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}
}