Datasets:

prakhya15
/

human-bacterial-isolates

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 ({'records_with_sequence_type', 'records_with_serotype', 'records', 'unique_strains', 'records_with_isolate'}) and 19 missing columns ({'sequence_type', 'host_scope', 'strain', 'serotype', 'final_decision', 'biosample_accession', 'geographic_location', 'species_taxid', 'human_infection', 'host', 'collection_date', 'zoonotic', 'assembly_accession', 'biosample_id', 'review_notes', 'identifier_type', 'isolate', 'sample_identifier', 'animal_associated'}).

This happened while the csv dataset builder was generating data using

hf://datasets/prakhya15/human-bacterial-isolates/HUMAN_BACTERIAL_ISOLATES_SUMMARY.csv (at revision 695d4ad1eb3d685cd266f835f12b669dadba84b5), ['hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/HUMAN_BACTERIAL_ISOLATES_FINAL.csv', 'hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/HUMAN_BACTERIAL_ISOLATES_SUMMARY.csv', 'hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/final_bacterial_species_audit.csv', 'hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/human_vs_humanhost_comparison.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 1848, 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 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              species: string
              records: int64
              unique_strains: int64
              records_with_isolate: int64
              records_with_serotype: int64
              records_with_sequence_type: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1052
              to
              {'species': Value('string'), 'species_taxid': Value('int64'), 'strain': Value('string'), 'isolate': Value('string'), 'serotype': Value('string'), 'sequence_type': Value('float64'), 'host': Value('string'), 'collection_date': Value('float64'), 'geographic_location': Value('float64'), 'assembly_accession': Value('string'), 'biosample_accession': Value('string'), 'biosample_id': Value('int64'), 'identifier_type': Value('string'), 'sample_identifier': Value('string'), 'human_infection': Value('bool'), 'zoonotic': Value('bool'), 'animal_associated': Value('bool'), 'host_scope': Value('string'), 'final_decision': Value('string'), 'review_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 1694, 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 1850, 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 5 new columns ({'records_with_sequence_type', 'records_with_serotype', 'records', 'unique_strains', 'records_with_isolate'}) and 19 missing columns ({'sequence_type', 'host_scope', 'strain', 'serotype', 'final_decision', 'biosample_accession', 'geographic_location', 'species_taxid', 'human_infection', 'host', 'collection_date', 'zoonotic', 'assembly_accession', 'biosample_id', 'review_notes', 'identifier_type', 'isolate', 'sample_identifier', 'animal_associated'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/prakhya15/human-bacterial-isolates/HUMAN_BACTERIAL_ISOLATES_SUMMARY.csv (at revision 695d4ad1eb3d685cd266f835f12b669dadba84b5), ['hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/HUMAN_BACTERIAL_ISOLATES_FINAL.csv', 'hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/HUMAN_BACTERIAL_ISOLATES_SUMMARY.csv', 'hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/final_bacterial_species_audit.csv', 'hf://datasets/prakhya15/human-bacterial-isolates@695d4ad1eb3d685cd266f835f12b669dadba84b5/human_vs_humanhost_comparison.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.

species string	species_taxid int64	strain string	isolate string	serotype null	sequence_type null	host string	collection_date null	geographic_location null	assembly_accession string	biosample_accession string	biosample_id int64	identifier_type string	sample_identifier string	human_infection bool	zoonotic bool	animal_associated bool	host_scope string	final_decision string	review_notes string
Acinetobacter baumannii	470	139BC	null	null	null	Homo sapiens	null	null	GCF_051294825.1	SAMN48311203	48,311,203	strain	SAMN48311203	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F02_FAO49464_BC01	not applicable	null	null	Homo sapiens	null	null	GCA_051933185.1	SAMN50012447	50,012,447	strain	SAMN50012447	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F06_FAQ08163_BC01	not applicable	null	null	Homo sapiens	null	null	GCA_051931625.1	SAMN50012495	50,012,495	strain	SAMN50012495	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F06_FAQ08163_BC11	not applicable	null	null	Homo sapiens	null	null	GCA_051932255.1	SAMN50012505	50,012,505	strain	SAMN50012505	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F06_FAQ08163_BC12	not applicable	null	null	Homo sapiens	null	null	GCA_051931635.1	SAMN50012506	50,012,506	strain	SAMN50012506	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F11_FAQ07850_BC01	not applicable	null	null	Homo sapiens	null	null	GCF_051932685.1	SAMN50012554	50,012,554	strain	SAMN50012554	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F11_FAQ07850_BC02	not applicable	null	null	Homo sapiens	null	null	GCA_051932295.1	SAMN50012555	50,012,555	strain	SAMN50012555	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144AB_F12_FAQ08076_BC07	not applicable	null	null	Homo sapiens	null	null	GCA_051932715.1	SAMN50012572	50,012,572	strain	SAMN50012572	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	144D	null	null	null	Homo sapiens	null	null	GCA_051294815.1	SAMN48311208	48,311,208	strain	SAMN48311208	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	169D	null	null	null	Homo sapiens	null	null	GCF_051294805.1	SAMN48311391	48,311,391	strain	SAMN48311391	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	17978rif	null	null	null	Homo sapiens	null	null	GCF_051941085.1	SAMN50235498	50,235,498	strain	SAMN50235498	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	19-046	null	null	null	Homo sapiens	null	null	GCA_041002735.1	SAMN42001262	42,001,262	strain	SAMN42001262	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	19-113	null	null	null	Homo sapiens	null	null	GCA_041002685.1	SAMN42001265	42,001,265	strain	SAMN42001265	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	19-226	null	null	null	Homo sapiens	null	null	GCA_041002475.1	SAMN42001268	42,001,268	strain	SAMN42001268	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	20-190	null	null	null	Homo sapiens	null	null	GCA_041001725.1	SAMN42001272	42,001,272	strain	SAMN42001272	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2022CK-00772	missing	null	null	Homo sapiens	null	null	GCF_027992645.1	SAMN32733976	32,733,976	strain	SAMN32733976	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2023CK-01274	missing	null	null	Homo sapiens	null	null	GCF_032634445.1	SAMN37709326	37,709,326	strain	SAMN37709326	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2023CK-01292	missing	null	null	Homo sapiens	null	null	GCF_045689365.1	SAMN38122020	38,122,020	strain	SAMN38122020	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00246	missing	null	null	Homo sapiens	null	null	GCF_037008745.1	SAMN40254326	40,254,326	strain	SAMN40254326	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00278	missing	null	null	Homo sapiens	null	null	GCF_037429075.1	SAMN40557119	40,557,119	strain	SAMN40557119	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00319	missing	null	null	Homo sapiens	null	null	GCF_039518815.1	SAMN40557123	40,557,123	strain	SAMN40557123	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00329	missing	null	null	Homo sapiens	null	null	GCF_037751415.1	SAMN40632425	40,632,425	strain	SAMN40632425	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00375	missing	null	null	Homo sapiens	null	null	GCF_038069235.1	SAMN40921371	40,921,371	strain	SAMN40921371	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00376	missing	null	null	Homo sapiens	null	null	GCF_038069255.1	SAMN40921370	40,921,370	strain	SAMN40921370	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00452	missing	null	null	Homo sapiens	null	null	GCF_038418265.1	SAMN41020280	41,020,280	strain	SAMN41020280	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00461	missing	null	null	Homo sapiens	null	null	GCF_038418285.1	SAMN41020282	41,020,282	strain	SAMN41020282	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00462	missing	null	null	Homo sapiens	null	null	GCF_038418365.1	SAMN41020287	41,020,287	strain	SAMN41020287	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00536	missing	null	null	Homo sapiens	null	null	GCF_038627275.1	SAMN41094846	41,094,846	strain	SAMN41094846	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00537	missing	null	null	Homo sapiens	null	null	GCF_038522965.1	SAMN41094845	41,094,845	strain	SAMN41094845	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00538	missing	null	null	Homo sapiens	null	null	GCF_038627255.1	SAMN41094844	41,094,844	strain	SAMN41094844	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00546	missing	null	null	Homo sapiens	null	null	GCF_038627335.1	SAMN41094848	41,094,848	strain	SAMN41094848	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00647	missing	null	null	Homo sapiens	null	null	GCF_039653385.1	SAMN41407424	41,407,424	strain	SAMN41407424	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00841	missing	null	null	Homo sapiens	null	null	GCA_040273435.2	SAMN41984685	41,984,685	strain	SAMN41984685	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00842	missing	null	null	Homo sapiens	null	null	GCA_040273095.2	SAMN41984684	41,984,684	strain	SAMN41984684	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-00843	missing	null	null	Homo sapiens	null	null	GCA_040273015.2	SAMN41984683	41,984,683	strain	SAMN41984683	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01048	missing	null	null	Homo sapiens	null	null	GCA_040898785.2	SAMN42837556	42,837,556	strain	SAMN42837556	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01097	missing	null	null	Homo sapiens	null	null	GCA_040939585.2	SAMN42837561	42,837,561	strain	SAMN42837561	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01224	missing	null	null	Homo sapiens	null	null	GCA_041292065.2	SAMN43185122	43,185,122	strain	SAMN43185122	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01225	missing	null	null	Homo sapiens	null	null	GCA_041292045.2	SAMN43185121	43,185,121	strain	SAMN43185121	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01226	missing	null	null	Homo sapiens	null	null	GCA_041292025.2	SAMN43185120	43,185,120	strain	SAMN43185120	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01227	missing	null	null	Homo sapiens	null	null	GCA_041292005.2	SAMN43185119	43,185,119	strain	SAMN43185119	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01357	missing	null	null	Homo sapiens	null	null	GCA_041760695.2	SAMN43497284	43,497,284	strain	SAMN43497284	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01384	missing	null	null	Homo sapiens	null	null	GCA_042209715.2	SAMN43585576	43,585,576	strain	SAMN43585576	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01385	missing	null	null	Homo sapiens	null	null	GCA_042209595.2	SAMN43585575	43,585,575	strain	SAMN43585575	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01386	missing	null	null	Homo sapiens	null	null	GCA_042209675.2	SAMN43585574	43,585,574	strain	SAMN43585574	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01391	missing	null	null	Homo sapiens	null	null	GCA_042165515.2	SAMN43815358	43,815,358	strain	SAMN43815358	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01407	missing	null	null	Homo sapiens	null	null	GCA_045182155.1	SAMN43963448	43,963,448	strain	SAMN43963448	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01444	missing	null	null	Homo sapiens	null	null	GCA_042445505.2	SAMN43963451	43,963,451	strain	SAMN43963451	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01445	missing	null	null	Homo sapiens	null	null	GCA_042443055.2	SAMN43963452	43,963,452	strain	SAMN43963452	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01459	missing	null	null	Homo sapiens	null	null	GCA_042443115.2	SAMN43963453	43,963,453	strain	SAMN43963453	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01503	missing	null	null	Homo sapiens	null	null	GCA_042700245.2	SAMN44063871	44,063,871	strain	SAMN44063871	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	2024CK-01504	missing	null	null	Homo sapiens	null	null	GCA_042945475.2	SAMN44063870	44,063,870	strain	SAMN44063870	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	209D	null	null	null	Homo sapiens	null	null	GCF_051294795.1	SAMN48311433	48,311,433	strain	SAMN48311433	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	241D	null	null	null	Homo sapiens	null	null	GCF_051294695.1	SAMN48311754	48,311,754	strain	SAMN48311754	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	361BC	null	null	null	Homo sapiens	null	null	GCF_051294735.1	SAMN48311536	48,311,536	strain	SAMN48311536	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	471CP	null	null	null	Homo sapiens	null	null	GCA_051294765.1	SAMN48311441	48,311,441	strain	SAMN48311441	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	580D	null	null	null	Homo sapiens	null	null	GCF_051294675.1	SAMN48311777	48,311,777	strain	SAMN48311777	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	600BC	null	null	null	Homo sapiens	null	null	GCF_051294685.1	SAMN48311801	48,311,801	strain	SAMN48311801	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	658U	null	null	null	Homo sapiens	null	null	GCF_051294705.1	SAMN48311733	48,311,733	strain	SAMN48311733	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	721D	null	null	null	Homo sapiens	null	null	GCF_051294655.1	SAMN48311827	48,311,827	strain	SAMN48311827	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	728D	null	null	null	Homo sapiens	null	null	GCA_051294725.1	SAMN48311582	48,311,582	strain	SAMN48311582	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	769BC	null	null	null	Homo sapiens	null	null	GCF_051294755.2	SAMN48311502	48,311,502	strain	SAMN48311502	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	800BC	null	null	null	Homo sapiens	null	null	GCA_051294745.1	SAMN48311511	48,311,511	strain	SAMN48311511	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	815D	null	null	null	Homo sapiens	null	null	GCF_051294665.1	SAMN48312002	48,312,002	strain	SAMN48312002	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	916D	null	null	null	Homo sapiens	null	null	GCA_051294715.1	SAMN48311668	48,311,668	strain	SAMN48311668	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	940BC	null	null	null	Homo sapiens	null	null	GCF_051294645.1	SAMN48312026	48,312,026	strain	SAMN48312026	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	966CSF	null	null	null	Homo sapiens	null	null	GCF_051294635.1	SAMN48312029	48,312,029	strain	SAMN48312029	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	986BC	null	null	null	Homo sapiens	null	null	GCA_051294605.1	SAMN48312064	48,312,064	strain	SAMN48312064	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	A1014	missing	null	null	Homo sapiens	null	null	GCF_042478285.1	SAMN36999747	36,999,747	strain	SAMN36999747	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	A207	missing	null	null	Homo sapiens	null	null	GCF_042474915.1	SAMN36998938	36,998,938	strain	SAMN36998938	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	A26326	missing	null	null	Homo sapiens	null	null	GCF_050164325.1	SAMN42539093	42,539,093	strain	SAMN42539093	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	A26329	missing	null	null	Homo sapiens	null	null	GCF_050164075.1	SAMN42539096	42,539,096	strain	SAMN42539096	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-10_FGL	null	null	null	Homo sapiens	null	null	GCF_052055455.1	SAMN42124024	42,124,024	strain	SAMN42124024	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-12_FGL	null	null	null	Homo sapiens	null	null	GCF_052055445.1	SAMN42124025	42,124,025	strain	SAMN42124025	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-14_FGL	null	null	null	Homo sapiens	null	null	GCF_052054865.1	SAMN42124026	42,124,026	strain	SAMN42124026	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-18_FGL	null	null	null	Homo sapiens	null	null	GCF_052054815.1	SAMN42124027	42,124,027	strain	SAMN42124027	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-1_FGL	null	null	null	Homo sapiens	null	null	GCF_052055475.1	SAMN42124021	42,124,021	strain	SAMN42124021	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-20_FGL	null	null	null	Homo sapiens	null	null	GCF_052054135.1	SAMN42124029	42,124,029	strain	SAMN42124029	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-25_FGL	null	null	null	Homo sapiens	null	null	GCF_052054115.1	SAMN42124030	42,124,030	strain	SAMN42124030	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-26_FGL	null	null	null	Homo sapiens	null	null	GCF_052053505.1	SAMN42124031	42,124,031	strain	SAMN42124031	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-34_FGL	null	null	null	Homo sapiens	null	null	GCF_052053485.1	SAMN42124034	42,124,034	strain	SAMN42124034	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-37_FGL	null	null	null	Homo sapiens	null	null	GCF_052052845.1	SAMN42124036	42,124,036	strain	SAMN42124036	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-38_FGL	null	null	null	Homo sapiens	null	null	GCF_052052835.1	SAMN42124037	42,124,037	strain	SAMN42124037	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-39_FGL	null	null	null	Homo sapiens	null	null	GCF_052052205.1	SAMN42124038	42,124,038	strain	SAMN42124038	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-3_FGL	null	null	null	Homo sapiens	null	null	GCF_052055465.1	SAMN42124022	42,124,022	strain	SAMN42124022	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-40_FGL	null	null	null	Homo sapiens	null	null	GCF_052052195.1	SAMN42124039	42,124,039	strain	SAMN42124039	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB-41_FGL	null	null	null	Homo sapiens	null	null	GCF_052051545.1	SAMN42124040	42,124,040	strain	SAMN42124040	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB0614	null	null	null	Homo sapiens	null	null	GCF_050562275.1	SAMN48330161	48,330,161	strain	SAMN48330161	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB11-AUFP	null	null	null	Homo sapiens	null	null	GCF_040543095.1	SAMN42110409	42,110,409	strain	SAMN42110409	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB16-AUFP	null	null	null	Homo sapiens	null	null	GCF_052040695.1	SAMN48008028	48,008,028	strain	SAMN48008028	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB17-AUFP	null	null	null	Homo sapiens	null	null	GCF_051397055.1	SAMN48008029	48,008,029	strain	SAMN48008029	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB1801	null	null	null	Homo sapiens	null	null	GCF_050562245.1	SAMN48330175	48,330,175	strain	SAMN48330175	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB191	null	null	null	Homo sapiens	null	null	GCF_028548795.2	SAMN32546230	32,546,230	strain	SAMN32546230	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB1944	null	null	null	Homo sapiens	null	null	GCF_053175725.1	SAMN48840873	48,840,873	strain	SAMN48840873	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB2012	null	null	null	Homo sapiens	null	null	GCF_053175715.1	SAMN48840874	48,840,874	strain	SAMN48840874	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB2016	null	null	null	Homo sapiens	null	null	GCF_053175705.1	SAMN48840875	48,840,875	strain	SAMN48840875	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB2038	null	null	null	Homo sapiens	null	null	GCF_053175695.1	SAMN48840876	48,840,876	strain	SAMN48840876	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB2039	null	null	null	Homo sapiens	null	null	GCF_053175685.1	SAMN48840877	48,840,877	strain	SAMN48840877	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB2041	null	null	null	Homo sapiens	null	null	GCF_053175675.1	SAMN48840878	48,840,878	strain	SAMN48840878	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.
Acinetobacter baumannii	470	AB26-AUFP	null	null	null	Homo sapiens	null	null	GCF_052040225.1	SAMN48008033	48,008,033	strain	SAMN48008033	true	false	true	primarily_human_associated	keep	Predominantly associated with human clinical infection; animal-associated records exist.

End of preview.

Human Bacterial Isolates

A literature- and NCBI-derived dataset of bacterial genome records associated with human hosts, restricted to a curated set of human-focused bacterial species.

Dataset summary

1,531 explicit human-host records
6 bacterial species
1,530 records with an explicit strain identifier
1 assembly-only record
Assembly and BioSample provenance retained

Included species

Acinetobacter baumannii
Clostridium tetani
Klebsiella pneumoniae
Pseudomonas aeruginosa
Vibrio cholerae
Vibrio vulnificus

Source

Genome and sample metadata were retrieved from NCBI Assembly and NCBI BioSample.

Only records whose BioSample host metadata explicitly indicated a human host (e.g. Homo sapiens / human / patient) were retained in the strict human-host dataset.

Fields

Field	Description
species	Bacterial species
species_taxid	NCBI Taxonomy ID
strain	NCBI BioSample strain identifier
isolate	Isolate metadata
serotype	Serotype when available
sequence_type	Sequence type when available
host	BioSample host
collection_date	Sample collection date
geographic_location	Sampling location
assembly_accession	NCBI Assembly accession
biosample_accession	NCBI BioSample accession
biosample_id	NCBI numeric BioSample ID
identifier_type	Type of available biological identifier
sample_identifier	Stable sample identifier
human_infection	Species-level human infection indicator
zoonotic	Species-level zoonotic review flag
animal_associated	Species-level animal association flag
host_scope	Curated host/ecological scope
final_decision	Species-level dataset inclusion decision
review_notes	Curatorial notes

Important interpretation

This dataset should be interpreted as a human-host isolate dataset, not as proof that the included bacterial species are biologically restricted to humans.

The human-host criterion is based on the NCBI BioSample metadata associated with the individual genome/sample record.

The species-level filtering layer was used to remove candidate species with clear zoonotic or strong animal-reservoir concerns from the strict human-focused dataset.

Quality control

The final dataset was checked for:

duplicated BioSample accessions
duplicated assembly accessions
repeated species × strain labels
missing or placeholder strain identifiers

The source pipeline found:

0 duplicated BioSample accessions
0 duplicated assembly accessions
0 repeated species × strain labels

Provenance

Primary database:

NCBI Assembly
NCBI BioSample
NCBI Taxonomy

Supporting literature:

PubMed

This dataset is intended for research, exploratory microbiology, comparative genomics, and downstream machine-learning dataset construction.

It should not be treated as a clinical or epidemiological registry.

Citation

If you use this dataset, please cite this Hugging Face dataset and the underlying NCBI resources.

Disclaimer

Metadata quality depends on the information submitted to NCBI by the original data producers. Missing values and inconsistent naming may therefore remain.

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