Datasets:

jackkuo
/

LLM-Enzyme-Kinetics-Archive-LLENKA

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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 6 new columns ({'Kcat/Km', 'Enzyme', 'Km', 'Kcat', 'Commentary[Cosubstrate]', 'Substrate'}) and 11 missing columns ({'km', 'Unit_Kobs', 'Ribozyme', 'Source', 'Km_kcat', 'Unit_Kcleav', 'Kcleav', 'kcat', 'Commentary[Others]', 'Variable_reactant', 'Kobs'}).

This happened while the csv dataset builder was generating data using

hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Archive-LLENKA/3435_merged_data_claude3.5_hu.csv (at revision 76d4700bfb6a5b338e79e0341eae13e819150698)

Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1870, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Enzyme: string
              Organism: string
              Substrate: string
              Km: string
              Unit_Km: string
              Kcat: string
              Unit_Kcat: string
              Kcat/Km: string
              Unit_Kcat/Km: string
              Commentary[Temp]: string
              Commentary[pH]: string
              Commentary[Mutant]: string
              Commentary[Cosubstrate]: string
              pubmed_id: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1948
              to
              {'Ribozyme': Value(dtype='string', id=None), 'Organism': Value(dtype='string', id=None), 'Variable_reactant': Value(dtype='string', id=None), 'Kobs': Value(dtype='float64', id=None), 'Unit_Kobs': Value(dtype='string', id=None), 'km': Value(dtype='float64', id=None), 'Unit_Km': Value(dtype='string', id=None), 'kcat': Value(dtype='float64', id=None), 'Unit_Kcat': Value(dtype='string', id=None), 'Unit_Kcat/Km': Value(dtype='string', id=None), 'Kcleav': Value(dtype='float64', id=None), 'Unit_Kcleav': Value(dtype='string', id=None), 'Commentary[Temp]': Value(dtype='string', id=None), 'Commentary[pH]': Value(dtype='string', id=None), 'Commentary[Mutant]': Value(dtype='string', id=None), 'Commentary[Others]': Value(dtype='string', id=None), 'pubmed_id': Value(dtype='string', id=None), 'Source': Value(dtype='string', id=None), 'Km_kcat': Value(dtype='float64', id=None)}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1438, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1050, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 924, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1000, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1872, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
              datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
              
              All the data files must have the same columns, but at some point there are 6 new columns ({'Kcat/Km', 'Enzyme', 'Km', 'Kcat', 'Commentary[Cosubstrate]', 'Substrate'}) and 11 missing columns ({'km', 'Unit_Kobs', 'Ribozyme', 'Source', 'Km_kcat', 'Unit_Kcleav', 'Kcleav', 'kcat', 'Commentary[Others]', 'Variable_reactant', 'Kobs'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Archive-LLENKA/3435_merged_data_claude3.5_hu.csv (at revision 76d4700bfb6a5b338e79e0341eae13e819150698)
              
              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.

Ribozyme string	Organism null	Variable_reactant string	Kobs null	Unit_Kobs null	km float64	Unit_Km string	kcat float64	Unit_Kcat string	Unit_Kcat/Km string	Kcleav null	Unit_Kcleav null	Commentary[Temp] string	Commentary[pH] string	Commentary[Mutant] string	Commentary[Others] string	pubmed_id string	Source string	Km_kcat float64
Hammerhead	null	S13	null	null	0.000038	mM	0.006667	s^-1	mM^-1s^-1	null	null	30°C	8	WT	10 mM MgCl2	1280808	Table	166.666667
Hammerhead	null	S13	null	null	0.000059	mM	0.148333	s^-1	mM^-1s^-1	null	null	30°C	8	DNA-armed	10 mM MgCl2	1280808	Table	2,500
rz.GH	null	rGAG	null	null	0.000038	mM	0.000317	s^-1	null	null	null	55°C	8.5	WT	null	1408757	Table	null
rz.GH	null	dGAGrUCA	null	null	0.000056	mM	0.00145	s^-1	null	null	null	55°C	8.5	WT	null	1408757	Table	null
rz.DRD	null	rGAG	null	null	0.000064	mM	0.000317	s^-1	null	null	null	55°C	8.5	DNA in base-pairing sequences and stem-loop II	null	1408757	Table	null
rz.DRD	null	dGAGrUCA	null	null	0.000196	mM	0.0004	s^-1	null	null	null	55°C	8.5	DNA in base-pairing sequences and stem-loop II	null	1408757	Table	null
rz.DRD	null	dGAGrUCA	null	null	0.000048	mM	0.0002	s^-1	null	null	null	50°C	8.5	DNA in base-pairing sequences and stem-loop II	null	1408757	Table	null
rz.RLoop	null	rGAG	null	null	0.000064	mM	0.0021	s^-1	null	null	null	55°C	8.5	DNA in base-pairing sequences only	null	1408757	Table	null
rz.RLoop	null	dGAGrUCA	null	null	0.000091	mM	0.0018	s^-1	null	null	null	55°C	8.5	DNA in base-pairing sequences only	null	1408757	Table	null
rz.GH	null	rGAG	null	null	null	null	0.000333	s^-1	null	null	null	55°C	8.5	WT	null	1408757	Text	null
RZ1	null	α-lac mRNA	null	null	0.00017	mM	0.3	mol/min	mM^-1s^-1	null	null	37°C	8	WT	20 mM MgCl2	1425576	Table	30
RZ2	null	α-lac mRNA	null	null	0.00027	mM	0.4	mol/min	mM^-1s^-1	null	null	37°C	8	WT	20 mM MgCl2	1425576	Table	25
RZ3	null	α-lac mRNA	null	null	0.00062	mM	1.1	mol/min	mM^-1s^-1	null	null	37°C	8	WT	20 mM MgCl2	1425576	Table	30
RZ4a	null	α-lac mRNA	null	null	0.00028	mM	0.3	mol/min	mM^-1s^-1	null	null	37°C	8	WT	20 mM MgCl2	1425576	Table	18.333333
RZ4b	null	α-lac mRNA	null	null	0.00028	mM	0.5	mol/min	mM^-1s^-1	null	null	37°C	8	WT	20 mM MgCl2	1425576	Table	30
RZ5	null	α-lac mRNA	null	null	0.00041	mM	1.5	mol/min	mM^-1s^-1	null	null	37°C	8	WT	20 mM MgCl2	1425576	Table	61.666667
Hammerhead	null	null	null	null	0.00088	mM	0.015667	s^-1	mM^-1s^-1	null	null	55°C	8	WT	10 mM Mg^2+	1570323	Table	18.333333
Hammerhead	null	null	null	null	0.0042	mM	0.000233	s^-1	mM^-1s^-1	null	null	55°C	8	I^10	10 mM Mg^2+	1570323	Table	0.055
Hammerhead	null	null	null	null	0.0069	mM	0.000095	s^-1	mM^-1s^-1	null	null	55°C	8	dG^10	10 mM Mg^2+	1570323	Table	0.013667
Hammerhead	null	null	null	null	0.013	mM	0.0008	s^-1	mM^-1s^-1	null	null	55°C	8	dG^13	10 mM Mg^2+	1570323	Table	0.058333
Hammerhead 6	null	null	null	null	0.000046	mM	0.025	s^-1	nM^-1·min^-1	null	null	25°C	7.5	null	10 mM MgCl2	1689847	Table	0.032
Hammerhead 8	null	null	null	null	0.000041	mM	0.016667	s^-1	nM^-1·min^-1	null	null	25°C	7.5	null	10 mM MgCl2	1689847	Table	0.024
Hammerhead 9	null	null	null	null	0.00016	mM	0.025	s^-1	nM^-1·min^-1	null	null	25°C	7.5	null	10 mM MgCl2	1689847	Table	0.0093
Hammerhead 10	null	null	null	null	0.0023	mM	0.016667	s^-1	nM^-1·min^-1	null	null	25°C	7.5	null	10 mM MgCl2	1689847	Table	0.00044
Hammerhead	null	null	null	null	0.000154	mM	0.0385	s^-1	mM^-1s^-1	null	null	25°C	7.5	WT	10 mM MgCl2	1736306	Table	250
Hammerhead	null	null	null	null	0.000041	mM	0.0001	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dG10	10 mM MgCl2	1736306	Table	1.666667
Hammerhead	null	null	null	null	0.000308	mM	0.000667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FG10	10 mM MgCl2	1736306	Table	3.333333
Hammerhead	null	null	null	null	0.000153	mM	0.013333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-NG10	10 mM MgCl2	1736306	Table	20
Hammerhead	null	null	null	null	0.000051	mM	0.000083	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dG13	10 mM MgCl2	1736306	Table	1.666667
Hammerhead	null	null	null	null	0.000227	mM	0.000133	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FG13	10 mM MgCl2	1736306	Table	0.666667
Hammerhead	null	null	null	null	0.00019	mM	0.002667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-NG13	10 mM MgCl2	1736306	Table	13.333333
Hammerhead	null	null	null	null	0.000158	mM	0.054833	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dG19	10 mM MgCl2	1736306	Table	346.666667
Hammerhead	null	null	null	null	0.000176	mM	0.046667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FG19	10 mM MgCl2	1736306	Table	265
Hammerhead	null	null	null	null	0.000095	mM	0.020167	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-NG19	10 mM MgCl2	1736306	Table	211.666667
Hammerhead	null	null	null	null	0.000087	mM	0.021667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dG24	10 mM MgCl2	1736306	Table	248.333333
Hammerhead	null	null	null	null	0.000116	mM	0.046667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FG24	10 mM MgCl2	1736306	Table	400
Hammerhead	null	null	null	null	0.000066	mM	0.013833	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-NG24	10 mM MgCl2	1736306	Table	210
Hammerhead	null	null	null	null	0.000242	mM	0.079667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dG27	10 mM MgCl2	1736306	Table	330
Hammerhead	null	null	null	null	0.00021	mM	0.005	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FG27	10 mM MgCl2	1736306	Table	23.333333
Hammerhead	null	null	null	null	0.000136	mM	0.015333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-NG27	10 mM MgCl2	1736306	Table	113.333333
NS83	null	YOKS501	null	null	0.000025	mM	0.00055	s^-1	mM^-1s^-1	null	null	37°C	7.6	null	12 mM MgCl2, 2 mM spermidine	1762907	Table	22
NS80	null	YOKS403	null	null	0.000023	mM	0.000133	s^-1	mM^-1s^-1	null	null	37°C	7.6	null	12 mM MgCl2, 2 mM spermidine	1762907	Table	5.5
(-)sTRSV	null	null	null	null	0.00003	mM	0.035	s^-1	mM^-1s^-1	null	null	null	null	WT	null	1762907	Table	1,166.666667
Hammerhead	null	null	null	null	0.00062	mM	0.008333	s^-1	mM^-1s^-1	null	null	55°C	null	null	null	1762907	Multisource	13.5
Hammerhead Ribozyme	null	null	null	null	0.00022	mM	0.683333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E_unmodified	Mn^2+	1911762	Table	3,100
Hammerhead Ribozyme	null	null	null	null	0.000217	mM	0.046667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E_unmodified	Mg^2+	1911762	Table	216.666667
Hammerhead Ribozyme	null	null	null	null	0.000276	mM	0.003333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_total	Mn^2+	1911762	Table	16.666667
Hammerhead Ribozyme	null	null	null	null	0.000107	mM	0.011667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_22,28-30	Mn^2+	1911762	Table	116.666667
Hammerhead Ribozyme	null	null	null	null	0.000187	mM	0.166667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_11,14	Mn^2+	1911762	Table	883.333333
Hammerhead Ribozyme	null	null	null	null	0.000269	mM	0.633333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_14	Mn^2+	1911762	Table	2,333.333333
Hammerhead Ribozyme	null	null	null	null	0.000321	mM	0.066667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_14	Mg^2+	1911762	Table	200
Hammerhead Ribozyme	null	null	null	null	0.000243	mM	0.366667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_28	Mn^2+	1911762	Table	1,500
Hammerhead Ribozyme	null	null	null	null	0.000187	mM	0.266667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_29	Mn^2+	1911762	Table	1,433.333333
Hammerhead Ribozyme	null	null	null	null	0.000091	mM	0.066667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-FA_30	Mn^2+	1911762	Table	733.333333
Hammerhead Ribozyme	null	null	null	null	0.000157	mM	0.01	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dA_total	Mn^2+	1911762	Table	66.666667
Hammerhead Ribozyme	null	null	null	null	0.000133	mM	0.133333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dA_11,14	Mn^2+	1911762	Table	950
Hammerhead Ribozyme	null	null	null	null	0.000264	mM	0.35	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dA_14	Mn^2+	1911762	Table	1,316.666667
Hammerhead Ribozyme	null	null	null	null	0.000168	mM	0.233333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dA_28	Mn^2+	1911762	Table	1,433.333333
Hammerhead Ribozyme	null	null	null	null	0.000179	mM	0.333333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dA_29	Mn^2+	1911762	Table	1,900
Hammerhead Ribozyme	null	null	null	null	0.000058	mM	0.083333	s^-1	mM^-1s^-1	null	null	25°C	7.5	E-dA_30	Mn^2+	1911762	Table	1,483.333333
Hammerhead Ribozyme	null	null	null	null	0.000178	mM	0.366667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E2_unmodified	Mn^2+	1911762	Table	2,000
Hammerhead Ribozyme	null	null	null	null	0.000184	mM	0.416667	s^-1	mM^-1s^-1	null	null	25°C	7.5	E2-FA_20-22	Mn^2+	1911762	Table	2,266.666667
Hammerhead	null	S	null	null	0.0013	mM	0.008333	s^-1	null	null	null	50°C	8.5	WT	20 mM MgCl2, S concentration 0.05-0.6 µM	2646593	Table	null
Hammerhead	null	S	null	null	0.00063	mM	0.008333	s^-1	null	null	null	50°C	8.5	WT	20 mM MgCl2	2646593	Table	null
Hammerhead	null	S	null	null	0.0075	mM	null	null	null	null	null	50°C	8.5	WT	20 mM MgCl2, S concentration >0.6 µM	2646593	Text	null
Tetrahymena IVS	null	32P-labeled RNA	null	null	0.025	mM	0.013333	s^-1	mM^-1s^-1	null	null	30°C	7.5	WT	200 mM NaCl, 6 mM MgCl2	2684642	Multisource	0.533333
Tetrahymena IVS	null	32P-labeled RNA	null	null	0.041	mM	0.0045	s^-1	mM^-1s^-1	null	null	30°C	7.5	C109G	200 mM NaCl, 6 mM MgCl2	2684642	Multisource	0.11
Tetrahymena IVS	null	32P-labeled RNA	null	null	0.12	mM	0.00012	s^-1	mM^-1s^-1	null	null	30°C	7.5	G212C	200 mM NaCl, 6 mM MgCl2	2684642	Multisource	0.001
Tetrahymena IVS	null	32P-labeled RNA	null	null	null	null	null	null	null	null	null	30°C	7.5	C109G:G212C	200 mM NaCl, 6 mM MgCl2	2684642	Table	null
Tetrahymena IVS	null	32P-labeled RNA	null	null	null	null	null	null	null	null	null	30°C	7.5	G212A	200 mM NaCl, 6 mM MgCl2	2684642	Table	null
Tetrahymena IVS	null	32P-labeled RNA	null	null	null	null	null	null	null	null	null	30°C	7.5	C211G	200 mM NaCl, 6 mM MgCl2	2684642	Table	null
Tetrahymena IVS	null	32P-labeled RNA	null	null	null	null	null	null	null	null	null	30°C	7.5	∆A210	200 mM NaCl, 6 mM MgCl2	2684642	Table	null
Tetrahymena IVS	null	32P-labeled RNA	null	null	null	null	null	null	null	null	null	30°C	7.5	C109G:C211G	200 mM NaCl, 6 mM MgCl2	2684642	Table	null
Tetrahymena ribozyme	null	32P-labeled RNA	null	null	null	null	null	null	null	null	null	42°C	7.5	G212C	200 mM NaCl, 10 mM MgCl2	2684642	Text	null
Hammerhead	null	null	null	null	0.0008	mM	0.004833	s^-1	mM^-1s^-1	null	null	37°C	7.9	WT	10 mM Mg^2+	7487885	Table	6
Hammerhead	null	null	null	null	0.0005	mM	0.000667	s^-1	mM^-1s^-1	null	null	37°C	7.9	^4H^C_3	10 mM Mg^2+	7487885	Table	1.333333
Hammerhead	null	null	null	null	0.0025	mM	0.000767	s^-1	mM^-1s^-1	null	null	37°C	7.9	^4H^C_4	10 mM Mg^2+	7487885	Table	0.316667
Hammerhead	null	null	null	null	0.0007	mM	0.0016	s^-1	mM^-1s^-1	null	null	37°C	7.9	^4S^U_4	10 mM Mg^2+	7487885	Table	2.333333
Hammerhead	null	null	null	null	0.0007	mM	0.003333	s^-1	mM^-1s^-1	null	null	37°C	7.9	^4H^C_7	10 mM Mg^2+	7487885	Table	4.5
Hammerhead	null	null	null	null	0.001	mM	0.003167	s^-1	mM^-1s^-1	null	null	37°C	7.9	^4S^U_16.1	10 mM Mg^2+	7487885	Table	3.166667
Hammerhead	null	null	null	null	0.0023	mM	0.001383	s^-1	mM^-1s^-1	null	null	37°C	7.9	^4H^C_17	10 mM Mg^2+	7487885	Table	0.616667
Hairpin	null	sTRSV-C8A	null	null	0.0025	mM	0.000633	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUA	12 mM MgCl2, 2 mM spermidine	7495810	Table	0.333333
Hairpin	null	sTRSV	null	null	0.000096	mM	0.006	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUC	12 mM MgCl2, 2 mM spermidine	7495810	Table	60
Hairpin	null	sTRSV-C8G	null	null	0.00054	mM	0.000167	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUG	12 mM MgCl2, 2 mM spermidine	7495810	Table	0.333333
Hairpin	null	sTRSV-C8U	null	null	0.00039	mM	0.00075	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUU	12 mM MgCl2, 2 mM spermidine	7495810	Table	2
Hairpin	null	sCYMV1	null	null	0.0004	mM	0.005333	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUA	12 mM MgCl2, 2 mM spermidine	7495810	Table	13.333333
Hairpin	null	sCYMV1-A8C	null	null	0.0015	mM	0.002333	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUC	12 mM MgCl2, 2 mM spermidine	7495810	Table	1.5
Hairpin	null	sCYMV1-A8G	null	null	null	null	null	null	null	null	null	37°C	7.5	GUG	12 mM MgCl2, 2 mM spermidine	7495810	Table	null
Hairpin	null	sCYMV1-A8U	null	null	null	null	null	null	null	null	null	37°C	7.5	GUU	12 mM MgCl2, 2 mM spermidine	7495810	Table	null
Hairpin	null	sArMV	null	null	0.0014	mM	0.003167	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUA	12 mM MgCl2, 2 mM spermidine	7495810	Table	2.333333
Hairpin	null	sArMV-A1C	null	null	0.00088	mM	0.004333	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUA	12 mM MgCl2, 2 mM spermidine	7495810	Table	5
Hairpin	null	sArMV-A1C-A8C	null	null	0.0054	mM	0.003667	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUC	12 mM MgCl2, 2 mM spermidine	7495810	Table	0.666667
Hairpin	null	sArMV-A1C-A8G	null	null	0.0017	mM	0.004333	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUG	12 mM MgCl2, 2 mM spermidine	7495810	Table	2.5
Hairpin	null	sArMV-A1C-A8U	null	null	0.003	mM	0.006667	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUU	12 mM MgCl2, 2 mM spermidine	7495810	Table	2.166667
Hairpin	null	sArMV	null	null	0.0026	mM	0.004833	s^-1	mM^-1s^-1	null	null	37°C	7.5	GUA	12 mM MgCl2, 2 mM spermidine	7495810	Table	1.833333
R32	null	all-RNA substrat	null	null	null	null	null	null	null	null	null	37°C	7	WT	25 mM CoCl2	7506830	Table	null
DRD32	null	all-RNA substrat	null	null	null	null	null	null	null	null	null	37°C	7	Chimeric DNA/RNA	25 mM CoCl2	7506830	Table	null
R32	null	all-RNA substrat	null	null	null	null	null	null	null	null	null	37°C	7	WT	25 mM MgCl2	7506830	Table	null
DRD32	null	all-RNA substrat	null	null	null	null	null	null	null	null	null	37°C	7	Chimeric DNA/RNA	25 mM MgCl2	7506830	Table	null
R32	null	all-RNA substrat	null	null	null	null	null	null	null	null	null	37°C	7	WT	25 mM MgSO4	7506830	Table	null

End of preview.

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Please cite the following paper if you use jackkuo/LLM-Enzyme-Kinetics-Archive-LLENKA in your work.

@article {Jiang2025.03.03.641178,
    author = {Jiang, Jinling and Hu, Jie and Xie, Siwei and Guo, Menghao and Dong, Yuhang and Fu, Shuai and Jiang, Xianyue and Yue, Zhenlei and Shi, Junchao and Zhang, Xiaoyu and Song, Minghui and Chen, Guangyong and Lu, Hua and Wu, Xindong and Guo, Pei and Han, Da and Sun, Zeyi and Qiu, Jiezhong},
    title = {Enzyme Co-Scientist: Harnessing Large Language Models for Enzyme Kinetic Data Extraction from Literature},
    elocation-id = {2025.03.03.641178},
    year = {2025},
    doi = {10.1101/2025.03.03.641178},
    publisher = {Cold Spring Harbor Laboratory},
    abstract = {The extraction of molecular annotations from scientific literature is critical for advancing data-driven research. However, traditional methods, which primarily rely on human curation, are labor-intensive and error-prone. Here, we present an LLM-based agentic workflow that enables automatic and efficient data extraction from literature with high accuracy. As a demonstration, our workflow successfully delivers a dataset containing over 91,000 enzyme kinetics entries from around 3,500 papers. It achieves an average F1 score above 0.9 on expert-annotated subsets of protein enzymes and can be extended to the ribozyme domain in fewer than 3 days at less than $90. This method opens up new avenues for accelerating the pace of scientific research.Competing Interest StatementThe authors have declared no competing interest.},
    URL = {https://www.biorxiv.org/content/early/2025/03/11/2025.03.03.641178},
    eprint = {https://www.biorxiv.org/content/early/2025/03/11/2025.03.03.641178.full.pdf},
    journal = {bioRxiv}
}

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