---
task_categories:
- feature-extraction
language:
- en
tags:
- nlp
pretty_name: CellTissue Data train/test
size_categories:
- n<1K
---
# CellTissue Data train/test

 *** ***Data curation parked due to consolidated curation strategy*** ***

Papers manually annotated and reviewed, for the following entity types, where applicable:

      - Cell type
      - Cell line
      - Tissue
      - Cell context
      - Cell component

### Dataset Description

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

### Dataset Sources

The following papers were annotated for use as training / testing text data:

--------------------------------------------------------------------------
PMCID  |  Journal  |  Year
--------------------------------------------------------------------------

PMC12115102  |  _Plants_  |  2025

PMC12101583	 |  _Cancer Biology & Therapy_  |  2025

PMC12081701  |  _Nature Communications_  |  2025

PMC11075828	 |  _PLoS Pathogens_  |  2024

PMC10442740	 |  _Biomedical Reports_  |  2023

PMC12141184	 |  _Saudi Pharmaceutical Journal_  |  2025

PMC12118871	 |  _PLoS One_	 |  2025

PMC12105127	 |  _BMC Complementary Medicine and Therapies_  |  2025

PMC12072392	 |  _International Journal of Molecular Sciences_  |  2025

PMC11699618	 |  _Iscience_  |  2024

PMC11641291	 |  _International Journal of Molecular Sciences_  |  2024

PMC11419360	 |  _PLoS Pathogens_  |  2024

--------------------------------------------------------------------------

## Uses

The aim for this data is for it to be used for the testing and correction of NER models generated in the OTAR3088 project.

## Dataset Structure

CoNLL format, friendly for the task of NER-model production.
An example of what a text annotation looks like in the CoNLL structure:

**- - - - - - -**

the -X- _ O

frequency -X- _ O

of -X- _ O

latently -X- _ B-CELL_CONTEXT

infected -X- _ I-CELL_CONTEXT

cells -X- _ B-CELL

and -X- _ O

**- - - - - - -**

### Curation Rationale

<!-- Motivation for the creation of this dataset. -->

This dataset was a first pass of data generation serving our aim to produce the CeLLaTe model.

We annotated with the inclusion of sub-type cell and tissue descriptors, being conscious of cell components also. 

A change in curation style and motivation led us to archiving this data.

### Source Data

<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->

Data was derived from articles, sourced via EuropePMC.


#### Who are the annotators?

<!-- This section describes the people or systems who created the annotations. -->

Christine Withers


## Bias, Risks, and Limitations

<!-- This section is meant to convey both technical and sociotechnical limitations. -->

This data has been annotated by one individual with no inter-annotator agreement calculated. Therefore this data cannot be considered gold standard and may contain erroneous annotations.

### Recommendations

<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->

It is recommended that should this data be used it should be revised. Contributions / corrections of this data are most welcome via HuggingFace should it prove useful.

We have decided to keep this data for traceability in the progression of our work.

## Dataset Card Authors

Christine Withers - _https://huggingface.co/christine-withers_

## Dataset Card Contact

Christine Withers - _https://huggingface.co/christine-withers_
withers@ebi.ac.uk