---
license: cc-by-sa-4.0
language:
- en
---

# Dataset Card: OTAR3088 Cellfinder (Cleaned & Filtered)

This dataset is a curated derivative of the CellFinder corpus, specifically adapted for the OTAR3088 project. It focuses on high-precision entity recognition for cellular and tissue-based nomenclature.


### Dataset Description
While the original CellFinder dataset provides 6(anatomical parts, cell components, cell lines, cell types, genes/protein and species) entity types,
this version has been adapted and restructured to focus on three core biological entities: CellLine, CellType, and Anatomy(equivalent to Tissue entity in our project). 
This version also resolves some annotation overlaps and inconsistencies found in the source material to improve training performance in Transformer-based models.

The original Cellfinder annotated texts was sourced from https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/resources/cellfinder/

Filters applied: 
  - Removal of "_Anatomy_" entities which are not fit for our use of "_Anatomy_" terms as "_Tissue_" equivalents
  - Resolution of cases where a term is given multiple labels in data sets, resolved by choosing the mode label / failing that a list of priorities is used for the entity label that is given
  - Drop entries of annotations which are outside of the entity types we care for, which are: "_CellType_", "_CellLine_" and "_Anatomy_"~Tissue


### Dataset info

- **Curated by:** Christine Withers
- **Funded by [optional]:** Open Targets
- **Shared by [optional]:** [More Information Needed]
- **Language(s) (NLP):** English

### Licensing & Attribution
- **License:** CC BY-SA 4.0

- **License Note** : This dataset is a derivative work based on the original CellFinder corpus (licensed under CC BY-SA 3.0). As permitted by the "Later Version" clause of the 3.0 license, this version is distributed under CC BY-SA 4.0.

- **Original Source**: [CellFinder - HU Berlin](https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/resources/cellfinder/)

- **Original Paper**: Neves M, et al. CellFinder: a corpus for multiclass annotations of cellular components and molecules in biomedical texts-> [PubMed](https://pubmed.ncbi.nlm.nih.gov/24304896/)


## Dataset Structure

- BRAT