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S0004-06142005000500011-1
0
DISEASE
50
73
alergias medicamentosas
S0004-06142005000500011-1
1
DISEASE
158
190
fracturas vertebrales y costales
S0004-06142005000500011-1
2
PROCEDURE
192
278
intervenido de enfermedad de Dupuytren en mano derecha y by-pass iliofemoral izquierdo
S0004-06142005000500011-1
3
DISEASE
207
230
enfermedad de Dupuytren
S0004-06142005000500011-1
4
DISEASE
280
305
Diabetes Mellitus tipo II
S0004-06142005000500011-1
5
DISEASE
307
326
hipercolesterolemia
S0004-06142005000500011-1
6
DISEASE
329
342
hiperuricemia
S0004-06142005000500011-1
7
DISEASE
344
359
enolismo activo
S0004-06142005000500011-1
8
DISEASE
361
368
fumador
S0004-06142005000500011-1
9
SYMPTOM
444
480
hematuria macroscópica postmiccional
S0004-06142005000500011-1
10
DISEASE
444
480
hematuria macroscópica postmiccional
S0004-06142005000500011-1
11
SYMPTOM
498
512
microhematuria
S0004-06142005000500011-1
12
SYMPTOM
545
563
micciones normales
S0004-06142005000500011-1
13
PROCEDURE
571
589
exploración física
S0004-06142005000500011-1
14
SYMPTOM
602
621
buen estado general
S0004-06142005000500011-1
15
SYMPTOM
627
655
abdomen y genitales normales
S0004-06142005000500011-1
16
PROCEDURE
657
669
tacto rectal
S0004-06142005000500011-1
17
DISEASE
685
704
adenoma de próstata
S0004-06142005000500011-1
18
PROCEDURE
723
741
analítica de orina
S0004-06142005000500011-1
19
PROCEDURE
818
827
sedimento
S0004-06142005000500011-1
20
PROCEDURE
836
845
Hemograma
S0004-06142005000500011-1
21
SYMPTOM
836
852
Hemograma normal
S0004-06142005000500011-1
22
PROCEDURE
860
870
bioquímica
S0004-06142005000500011-1
23
CHEMICAL
907
920
triglicéridos
S0004-06142005000500011-1
24
PROCEDURE
935
959
función hepática y renal
S0004-06142005000500011-1
25
SYMPTOM
935
966
función hepática y renal normal
S0004-06142005000500011-1
26
PROTEIN
968
971
PSA
S0004-06142005000500011-1
27
PROCEDURE
991
1,010
citologías de orina
S0004-06142005000500011-1
28
PROCEDURE
1,062
1,085
placa simple de abdomen
S0004-06142005000500011-1
29
SYMPTOM
1,097
1,136
cambios degenerativos en columna lumbar
S0004-06142005000500011-1
30
DISEASE
1,097
1,136
cambios degenerativos en columna lumbar
S0004-06142005000500011-1
31
SYMPTOM
1,139
1,199
calcificaciones vasculares en ambos hipocondrios y en pelvis
S0004-06142005000500011-1
32
DISEASE
1,139
1,199
calcificaciones vasculares en ambos hipocondrios y en pelvis
S0004-06142005000500011-1
33
PROCEDURE
1,204
1,223
ecografía urológica
S0004-06142005000500011-1
34
DISEASE
1,260
1,295
quistes corticales simples en riñón
S0004-06142005000500011-1
35
SYMPTOM
1,305
1,328
vejiga sin alteraciones
S0004-06142005000500011-1
36
PROCEDURE
1,387
1,390
UIV
S0004-06142005000500011-1
37
SYMPTOM
1,402
1,436
normofuncionalismo renal bilateral
S0004-06142005000500011-1
38
SYMPTOM
1,438
1,481
calcificaciones sobre silueta renal derecha
S0004-06142005000500011-1
39
DISEASE
1,438
1,492
calcificaciones sobre silueta renal derecha y uréteres
S0004-06142005000500011-1
40
SYMPTOM
1,484
1,505
uréteres arrosariados
S0004-06142005000500011-1
41
DISEASE
1,585
1,614
pseudodiverticulosis ureteral
S0004-06142005000500011-1
42
PROCEDURE
1,619
1,629
cistograma
S0004-06142005000500011-1
43
SYMPTOM
1,644
1,670
vejiga con buena capacidad
S0004-06142005000500011-1
44
DISEASE
1,712
1,730
vejiga de esfuerzo
S0004-06142005000500011-1
45
PROCEDURE
1,735
1,747
TC abdominal
S0004-06142005000500011-1
46
SYMPTOM
1,735
1,757
TC abdominal es normal
S0004-06142005000500011-1
47
PROCEDURE
1,763
1,774
cistoscopia
S0004-06142005000500011-1
48
SYMPTOM
1,810
1,832
tumoraciones vesicales
S0004-06142005000500011-1
49
DISEASE
1,810
1,832
tumoraciones vesicales
S0004-06142005000500011-1
50
PROCEDURE
1,847
1,869
resección transuretral
S0004-06142005000500011-1
51
PROCEDURE
1,877
1,904
resultado anatomopatológico
S0004-06142005000500011-1
52
DISEASE
1,908
1,949
carcinoma urotelial superficial de vejiga
S0004-06142005000700014-1
0
SYMPTOM
78
102
dolores osteoarticulares
S0004-06142005000700014-1
1
SYMPTOM
147
153
fiebre
S0004-06142005000700014-1
2
DISEASE
486
496
brucelosis
S0004-06142005000700014-1
3
SYMPTOM
534
549
síndrome febril
S0004-06142005000700014-1
4
DISEASE
638
655
orquiepididimitis
S0004-06142005000700014-1
5
PROCEDURE
668
686
exploración física
S0004-06142005000700014-1
6
SYMPTOM
750
760
consciente
S0004-06142005000700014-1
7
SYMPTOM
762
771
orientado
S0004-06142005000700014-1
8
SYMPTOM
773
781
sudoroso
S0004-06142005000700014-1
9
SYMPTOM
783
791
eupneico
S0004-06142005000700014-1
10
SYMPTOM
797
835
buen estado de nutrición e hidratación
S0004-06142005000700014-1
11
DISEASE
869
880
adenopatías
S0004-06142005000700014-1
12
DISEASE
885
890
bocio
S0004-06142005000700014-1
13
SYMPTOM
894
923
ingurgitación de vena yugular
S0004-06142005000700014-1
14
SYMPTOM
929
957
pulsos carotídeos simétricos
S0004-06142005000700014-1
15
PROCEDURE
959
980
Auscultación cardíaca
S0004-06142005000700014-1
16
SYMPTOM
959
988
Auscultación cardíaca rítmica
S0004-06142005000700014-1
17
SYMPTOM
994
1,000
soplos
S0004-06142005000700014-1
18
SYMPTOM
1,002
1,007
roces
S0004-06142005000700014-1
19
SYMPTOM
1,011
1,021
extratonos
S0004-06142005000700014-1
20
PROCEDURE
1,023
1,044
Auscultación pulmonar
S0004-06142005000700014-1
21
SYMPTOM
1,049
1,084
conservación del murmullo vesicular
S0004-06142005000700014-1
22
SYMPTOM
1,086
1,112
Abdomen blando, depresible
S0004-06142005000700014-1
23
SYMPTOM
1,118
1,123
masas
S0004-06142005000700014-1
24
SYMPTOM
1,127
1,135
megalias
S0004-06142005000700014-1
25
PROCEDURE
1,143
1,166
exploración neurológica
S0004-06142005000700014-1
26
SYMPTOM
1,182
1,198
signos meníngeos
S0004-06142005000700014-1
27
DISEASE
1,239
1,246
varices
S0004-06142005000700014-1
28
SYMPTOM
1,250
1,256
edemas
S0004-06142005000700014-1
29
SYMPTOM
1,258
1,299
Pulsos periféricos presentes y simétricos
S0004-06142005000700014-1
30
PROCEDURE
1,307
1,328
exploración urológica
S0004-06142005000700014-1
31
SYMPTOM
1,343
1,396
teste derecho aumentado de tamaño, no adherido a piel
S0004-06142005000700014-1
32
SYMPTOM
1,438
1,461
doloroso a la palpación
S0004-06142005000700014-1
33
PROCEDURE
1,452
1,461
palpación
S0004-06142005000700014-1
34
SYMPTOM
1,467
1,506
pérdida del límite epidídimo-testicular
S0004-06142005000700014-1
35
PROCEDURE
1,509
1,525
transiluminación
S0004-06142005000700014-1
36
SYMPTOM
1,509
1,534
transiluminación positiva
S0004-06142005000700014-1
37
PROCEDURE
1,592
1,601
Hemograma
S0004-06142005000700014-1
38
PROTEIN
1,603
1,605
Hb
S0004-06142005000700014-1
39
PROCEDURE
1,702
1,713
Coagulación
S0004-06142005000700014-1
40
PROCEDURE
1,738
1,748
Bioquímica
S0004-06142005000700014-1
41
CHEMICAL
1,750
1,757
Glucosa
S0004-06142005000700014-1
42
CHEMICAL
1,769
1,773
urea
S0004-06142005000700014-1
43
CHEMICAL
1,784
1,794
creatinina
S0004-06142005000700014-1
44
CHEMICAL
1,806
1,811
sodio
S0004-06142005000700014-1
45
CHEMICAL
1,823
1,830
potasio
S0004-06142005000700014-1
46
PROTEIN
1,842
1,845
GOT

Dataset

Description

The merged dataset utilized in this project combines four distinct annotated datasets, all based on the Spanish Clinical Case Corpus (SPACCC), a compilation of clinical case reports from Spanish medical publications. This merged dataset encompasses a total of 16,504 sentences across 1,000 clinical cases. The dataset focuses on identifying various medical entities within clinical narratives, including symptoms, medical procedures, diseases, proteins, and chemicals.

The dataset is further provided on Zenodo, and construction is detailed in our GitHub repository.

In order to use this dataset, the documents are also provided.

Origin

The constituent datasets include:

  • SympTEMIST: Designed for symptom, signs, and findings annotations, contributing 12,193 annotations.
  • MedProcNER: Focused on medical procedure identification with 14,683 instances.
  • DisTEMIST: Targeting disease identification, containing 10,663 annotations.
  • PharmaCoNER: Primarily for identifying chemicals and proteins, with 7,624 entities.

Annotations and Classes

The annotations are normalized to SNOMED CT, ensuring consistency across datasets. Classes include symptoms, procedures, diseases, proteins, and chemicals. Intra-class overlapping entities are addressed, ensuring model training on the longest span.

Statistics

The dataset is split into training and test sets, with consistent splits across corpora. For detailed statistics, refer to Table 1 and Table 2 below.

Use Case

The dataset serves as a resource for training and evaluating models for medical entity recognition and normalization tasks in Spanish clinical text.

References

  1. Miranda-Escalada, A., Gascó, L., Lima-López, S., Farré-Maduell, E., Estrada, D., Nentidis, A., Krithara, A., Katsimpras, G., Paliouras, G., & Krallinger, M. (2022). Overview of DisTEMIST at BioASQ: Automatic detection and normalization of diseases from clinical texts: results, methods, evaluation and multilingual resources. Working Notes of Conference and Labs of the Evaluation (CLEF) Forum. CEUR Workshop Proceedings
  2. Lima-López S, Farré-Maduell E, Gascó L, Nentidis A, Krithara A, Katsimpras G, Paliouras G, Krallinger M. Overview of MedProcNER task on medical procedure detection and entity linking at BioASQ 2023. Working Notes of CLEF. 2023.
  3. Lima-López, S., Farré-Maduell, E., Gasco-Sánchez, L., Rodríguez-Miret, J. and Krallinger, M. (2023). Overview of SympTEMIST at BioCreative VIII: corpus, guidelines and evaluation of systems for the detection and normalization of symptoms, signs and findings from text. In: Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models.
  4. A. G. Agirre, M. Marimon, A. Intxaurrondo, O. Rabal, M. Villegas, M. Krallinger, Pharmaconer: Pharmacological substances, compounds and proteins named entity recognition track, in: Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, 2019, pp. 1–10.
  5. Ander Intxaurrondo, & Krallinger, M. (2018). SPACCC (2019-02-01) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.2560316

Table 1: Datasets statistics with the number of entity mentions.

Dataset Train Test Total
SympTEMIST 9,091 3,102 12,193
MedProcNER 11,065 3,618 14,683
DisTEMIST 8,065 2,598 10,663
PharmaCoNER 4,665 1,959 7,624
Total 32,886 11,277 45,163

Table 2: Total number of overlapping entities within the datasets.

Subset Train Test Total
SympTEMIST 57 39 96
MedProcNER 418 143 561
DisTEMIST 323 90 413
PharmaCoNER 0 0 0
Total 798 272 1070

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Collection including IEETA/SPACCC-Spanish-NER