LivingNER corpus: recognition and normalization of species

LivingNER corpus - training and validation sets

The LivingNER corpus is a collection of 2000 clinical cases from over 10 different medical areas annotated with SPECIES mentions, that are mapped to NCBI Taxonomy. It is used for the LivingNER Shared Task on occupations and employment status detection and normalization in Spanish medical documents, which will be celebrated as part of IberLEF 2022.

The training set is composed of 1000 clinical cases extracted from miscellaneous medical specialties including COVID, oncology, infectious diseases, tropical medicine, urology, pediatrics, and others. The files are distributed as follows:

- For subtask 1 (LivingNER-Species NER track), annotations are distributed in a tab-separated file (TSV) file with the following columns:

• filename: document name
• mark: identifier mention mark 
• label: mention type (SPECIES or HUMAN)
• off0: starting position of the mention in the document
• off1: ending position of the mention in the document
• span: textual span

 - For subtask 2 (LivingNER-Species Norm track), annotations are distributed in a TSV file with the same columns as the previous one, plus:

• isH: whether the span is narrower than the NCBITax assigned code 
• isN: whether the mention corresponds to a nosocomial infection
• iscomplex: whether the span has assigned a combination of NCBITax codes
• NCBITax: mention code in the NCBI Taxonomy

- For subtask 3 (LivingNER-Clinical IMPACT track), annotations are distributed in a (TSV). In this version of the dataset, the data for this subtask is pending.

All text files are distributed as plain UTF-8 text files.

Resources

• Web
• Annotation guidelines
• Evaluation library
• LivingNER terminology

For further information, please visit https://temu.bsc.es/livingner/ or email us at encargo-pln-life@bsc.es