
196,275	Bacteria	Deinococcota	Deinococci	Deinococcales	Deinococcaceae	Deinococcus	Deinococcus geothermalis	196,275	true	100	0.01	v232
425,585	Bacteria	Bacteroidota	Bacteroidia	Chitinophagales	Chitinophagaceae	Terrimonas	Terrimonas ferruginea	425,585	true	99.99	0.03	v232
3,350,405	Bacteria	Pseudomonadota	Alphaproteobacteria	Acetobacterales	Acetobacteraceae	Gluconacetobacter	Gluconacetobacter liquefaciens	3,350,405	true	100	0.42	v232
29,846,315	Bacteria	Pseudomonadota	Gammaproteobacteria	Pseudomonadales	Halomonadaceae	Cobetia	Cobetia amphilecti	30,010,415	false	99.97	5.84	v232
341,105	Bacteria	Actinomycetota	Actinomycetes	Streptosporangiales	Streptosporangiaceae	Nocardiopsis_A	Nocardiopsis_A potens	341,105	true	99.44	0.22	v232
526,415	Bacteria	Chloroflexota	Chloroflexia	Chloroflexales	Kallotenuaceae	Kallotenue	Kallotenue papyrolyticum	526,415	true	99.39	0.5	v232
47,836,735	Bacteria	Actinomycetota	Actinomycetes	Actinomycetales	Bifidobacteriaceae	Bombiscardovia	Bombiscardovia crudilactis	738,005	false	99.99	0.35	v232
973,105	Bacteria	Bacteroidota	Bacteroidia	Flavobacteriales	Flavobacteriaceae	Zobellia	Zobellia galactanivorans	973,105	true	100	0.03	v232
900,104,045	Bacteria	Desulfobacterota	Desulfovibrionia	Desulfovibrionales	Desulfonatronovibrionaceae	Desulfonauticus	Desulfonauticus submarinus	900,104,045	true	98.6	0.07	v232
3,286,915	Bacteria	Bacteroidota	Bacteroidia	Cytophagales	Cyclobacteriaceae	Ohtaekwangia	Ohtaekwangia flava	3,286,915	true	99.27	0.54	v232
2,067,135	Bacteria	Bacteroidota	Bacteroidia	Cytophagales	Spirosomataceae	Spirosoma	Spirosoma rigui	2,067,135	true	99.81	0.01	v232
14,705	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Shewanellaceae	Shewanella	Shewanella frigidimarina	3,797,125	false	100	0.16	v232
14,192,095	Bacteria	Pseudomonadota	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	Phyllobacterium	Phyllobacterium trifolii	14,192,095	true	99.99	0.28	v232
39,532,925	Bacteria	Actinomycetota	Actinomycetes	Streptomycetales	Streptomycetaceae	Streptomyces	Streptomyces violaceusniger	39,532,925	true	100	1.05	v232
1,270,065	Bacteria	Pseudomonadota	Gammaproteobacteria	Burkholderiales	Burkholderiaceae_C	Limnohabitans_A	Limnohabitans_A planktonicus	1,270,065	true	100	0.04	v232

End of preview.

IMAGINE-AI data package v0.2

Analysis-ready phenotype labels and genome tables for microbial genotype-to-phenotype modelling, built for the DOE GENESIS IMAGINE-AI project (PI: Ember Morrissey, West Virginia University). Version 0.2 applies twelve cleanup steps to version 0.1; CHANGES.md lists every change with its count, and DATA_DICTIONARY.md describes every column.

Tables

File	One row per	Use as
`taxa.csv`	species	backbone and NCBI lineage
`strains.csv`	BacDive strain	strain keys
`genomes.csv`	genome assembly	genotype side only, incl. `nitrogenase_carrier`
`genome_taxonomy_gtdb.csv`	genome assembly	GTDB taxonomy, GTDB species cluster, CheckM2 (CC BY-SA 4.0)
`traits_long.csv`	species × trait × source	species-tier labels with `source_type`
`strain_traits_long.csv.gz`	strain × trait × value	strain-tier BacDive observations, controlled vocabulary
`metabolic_profiles_long.csv.gz`	strain × test	BacDive metabolic profiles
`nfix_labels.csv`	species	nitrogen-fixation phenotype label
`nfix_genome_labels.csv`	genome	N-fixation label per genome, strain or species tier, genotype veto
`nfix_evidence_long.csv`	evidence row	every phenotype or genotype statement behind the labels, with tier and quote
`growth_rates.csv`	observation	growth rate per hour, doubling time
`modelling_view.csv`	species with a genome	starting table for models

Rules

Genotype never labels phenotype. nitrogenase_carrier is a genome-derived target; the N-fixation phenotype labels come only from experiments, assays or explicit claims.
A genome-derived fact can remove an impossible label, never add one.
source_type = curated, text_mined or curated_may_include_predicted are labels. The last marks Madin values whose sources include ProTraits, a predictor: they count, and every consensus they feed carries <trait>_may_include_predicted. predicted (FAPROTAX) and culture_condition rows are kept for reference only.
Split by lineage (GTDB genus or species cluster), never at random.
Empty is not negative.

Licences and attribution

BacDive (DSMZ), CC BY 4.0: Schober et al. 2025, Nucleic Acids Research, "BacDive in 2025: the core database for prokaryotic strain data".
Madin et al. 2020, Scientific Data, "A synthesis of bacterial and archaeal phenotypic trait data", CC BY 4.0 (figshare collection 10.6084/m9.figshare.c.4843290).
GTDB (genome_taxonomy_gtdb.csv), CC BY-SA 4.0: Parks et al., Genome Taxonomy Database.
NCBI Taxonomy and assembly metadata: public domain (US government work).
Literature-mined N-fixation evidence: facts with short quotations (at most 300 characters) from the cited papers, identified by PMC ID or DOI.
NFixDB gene calls are not included: the source declares no licence.

The rest of the package is released under CC BY 4.0.

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