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smamooler
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PICLe

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bc2gm

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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 2 new columns ({'pmid', 'offsets'}) and 1 missing columns ({'id'}).

This happened while the json dataset builder was generating data using

hf://datasets/smamooler/PICLe/chemprotchem/test_sentence.json (at revision 46c05f4a01c03d19caaf49217a4eb945726a10c5)

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 1871, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 623, 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 2293, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2241, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              pmid: string
              text: string
              type: string
              entities: list<item: string>
                child 0, item: string
              offsets: list<item: list<item: int64>>
                child 0, item: list<item: int64>
                    child 0, item: int64
              -- schema metadata --
              pandas: '{"index_columns": [], "column_indexes": [], "columns": [{"name":' + 672
              to
              {'id': Value(dtype='string', id=None), 'type': Value(dtype='string', id=None), 'text': Value(dtype='string', id=None), 'entities': Sequence(feature=Value(dtype='string', id=None), length=-1, 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 925, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1001, 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 1742, 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 1873, 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 2 new columns ({'pmid', 'offsets'}) and 1 missing columns ({'id'}).
              
              This happened while the json dataset builder was generating data using
              
              hf://datasets/smamooler/PICLe/chemprotchem/test_sentence.json (at revision 46c05f4a01c03d19caaf49217a4eb945726a10c5)
              
              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 string	type string	text string	entities sequence
0	gene	Physical mapping 220 kb centromeric of the human MHC and DNA sequence analysis of the 43 - kb segment including the RING1 , HKE6 , and HKE4 genes .	[ "human MHC", "RING1", "HKE6", "HKE4 genes" ]
1	gene	The synthesis of endo - adduct [ 4aS , 5S , 8R , 8aR , SS ] - 9d resulting from cycloaddition on the substituted C ( 2 ) - C ( 3 ) double bond was achieved in a chemo - and diastereoselective way from quinone 1d in the presence of ZnBr ( 2 ) .	[]
2	gene	DNA elements recognizing NF - Y and Sp1 regulate the human multidrug - resistance gene promoter .	[ "NF - Y", "Sp1", "human multidrug - resistance gene promoter" ]
3	gene	Radioimmunoassay of plasma gonadotropins ; problems of specificity	[ "plasma gonadotropins" ]
4	gene	Patients randomized into the active treatment groups A30 ( n = 49 ) and A60 ( n = 48 ) received topical treatment with 3 . 0 % diclofenac in 2 . 5 % hyaluronan gel 0 . 5 g twice daily for 30 or 60 days , respectively .	[]
5	gene	As tat itself dramatically increases HIV - 1 gene expression , it too is presumably regulated in the latent state , and may also be activated by mitogenic stimulation .	[ "tat" ]
6	gene	To clarify the difference , both the Crk II and Crk II - 23 , proteins were expressed in E . coli and examined their binding capacity in vitro .	[ "Crk II", "Crk II - 23" ]
7	gene	CONCLUSIONS : Systemic factors that increase bone mineral density appear to be involved in the pathogenesis of ossification of the posterior longitudinal ligament , and these factors may be activated after middle age .	[]
8	gene	Thus , in V . furnissii , the E . coli manX equivalent comprises two genes , which are separated in the genome by two other genes of the ptsM complex .	[ "E . coli manX equivalent", "ptsM complex" ]
9	gene	Id - 1H and Id - 2H seem to be human homologues of mouse Id - 1 and Id - 2 , respectively , and have potential to encode 154 and 135 amino acid proteins .	[ "Id - 1H", "Id - 2H", "mouse Id - 1", "Id - 2" ]
10	gene	Characterization of insertion mutations in the Saccharomyces cerevisiae MSH1 and MSH2 genes : evidence for separate mitochondrial and nuclear functions .	[ "Saccharomyces cerevisiae MSH1", "MSH2 genes" ]
11	gene	Transcription of FN promoter - chloramphenicol acetyltransferase fusion genes carrying the base substitution in one or more of these G - rich sequences both in vivo and in vitro revealed that the base substitution in any G - rich sequence results in reduction of promoter activity , although the downstream GC box ( GCd ) plays a primary role .	[ "FN promoter", "chloramphenicol acetyltransferase" ]
12	gene	Morphologically , corrugation of the internal elastic lamina of vessels was often observed in the vehicle - treated group , but was not prominent in the GLNVA - treated groups or healthy controls .	[]
13	gene	A GT - rich sequence binding the transcription factor Sp1 is crucial for high expression of the human type VII collagen gene ( COL7A1 ) in fibroblasts and keratinocytes .	[ "transcription factor Sp1", "human type VII collagen gene", "COL7A1" ]
14	gene	Each received 20 mL of one of three test solutions : levobupivacaine control , levobupivacaine and fentanyl 2 microg / mL , or levobupivacaine and fentanyl 3 microg / mL .	[]
15	gene	The XPR2 gene from Yarrowia lipolytica encodes an inducible alkaline extracellular protease .	[ "XPR2 gene", "alkaline extracellular protease" ]
16	gene	CONCLUSIONS : This study shows that the annual rate of de novo aneurysm formation is relatively high ( 0 . 89 % ) and that the cumulative risk becomes significant after 9 years .	[]
17	gene	It was found that Nopp140 binds primarily to the CK2 regulatory subunit , beta .	[ "Nopp140", "CK2 regulatory subunit , beta" ]
18	gene	Juvenile idiopathic inflammatory myopathies : the value of magnetic resonance imaging in the detection of muscle involvement .	[]
19	gene	Previous analysis of this motif in the lactose permease ( A .	[ "lactose permease" ]
20	gene	Combined chemotherapy with VM 26 and BCNU for recurrent malignant gliomas after operation and irradiation .	[]
21	gene	Like other IAPs , ch - IAP1 contains the N - terminal baculovirus IAP repeats and C - terminal RING finger motifs .	[ "IAPs", "ch - IAP1", "N - terminal baculovirus IAP repeats" ]
22	gene	Effects of long - term use of raloxifene , a selective estrogen receptor modulator , on thyroid function test profiles .	[ "estrogen receptor" ]
23	gene	The donors of 10 patients were ABO - incompatible , and for five pairs the ABO incompatibility was major .	[]
24	gene	Alternative splicing of the human serotonin transporter gene .	[ "human serotonin transporter gene" ]
25	gene	Interestingly , basal MAPK , but not Raf - 1 , activity was constitutively enhanced in Jak1 - deficient HeLa cells .	[ "MAPK", "Raf - 1", "Jak1" ]
26	gene	This case report describes the treatment of a patient with periodontosis .	[]
27	gene	The aim of this work was to organize chemical data in a client - server environment using Database Management System and Web fashion for the client interface .	[]
28	gene	Cerumen management in hearing conservation : the Dallas ( Texas ) Independent School District program .	[]
29	gene	Lactate , pyruvate and actual pH values in the venous blood of newborn calves	[]
30	gene	This article focuses on a general approach to the use of ARV agents .	[]
31	gene	Platelets and RBCs from each animal were labeled with 51Cr and 99mTc , respectively , and were rapidly injected into the right atrium while blood was sampled from the ascending aorta .	[]
32	gene	The comparisons of swimming performance before and after treatments with deltamethrin have shown a significant effect on locomotory ability of rainbow trout which at the end of strong exposure ( e . g .	[]
33	gene	Protection levels of 33 . 3 % , 36 . 6 % and 37 . 0 % were achieved in groups which had received , respectively , 1000 20 - krad cercariae , 1000 10 - krad cercariae , 2000 40 - krad cercariae and 2000 60 - krad cercariae .	[]
34	gene	In Types I and II , capillary walls became thinner and more capillary lumens were visiable .	[]
35	gene	Thus , primate vs . rodent promoter selectivity mediated by the TBP - TAFI complex is likely to be the result of cumulative subtle differences between individual subunits that lead to species - specific properties of RNA polymerase I transcription .	[ "TBP", "TAFI", "RNA polymerase I" ]
36	gene	The effects of pretreatment with the non - competitive NMDA antagonist ( + ) MK - 801 on the behavioral alterations induced by repeated restraint stress were investigated .	[]
37	gene	When gene conversion is initiated by a double - strand break ( DSB ) , any nonhomologous DNA that may be present at the ends must be removed before new DNA synthesis can be initiated .	[]
38	gene	In this reconstituted system , RNAP IIA , but not RNAP IIB , can transcribe from the DHFR promoter .	[ "RNAP IIA", "RNAP IIB", "DHFR promoter" ]
39	gene	The cDNA clones encode a polypeptide of 657 amino acids with a bHLH ( basic - helix - loop - helix ) domain , characteristic of a large family of transcription factors , and a PAS ( Per - Arnt - Sim ) domain in the amino - terminal half region .	[ "PAS", "Per", "Arnt", "Sim" ]
40	gene	FTF ( Joint Council of Civil Servants and Functionaries ) : clarification about membership in the main organizations	[]
41	gene	Lumbar spine bone mineral density ( BMD ) by dual - energy X - ray absorptiometry ( DXA ) increased by 0 . 6 % , 3 . 6 % and 8 . 1 % after 48 weeks in groups L , M and H respectively , responses in groups M and H being significantly higher than in L ( p < 0 . 05 , Mann - Whitney U - test ) .	[]
42	gene	Synergy between interferon - gamma and tumor necrosis factor - alpha in transcriptional activation is mediated by cooperation between signal transducer and activator of transcription 1 and nuclear factor kappaB .	[ "interferon - gamma", "tumor necrosis factor - alpha", "signal transducer and activator of transcription 1", "nuclear factor kappaB" ]
43	gene	1H and 15N magnetic resonance assignments , secondary structure , and tertiary fold of Escherichia coli DnaJ ( 1 - 78 ) .	[ "Escherichia coli DnaJ ( 1 - 78 )" ]
44	gene	A cDNA for human microfibril - associated glycoprotein - 2 ( MAGP - 2 ) was used to screen a human leukocyte genomic DNA library in EMBL - 3 vector .	[ "human microfibril - associated glycoprotein - 2", "MAGP - 2" ]
45	gene	Furthermore , ERK phosphorylation was substantially prolonged in LC / BRY - treated cells compared to those exposed to BRY alone , and pretreatment with the highly specific MEK inhibitors , PD98059 , U0126 , and SL327 , opposed ERK activation while protecting cells from LC / BRY - induced lethality .	[ "ERK", "MEK", "ERK" ]
46	gene	The cholesterol 7alpha - hydroxylase gene ( CYP7A ) is transcriptionally regulated by a number of factors , including hormones , bile acids , and diurnal rhythm .	[ "cholesterol 7alpha - hydroxylase gene", "CYP7A" ]
47	gene	CNS preventive treatment without cranial irradiation was effective in all the groups of ALL patients .	[]
48	gene	Additionally , the members of this family display strong sequence homologies between their larger C - terminal effector binding / oligomerization domains .	[]
49	gene	Aspartame is a synthetic sweetener commonly used in soft drinks and many foods .	[]
50	gene	The rat anococcygeus muscle was used in postsynaptic studies .	[]
51	gene	The purpose of this presentation is to review the current state of knowledge regarding 5 , 8 , 11 , 14 - eicosatetraynoic acid ( ETYA , Ro 3 - 1428 ) and its effects on lipid metabolism .	[]
52	gene	A Meis1 cDNA clone that encoded a novel member of the homeobox gene family was identified .	[ "Meis1 cDNA", "homeobox gene family" ]
53	gene	The S . typhimurium aspartyl / asparaginyl beta - hydroxylase homologue ( designated lpxO ) was cloned into pBluescriptSK and expressed in Escherichia coli K - 12 , which does not contain lpxO .	[ "S . typhimurium aspartyl / asparaginyl beta - hydroxylase homologue", "lpxO", "lpxO" ]
54	gene	The levels of soluble L - selectin and ICAM - 1 in the serum were determined by the ELISA method .	[ "L - selectin", "ICAM - 1" ]
55	gene	The highest TTX content is 10 . 0 microg / g in N . livescens .	[ "TTX" ]
56	gene	On the other hand hypokalemia , induced by diuretics , may also be accompanied by a significant depletion of total body K , bringing about more general consequences .	[]
57	gene	Glutathione reductase activities in liver , kidney , lung , and brain were not affected by diet .	[ "Glutathione reductase" ]
58	gene	Here , we describe the nucleotide ( nt ) sequence and genomic organization of ipiB and ipiO .	[ "ipiB", "ipiO" ]
59	gene	Vancomycin and tetracycline eliminated toxin in stools and delayed death .	[]
60	gene	Soluble fibrin monomer complexes in thromboembolism	[ "fibrin" ]
61	gene	Comparison to the murine homologues of these molecules reveals a high degree of conservation between the products of one of these genes , Fc gamma RIIb , and the murine beta gene in primary sequence , splicing pattern , and tissue distribution .	[ "Fc gamma RIIb", "murine beta gene" ]
62	gene	Acidosis provoked by 30 % CO2 irreversibly increased the BDRT , however the TRT were not changed .	[]
63	gene	Others as for example C - 11 labeled short chain fatty acids are on the horizon .	[]
64	gene	The average progression was 11 . 6 ( SD 9 . 0 ) .	[]
65	gene	80 bp ) surrounding the site of transcription initiation .	[]
66	gene	Ultrastructure and toxin formation of Cor . diphtheriae PW - 8 cultured in the presence of penicillin	[]
67	gene	EMT was localized to chromosome 5q31 - 32 , a region that contains the genes for several growth factors and receptors as well as early activation genes , particularly those involved in the hematopoietic system .	[ "EMT" ]
68	gene	Tbx6 maps to chromosome 7 and does not appear to be linked to any known mutation .	[ "Tbx6" ]
69	gene	Kaposi ' s eruptive disease .	[]
70	gene	It is not tested yet , whether the extent of glaucoma damage should be better quantified using reference plane 1 or 2 .	[]
71	gene	Importin beta mediates nuclear translocation of Smad 3 .	[ "Importin beta", "Smad 3" ]
72	gene	The encoded protein contains an amino terminal PDZ domain , followed by a predicted coiled - coil region , a PEST domain , and a carboxy - terminal SAM domain .	[ "PDZ" ]
73	gene	Using lasers , PRK involves reshaping the cornea so that its refractive power is increased .	[]
74	gene	However , sphincter length decreased with age from 24 . 3 to 14 . 8 mm . , maximal urethral pressure from 88 . 7 to 55 cm . water and maximal urethral pressure during voluntary contraction from 221 . 4 to 166 . 3 cm . water .	[]
75	gene	Several studies have demonstrated that the corticotropin - releasing factor test ( CRF ) is useful for the aetiological diagnosis of Cushing ' s syndrome : in Cushing ' s disease , as opposed to ectopic ACTH secretion syndrome , the hypothalamus - pituitary - adrenal ( HPA ) axis can still be stimulated by CRF .	[ "corticotropin - releasing factor", "CRF", "ACTH", "CRF" ]
76	gene	Transcription initiation from this region was also detected in vivo , when the cloned rRNA gene cluster was present on a multi - copy plasmid .	[]
77	gene	The results of the transient - transfection assay showed that the Sp1 binding element located in the core region ( positions - - 64 to + 1 ) of the alpha2 - integrin promoter plays an essential role in the alpha2 - integrin promoter activity and its downregulation by Erb - B2 .	[ "Sp1 binding element", "alpha2 - integrin promoter", "alpha2 - integrin promoter", "Erb", "B2" ]
78	gene	Principal component analysis using psychosocial factors in women showed two psychosocial structures , i . e . the second principal ( high SOC , high lifestyle , and low stress ) and the 4th principal components ( high supernatural HLC , and high PHLC ) .	[]
79	gene	Expression of FNCAT increased on serum treatment indicating that the region of the FN gene between positions + 69 and - 510 bp mediated serum responsiveness .	[ "FNCAT", "FN gene" ]
80	gene	Interaction of the v - rel protein with an NF - kappa B DNA binding site .	[ "v - rel protein", "NF - kappa B DNA binding site" ]
81	gene	This increase is not the result of alterations in the deposition of inhaled particles of capsaicin brought about by volume restriction .	[]
82	gene	Providing appropriate care to both sexes .	[]
83	gene	To test this hypothesis , we developed a system of transient transfection of rat adipocytes with constructs containing glyceraldehyde - 3 - phosphate dehydrogenase ( GAPDH ) and fatty acid synthetase ( FAS ) promoters fused to gene reporter CAT .	[ "glyceraldehyde - 3 - phosphate dehydrogenase", "GAPDH", "fatty acid synthetase", "FAS", "gene reporter CAT" ]
84	gene	In the green unicellular alga Chlamydomonas eugametos , cellular division is readily synchronized by light / dark cycles .	[]
85	gene	SHBG concentrations in women were also significantly higher at T - 2 and T - 3 when compared to T - 1 values .	[ "SHBG" ]
86	gene	Simvastatin decreased levels of total cholesterol by 20 . 8 % , LDL cholesterol by 29 . 7 % , triglycerides by 13 . 6 % , apolipoprotein B by 22 . 4 % , alpha - tocopherol by 16 . 2 % , beta - carotene by 19 . 5 % , and ubiquinol - 10 by 22 . 0 % ( P < . 001 for all ) and increased levels of HDL cholesterol by 7 . 0 % ( P < . 001 ) and serum insulin by 13 . 2 % ( P = . 005 ) .	[ "LDL cholesterol", "apolipoprotein B", "HDL cholesterol", "serum insulin" ]
87	gene	The more severe the CRF , the more likely that total HDL and HDL2 cholesterol will be low .	[ "HDL", "HDL2 cholesterol" ]
88	gene	They are growth - inhibited by TGF - beta1 .	[ "TGF - beta1" ]
89	gene	To investigate the in vivo role of this chimeric bZIP protein in oncogenic transformation , its expression was directed to the lymphoid compartments of transgenic mice .	[ "chimeric bZIP protein" ]
90	gene	This is consistent with the need for a nuclear retinoid receptor function in RA - induced ERK2 activation .	[ "retinoid receptor", "ERK2" ]
91	gene	In the virus - infected cells , translation of the M1 protein was reduced to 10 to 20 % of that of the wild - type virus ; however , the translation of neither the nucleoprotein nor NS1 was significantly interfered with , indicating the important role of NS1 in translational stimulation of the M1 protein .	[ "M1 protein", "NS1", "NS1", "M1 protein" ]
92	gene	Some cells were excited , others inhibited by , and only some were directionally sensitive to the optomotor stimulus .	[]
93	gene	LT - beta transcription is maximal in the thymic medulla and in splenic white pulp .	[ "LT - beta" ]
94	gene	A novel Cdc42Hs mutant induces cellular transformation .	[ "Cdc42Hs mutant" ]
95	gene	Interactions were also detected between full - length HSF1 and the small subunit ( gamma ) of TFIIA .	[ "HSF1", "TFIIA" ]
96	gene	We report that Nim1 possesses intrinsic serine - kinase , threonine - kinase and tyrosine - kinase activities .	[ "Nim1", "serine - kinase", "threonine - kinase", "tyrosine - kinase" ]
97	gene	A short conserved motif is required for repressor domain function in the myeloid - specific transcription factor CCAAT / enhancer - binding protein epsilon .	[ "CCAAT / enhancer - binding protein epsilon" ]
98	gene	Androgen ablation - - 50 years later .	[]
99	gene	In conclusion , ORCA3 regulates jasmonate - responsive expression of the Str gene via direct interaction with the JERE .	[ "ORCA3", "Str gene" ]

End of preview.

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