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LLM-Enzyme-Kinetics-Golden-Benchmark

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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 18 new columns ({' Variable_reactant ', ' Unit_Kobs ', 'km_kcat', 'km', ' Commentary[Others] ', ' Commentary[pH] ', 'kcat', ' Commentary[Mutant] ', 'Kcleav', ' Unit_Kcat/Km ', ' Commentary[Temp] ', ' Organism ', ' Unit_Kcleav ', 'Kobs', 'Source', ' Ribozyme ', ' Unit_Kcat ', ' Unit_Km '}) and 12 missing columns ({'km_kcat(mM^-1s^-1)', 'Commentary[Cosubstrate]', 'Commentary[pH]', 'Commentary[Mutant]', 'Enzyme', 'kcat(s^-1)', 'ID_gold', 'Commentary[Temp]', 'Organism', 'Substrate', 'Reference[Table/Text]', 'km(mM)'}).

This happened while the csv dataset builder was generating data using

hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark/20241213_Ribozyme_benchmark.csv (at revision fec27341c9fe117dbfb7756a065f5b6c72f3d630), [/tmp/hf-datasets-cache/medium/datasets/40258543484657-config-parquet-and-info-jackkuo-LLM-Enzyme-Kineti-f753539c/hub/datasets--jackkuo--LLM-Enzyme-Kinetics-Golden-Benchmark/snapshots/fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241212_Golden_Benchmark_for_Enzyme_Kinetics_converted.csv (origin=hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark@fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241212_Golden_Benchmark_for_Enzyme_Kinetics_converted.csv), /tmp/hf-datasets-cache/medium/datasets/40258543484657-config-parquet-and-info-jackkuo-LLM-Enzyme-Kineti-f753539c/hub/datasets--jackkuo--LLM-Enzyme-Kinetics-Golden-Benchmark/snapshots/fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241213_Ribozyme_benchmark.csv (origin=hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark@fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241213_Ribozyme_benchmark.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/python3.12/site-packages/datasets/builder.py", line 1887, in _prepare_split_single
                  writer.write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 674, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2272, in table_cast
                  return cast_table_to_schema(table, schema)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2218, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
               Ribozyme : string
               Organism : string
               Variable_reactant : string
              Kobs: string
               Unit_Kobs : string
              km: string
               Unit_Km : string
              kcat: string
               Unit_Kcat : string
              km_kcat: string
               Unit_Kcat/Km : string
              Kcleav: string
               Unit_Kcleav : string
               Commentary[Temp] : string
               Commentary[pH] : string
               Commentary[Mutant] : string
               Commentary[Others] : string
              pubmed_id: string
              Source: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 2580
              to
              {'ID_gold': Value('int64'), 'pubmed_id': Value('int64'), 'Enzyme': Value('string'), 'Organism': Value('string'), 'Substrate': Value('string'), 'km(mM)': Value('string'), 'kcat(s^-1)': Value('string'), 'km_kcat(mM^-1s^-1)': Value('string'), 'Commentary[Temp]': Value('string'), 'Commentary[pH]': Value('string'), 'Commentary[Mutant]': Value('string'), 'Commentary[Cosubstrate]': Value('string'), 'Reference[Table/Text]': Value('string')}
              because column names don't match
              
              During handling of the above exception, another exception occurred:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1347, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
                  builder.download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 884, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 947, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1736, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1889, 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 18 new columns ({' Variable_reactant ', ' Unit_Kobs ', 'km_kcat', 'km', ' Commentary[Others] ', ' Commentary[pH] ', 'kcat', ' Commentary[Mutant] ', 'Kcleav', ' Unit_Kcat/Km ', ' Commentary[Temp] ', ' Organism ', ' Unit_Kcleav ', 'Kobs', 'Source', ' Ribozyme ', ' Unit_Kcat ', ' Unit_Km '}) and 12 missing columns ({'km_kcat(mM^-1s^-1)', 'Commentary[Cosubstrate]', 'Commentary[pH]', 'Commentary[Mutant]', 'Enzyme', 'kcat(s^-1)', 'ID_gold', 'Commentary[Temp]', 'Organism', 'Substrate', 'Reference[Table/Text]', 'km(mM)'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark/20241213_Ribozyme_benchmark.csv (at revision fec27341c9fe117dbfb7756a065f5b6c72f3d630), [/tmp/hf-datasets-cache/medium/datasets/40258543484657-config-parquet-and-info-jackkuo-LLM-Enzyme-Kineti-f753539c/hub/datasets--jackkuo--LLM-Enzyme-Kinetics-Golden-Benchmark/snapshots/fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241212_Golden_Benchmark_for_Enzyme_Kinetics_converted.csv (origin=hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark@fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241212_Golden_Benchmark_for_Enzyme_Kinetics_converted.csv), /tmp/hf-datasets-cache/medium/datasets/40258543484657-config-parquet-and-info-jackkuo-LLM-Enzyme-Kineti-f753539c/hub/datasets--jackkuo--LLM-Enzyme-Kinetics-Golden-Benchmark/snapshots/fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241213_Ribozyme_benchmark.csv (origin=hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark@fec27341c9fe117dbfb7756a065f5b6c72f3d630/20241213_Ribozyme_benchmark.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.

ID_gold
int64
pubmed_id
int64
Enzyme
string
Organism
string
Substrate
string
km(mM)
string
kcat(s^-1)
string
km_kcat(mM^-1s^-1)
string
Commentary[Temp]
string
Commentary[pH]
string
Commentary[Mutant]
string
Commentary[Cosubstrate]
string
Reference[Table/Text]
string
1
11,900,558
BglB
Pyrococcus horikoshii
pNP-Glc
13.5
34.4
2.58
90°C
4.75
WT
0.1 M Sodium Citrate/0.1 M NaPi
Table
2
11,900,558
BglB
Pyrococcus horikoshii
pNP-Gal
7.3
13.5
1.9
90°C
4.75
WT
0.1 M Sodium Citrate/0.1 M NaPi
Table
3
11,900,558
BglB
Pyrococcus horikoshii
pNP-Man
0.44
4.2
9.8
90°C
4.75
WT
0.1 M Sodium Citrate/0.1 M NaPi
Table
4
11,900,558
BglB
Pyrococcus horikoshii
pNP-Glc
16.2
25.5
1.6
90°C
4.75
Q77R
0.1 M Sodium Citrate/0.1 M NaPi
Table
5
11,900,558
BglB
Pyrococcus horikoshii
pNP-Gal
16.8
14.2
0.85
90°C
4.75
Q77R
0.1 M Sodium Citrate/0.1 M NaPi
Table
6
11,900,558
BglB
Pyrococcus horikoshii
pNP-Man
1.1
1.6
1.4
90°C
4.75
Q77R
0.1 M Sodium Citrate/0.1 M NaPi
Table
7
11,900,558
BglB
Pyrococcus horikoshii
pNP-Glc
0.3
252
870
90°C
4.75
D206N
0.1 M Sodium Citrate/0.1 M NaPi
Table
8
11,900,558
BglB
Pyrococcus horikoshii
pNP-Gal
7.8
571
75.8
90°C
4.75
D206N
0.1 M Sodium Citrate/0.1 M NaPi
Table
9
11,900,558
BglB
Pyrococcus horikoshii
pNP-Man
3.2
45
14.7
90°C
4.75
D206N
0.1 M Sodium Citrate/0.1 M NaPi
Table
10
11,900,558
BglB
Pyrococcus horikoshii
pNP-Glc
30.4
439
14.4
90°C
4.75
Q77R/D206N
0.1 M Sodium Citrate/0.1 M NaPi
Table
11
11,900,558
BglB
Pyrococcus horikoshii
pNP-Gal
36.1
66.5
1.8
90°C
4.75
Q77R/D206N
0.1 M Sodium Citrate/0.1 M NaPi
Table
12
11,900,558
BglB
Pyrococcus horikoshii
pNP-Man
0.68
6.8
9.9
90°C
4.75
Q77R/D206N
0.1 M Sodium Citrate/0.1 M NaPi
Table
13
11,900,558
CelB
Pyrococcus furiosus
pNP-Glc
0.19
1140
7337
90°C
4.75
WT
0.1 M Sodium Citrate/0.1 M NaPi
Table
14
11,900,558
CelB
Pyrococcus furiosus
pNP-Gal
5
2827
561
90°C
4.75
WT
0.1 M Sodium Citrate/0.1 M NaPi
Table
15
11,900,558
CelB
Pyrococcus furiosus
pNP-Man
1.3
65.9
49.8
90°C
4.75
WT
0.1 M Sodium Citrate/0.1 M NaPi
Table
16
11,900,558
CelB
Pyrococcus furiosus
pNP-Glc
13.8
207
14.9
90°C
4.75
R77Q
0.1 M Sodium Citrate/0.1 M NaPi
Table
17
11,900,558
CelB
Pyrococcus furiosus
pNP-Gal
21.7
69.2
3.2
90°C
4.75
R77Q
0.1 M Sodium Citrate/0.1 M NaPi
Table
18
11,900,558
CelB
Pyrococcus furiosus
pNP-Man I
0.64
1.22
1.9
90°C
4.75
R77Q
0.1 M Sodium Citrate/0.1 M NaPi
Table
19
11,900,558
CelB
Pyrococcus furiosus
pNP-Man II
0.15
0.85
5.7
90°C
4.75
R77Q
0.1 M Sodium Citrate/0.1 M NaPi
Table
20
11,900,558
CelB
Pyrococcus furiosus
pNP-Gal
15.7
180
11.5
90°C
4.75
N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
21
11,900,558
CelB
Pyrococcus furiosus
pNP-Glc
4.6
116
24.9
90°C
4.75
N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
22
11,900,558
CelB
Pyrococcus furiosus
pNP-Man
0.63
1.97
3.1
90°C
4.75
N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
23
11,900,558
CelB
Pyrococcus furiosus
pNP-Glc
13.9
172
12.3
90°C
4.75
R77Q/N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
24
11,900,558
CelB
Pyrococcus furiosus
pNP-Gal
22
29.2
1.3
90°C
4.75
R77Q/N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
25
11,900,558
CelB
Pyrococcus furiosus
pNP-Man I
1.5
1.9
1.3
90°C
4.75
R77Q/N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
26
11,900,558
CelB
Pyrococcus furiosus
pNP-Man II
0.1
1.02
10.2
90°C
4.75
R77Q/N206D
0.1 M Sodium Citrate/0.1 M NaPi
Table
27
11,900,558
CelB
Pyrococcus furiosus
pNP-Glc
12
309
26
90°C
4.75
N206S
0.1 M Sodium Citrate/0.1 M NaPi
Table
28
11,900,558
CelB
Pyrococcus furiosus
pNP-Gal
200
1090
5.5
90°C
4.75
N206S
0.1 M Sodium Citrate/0.1 M NaPi
Table
29
11,900,558
CelB
Pyrococcus furiosus
pNP-Man
4.7
15
3.2
90°C
4.75
N206S
0.1 M Sodium Citrate/0.1 M NaPi
Table
30
19,004,819
SDH
S. novella
sulfite
0.0006
63.5
106000
25°C
6.0
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
31
19,004,819
SDH
S. novella
sulfite
0.0011
86.2
75500
25°C
6.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
32
19,004,819
SDH
S. novella
sulfite
0.0037
158.8
42700
25°C
7.0
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
33
19,004,819
SDH
S. novella
sulfite
0.0071
293.4
40300
25°C
7.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
34
19,004,819
SDH
S. novella
sulfite
0.022
345.3
15300
25°C
8.0
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
35
19,004,819
SDH
S. novella
sulfite
0.086
410
4880
25°C
8.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
36
19,004,819
SDH
S. novella
sulfite
0.324
519
1500
25°C
9.0
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
37
19,004,819
SDH
S. novella
sulfite
1.66
431
251
25°C
9.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
38
19,004,819
SDH
S. novella
sulfite
3.389
23.7
6.77
25°C
10.0
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
39
19,004,819
SDH
S. novella
sulfite
0.004
36.8
8420
25°C
6.0
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
40
19,004,819
SDH
S. novella
sulfite
0.007
41.6
5600
25°C
6.5
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
41
19,004,819
SDH
S. novella
sulfite
0.026
51.8
1970
25°C
7.0
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
42
19,004,819
SDH
S. novella
sulfite
0.042
48.3
1140
25°C
7.5
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
43
19,004,819
SDH
S. novella
sulfite
0.114
53.4
461
25°C
8.0
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
44
19,004,819
SDH
S. novella
sulfite
0.332
58.3
173
25°C
8.5
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
45
19,004,819
SDH
S. novella
sulfite
1.155
64
54.5
25°C
9.0
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
46
19,004,819
SDH
S. novella
sulfite
4.456
52.7
11.6
25°C
9.5
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
47
19,004,819
SDH
S. novella
sulfite
15.487
44.8
2.84
25°C
10.0
Y236F
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
48
19,004,819
SDH
S. novella
sulfite
0.812
70.5
86.8
25°C
5.8
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
49
19,004,819
SDH
S. novella
sulfite
1.087
64
58.9
25°C
6.2
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
50
19,004,819
SDH
S. novella
sulfite
1.63
64
39.3
25°C
6.6
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
51
19,004,819
SDH
S. novella
sulfite
1.95
66.3
34
25°C
7.0
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
52
19,004,819
SDH
S. novella
sulfite
3.62
68.3
18.9
25°C
7.5
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
53
19,004,819
SDH
S. novella
sulfite
8.17
73.4
8.98
25°C
7.9
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
54
19,004,819
SDH
S. novella
sulfite
33.27
109.88
3.3
25°C
8.3
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
55
19,004,819
SDH
S. novella
sulfite
0.667
238.8
358
25°C
6.0
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
56
19,004,819
SDH
S. novella
sulfite
0.29
226.5
782
25°C
6.5
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
57
19,004,819
SDH
S. novella
sulfite
0.189
214.5
1130
25°C
7.0
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
58
19,004,819
SDH
S. novella
sulfite
0.22
220.5
1010
25°C
7.5
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
59
19,004,819
SDH
S. novella
sulfite
0.27
214.6
799
25°C
8.0
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
60
19,004,819
SDH
S. novella
sulfite
0.452
222.4
492
25°C
8.5
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
61
19,004,819
SDH
S. novella
sulfite
1.46
192.5
132
25°C
9.0
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
62
19,004,819
SDH
S. novella
sulfite
12.2
148.4
12.2
25°C
9.5
H57A
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
63
19,004,819
SDH
S. novella
sulfite
0.0032
730
225000
10°C
6
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
64
19,004,819
SDH
S. novella
sulfite
0.0036
847
239000
10°C
6.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
65
19,004,819
SDH
S. novella
sulfite
0.0014
782
55800
10°C
7
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
66
19,004,819
SDH
S. novella
sulfite
0.0031
677
21800
10°C
7.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
67
19,004,819
SDH
S. novella
sulfite
0.0087
776
8890
10°C
8
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
68
19,004,819
SDH
S. novella
sulfite
0.412
829
2010
10°C
8.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
69
19,004,819
SDH
S. novella
sulfite
1.183
731
618
10°C
9
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
70
19,004,819
SDH
S. novella
sulfite
3.811
674
177
10°C
9.5
WT
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
71
19,004,819
SDH
S. novella
sulfite
4.53
746
165
10°C
5.5
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
72
19,004,819
SDH
S. novella
sulfite
6.48
662
102
10°C
6
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
73
19,004,819
SDH
S. novella
sulfite
22.8
240
10.5
10°C
7
R55M
20 mM Tris acetate buffer，0.04 mM cytochrome c，sulfite dehydrogenase mM cytochrome c
Table
98
21,105,905
TCME1
Trypanosoma cruzi
L-Malate
0.13
518
3981
null
7.4
WT
NADP+(0.5), Mn2+(0.5)
Table
99
21,105,905
TCME1
Trypanosoma cruzi
NADP+
0.027
504
18681
null
7.4
WT
L-Malate (5), Mn2+(0.5)
Table
100
21,105,905
TCME1
Trypanosoma cruzi
Pyruvate
7.6
8.3
1.1
null
7.4
WT
NADPH(0.5), Mn2+(0.5), HCO3-(5)
Table
101
21,105,905
TCME1
Trypanosoma cruzi
Mg2+
0.04
461
11513
null
7.4
WT
L-Malate (5), NADP+(0.5)
Table
102
21,105,905
TCME1
Trypanosoma cruzi
Mn2+
0.0043
518
120361
null
7.4
WT
L-Malate (5), NADP+(0.5)
Table
103
21,105,905
TcME2
Trypanosoma cruzi
L-Malate
2.3
683
297
null
7.4
WT
NADP+(0.5), Mn2+(0.5)
Table
104
21,105,905
TcME2
Trypanosoma cruzi
NADP+
0.032
691
21599
null
7.4
WT
L-Malate (35), Mn2+(0.5)
Table
105
21,105,905
TcME2
Trypanosoma cruzi
Pyruvate
5.1
39
8
null
7.4
WT
NADPH(0.5), Mn2+(0.5), HCO3-(5)
Table
106
21,105,905
TcME2
Trypanosoma cruzi
Mg2+
0.57
864
1516
null
7.4
WT
L-Malate (35), NADP+(0.5)
Table
107
21,105,905
TcME2
Trypanosoma cruzi
Mn2+
0.0091
687
75479
null
7.4
WT
L-Malate (35), NADP+(0.5)
Table
108
21,105,905
TbME1
Trypanosoma brucei
L-Malate
0.32
1132
3536
null
7.4
WT
NADP+(0.5), Mn2+(0.5)
Table
109
21,105,905
TbME1
Trypanosoma brucei
NADP+
0.048
1206
25166
null
7.4
WT
L-Malate (5), Mn2+(0.5)
Table
110
21,105,905
TbME1
Trypanosoma brucei
Pyruvate
4.3
113
26
null
7.4
WT
NADPH(0.5), Mn2+(0.5), HCO3-(5)
Table
111
21,105,905
TbME1
Trypanosoma brucei
Mg2+
0.27
1280
4739
null
7.4
WT
L-Malate (5), NADP+(0.5)
Table
112
21,105,905
TbME1
Trypanosoma brucei
Mn2+
0.0024
905
377192
null
7.4
WT
L-Malate (5), NADP+(0.5)
Table
113
21,105,905
TbME2
Trypanosoma brucei
L-Malate
0.49
242
494
null
7.4
WT
NADP+(0.5), Mn2+(0.5)
Table
114
21,105,905
TbME2
Trypanosoma brucei
NADP+
0.016
284
17775
null
7.4
WT
L-Malate (5), Mn2+(0.5)
Table
115
21,105,905
TbME2
Trypanosoma brucei
Pyruvate
5.3
34
6
null
7.4
WT
NADPH(0.5), Mn2+(0.5), HCO3-(5)
Table
116
21,105,905
TbME2
Trypanosoma brucei
Mg2+
0.58
208
359
null
7.4
WT
L-Malate (5), NADP+(0.5)
Table
117
21,105,905
TbME2
Trypanosoma brucei
Mn2+
0.0066
246
37302
null
7.4
WT
L-Malate (5), NADP+(0.5)
Table
118
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
0.024
59.1
2460
Room temperature
7
WT
potassium phosphate buffer
Table
119
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
null
20.8
null
Room temperature
7
E16G
potassium phosphate buffer
Table
120
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
0.0167
3.17
190
Room temperature
7
R18G
potassium phosphate buffer
Table
121
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
0.0126
140
11110
Room temperature
7
R21G
potassium phosphate buffer
Table
122
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
0.0288
6.61
230
Room temperature
7
L59G
potassium phosphate buffer
Table
123
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
0.0335
21.1
630
Room temperature
7
W62A
potassium phosphate buffer
Table
124
22,387,379
AzoA
Enterococcus faecalis
Methyl Red
0.0053
77.3
14580
Room temperature
7
R66A
potassium phosphate buffer
Table
End of preview.

🚩Citation

Please cite the following paper if you use jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark 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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