LivingNER corpus: recognition and normalization of species

LivingNER corpus - trainining set

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 the training set from four different specialties: COVID, oncology, infectious diseases and tropical medicine. The files are distributed as follows:

- For the subtask 1 (LivingNER - NER), 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 the subtask 2 (LivingNER - NORM), 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 the subtask 3 (LivingNER -  Application), annotations are distributed in a (TSV). In this version of the sample set, the data for this subtask is pending.

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

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