BIOMAT-CellNER Corpus: Train and Validation Sets

BIOMAT-CellNER Train and Validation Sets

BIOMAT-CellNER stands for BIOMATerials Cell Named Entity Recognition. It is a corpus developed within the scope of the Horizon Europe BIOMATDB project to support the extraction and classification of cell entity mentions from the scientific literature in the biomaterials domain. It focuses on the annotation of cell mentions, including both cell types (e.g., fibroblasts, stem cells) and cell lines (e.g., HeLa, MC3T3), particularly those that are studied in interaction with biomaterials in experimental settings. The corpus was created through a collaborative effort involving domain experts, who were tasked with the establishment of comprehensive and accurate annotation guidelines for the manual annotation of the final gold standard corpus. To ensure domain relevance and terminological coverage, PubMed abstracts were carefully selected based on relevant MeSH (Medical Subject Headings) categories associated with biomaterials, tissue engineering, and related fields. The abstracts were then manually annotated according to the predefined rules in the annotation guidelines.

This repository contains the train (750 documents) and validation (100 documents) sets of the BIOMAT-CellNER Corpus, which are made available under open access for public use. These sets have been released to support the development of Named Entity Recognition (NER) models for biomaterials-related concept extraction from scientific literature, particularly those mentions referring to cell lines and cell types.

The test set is not included in this repository, as it is reserved for a future shared task planned within the scope of the project. For this reason, access to the full corpus remains restricted, but will be made publicly available upon completion of the shared task.

Resources

Project Website

Biomaterials Marketplace

Biomaterials Database

BIOMAT-CellNER full corpus

Annotation Guidelines