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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
- 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
- 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.
- 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.
- 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.
- 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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