--- 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} } ```