|
--- |
|
language: |
|
- es |
|
license: cc-by-4.0 |
|
multilinguality: monolingual |
|
pretty_name: CANTEMIST |
|
bigbio_language: |
|
- Spanish |
|
bigbio_license_shortname: CC_BY_4p0 |
|
homepage: https://temu.bsc.es/cantemist/?p=4338 |
|
bigbio_pubmed: false |
|
bigbio_public: true |
|
bigbio_tasks: |
|
- NAMED_ENTITY_RECOGNITION |
|
- NAMED_ENTITY_DISAMBIGUATION |
|
- TEXT_CLASSIFICATION |
|
dataset_info: |
|
- config_name: cantemist_bigbio_kb |
|
features: |
|
- name: id |
|
dtype: string |
|
- name: document_id |
|
dtype: string |
|
- name: passages |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: text |
|
sequence: string |
|
- name: offsets |
|
sequence: |
|
list: int32 |
|
- name: entities |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: text |
|
sequence: string |
|
- name: offsets |
|
sequence: |
|
list: int32 |
|
- name: normalized |
|
list: |
|
- name: db_name |
|
dtype: string |
|
- name: db_id |
|
dtype: string |
|
- name: events |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: trigger |
|
struct: |
|
- name: text |
|
sequence: string |
|
- name: offsets |
|
sequence: |
|
list: int32 |
|
- name: arguments |
|
list: |
|
- name: role |
|
dtype: string |
|
- name: ref_id |
|
dtype: string |
|
- name: coreferences |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: entity_ids |
|
sequence: string |
|
- name: relations |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: arg1_id |
|
dtype: string |
|
- name: arg2_id |
|
dtype: string |
|
- name: normalized |
|
list: |
|
- name: db_name |
|
dtype: string |
|
- name: db_id |
|
dtype: string |
|
splits: |
|
- name: train |
|
num_bytes: 3431289 |
|
num_examples: 501 |
|
- name: test |
|
num_bytes: 1883309 |
|
num_examples: 300 |
|
- name: validation |
|
num_bytes: 3111616 |
|
num_examples: 500 |
|
download_size: 4000409 |
|
dataset_size: 8426214 |
|
- config_name: cantemist_bigbio_text |
|
features: |
|
- name: id |
|
dtype: string |
|
- name: document_id |
|
dtype: string |
|
- name: text |
|
dtype: string |
|
- name: labels |
|
list: string |
|
splits: |
|
- name: train |
|
num_bytes: 2704288 |
|
num_examples: 501 |
|
- name: test |
|
num_bytes: 1468362 |
|
num_examples: 300 |
|
- name: validation |
|
num_bytes: 2425597 |
|
num_examples: 500 |
|
download_size: 3605238 |
|
dataset_size: 6598247 |
|
- config_name: cantemist_source |
|
features: |
|
- name: id |
|
dtype: string |
|
- name: document_id |
|
dtype: string |
|
- name: text |
|
dtype: string |
|
- name: labels |
|
list: string |
|
- name: text_bound_annotations |
|
list: |
|
- name: offsets |
|
sequence: |
|
list: int32 |
|
- name: text |
|
sequence: string |
|
- name: type |
|
dtype: string |
|
- name: id |
|
dtype: string |
|
- name: events |
|
list: |
|
- name: trigger |
|
dtype: string |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: arguments |
|
sequence: |
|
- name: role |
|
dtype: string |
|
- name: ref_id |
|
dtype: string |
|
- name: relations |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: head |
|
struct: |
|
- name: ref_id |
|
dtype: string |
|
- name: role |
|
dtype: string |
|
- name: tail |
|
struct: |
|
- name: ref_id |
|
dtype: string |
|
- name: role |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: equivalences |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: ref_ids |
|
sequence: string |
|
- name: attributes |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: ref_id |
|
dtype: string |
|
- name: value |
|
dtype: string |
|
- name: normalizations |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: ref_id |
|
dtype: string |
|
- name: resource_name |
|
dtype: string |
|
- name: cuid |
|
dtype: string |
|
- name: text |
|
dtype: string |
|
- name: notes |
|
list: |
|
- name: id |
|
dtype: string |
|
- name: type |
|
dtype: string |
|
- name: ref_id |
|
dtype: string |
|
- name: text |
|
dtype: string |
|
splits: |
|
- name: train |
|
num_bytes: 3451245 |
|
num_examples: 501 |
|
- name: test |
|
num_bytes: 1892436 |
|
num_examples: 300 |
|
- name: validation |
|
num_bytes: 3126466 |
|
num_examples: 500 |
|
download_size: 3927340 |
|
dataset_size: 8470147 |
|
configs: |
|
- config_name: cantemist_bigbio_kb |
|
data_files: |
|
- split: train |
|
path: cantemist_bigbio_kb/train-* |
|
- split: test |
|
path: cantemist_bigbio_kb/test-* |
|
- split: validation |
|
path: cantemist_bigbio_kb/validation-* |
|
- config_name: cantemist_bigbio_text |
|
data_files: |
|
- split: train |
|
path: cantemist_bigbio_text/train-* |
|
- split: test |
|
path: cantemist_bigbio_text/test-* |
|
- split: validation |
|
path: cantemist_bigbio_text/validation-* |
|
- config_name: cantemist_source |
|
data_files: |
|
- split: train |
|
path: cantemist_source/train-* |
|
- split: test |
|
path: cantemist_source/test-* |
|
- split: validation |
|
path: cantemist_source/validation-* |
|
default: true |
|
--- |
|
|
|
|
|
# Dataset Card for CANTEMIST |
|
|
|
## Dataset Description |
|
|
|
- **Homepage:** https://temu.bsc.es/cantemist/?p=4338 |
|
- **Pubmed:** False |
|
- **Public:** True |
|
- **Tasks:** NER,NED,TXTCLASS |
|
|
|
|
|
Collection of 1301 oncological clinical case reports written in Spanish, with tumor morphology mentions manually annotated and mapped by clinical experts to a controlled terminology. Every tumor morphology mention is linked to an eCIE-O code (the Spanish equivalent of ICD-O). |
|
|
|
The original dataset is distributed in Brat format, and was randomly sampled into 3 subsets. The training, development and test sets contain 501, 500 and 300 documents each, respectively. |
|
|
|
This dataset was designed for the CANcer TExt Mining Shared Task, sponsored by Plan-TL. The task is divided in 3 subtasks: CANTEMIST-NER, CANTEMIST_NORM and CANTEMIST-CODING. |
|
|
|
CANTEMIST-NER track: requires finding automatically tumor morphology mentions. All tumor morphology mentions are defined by their corresponding character offsets in UTF-8 plain text medical documents. |
|
|
|
CANTEMIST-NORM track: clinical concept normalization or named entity normalization task that requires to return all tumor morphology entity mentions together with their corresponding eCIE-O-3.1 codes i.e. finding and normalizing tumor morphology mentions. |
|
|
|
CANTEMIST-CODING track: requires returning for each of document a ranked list of its corresponding ICD-O-3 codes. This it is essentially a sort of indexing or multi-label classification task or oncology clinical coding. |
|
|
|
For further information, please visit https://temu.bsc.es/cantemist or send an email to encargo-pln-life@bsc.es |
|
|
|
|
|
|
|
## Citation Information |
|
|
|
``` |
|
@article{miranda2020named, |
|
title={Named Entity Recognition, Concept Normalization and Clinical Coding: Overview of the Cantemist Track for Cancer Text Mining in Spanish, Corpus, Guidelines, Methods and Results.}, |
|
author={Miranda-Escalada, Antonio and Farr{'e}, Eul{\`a}lia and Krallinger, Martin}, |
|
journal={IberLEF@ SEPLN}, |
|
pages={303--323}, |
|
year={2020} |
|
} |
|
|
|
``` |
|
|
