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license: mit
task_categories:
- text-classification
language:
- en
tags:
- biology
- ner
- nlp
pretty_name: Cell/Tissue Dictionary
size_categories:
- 1K<n<10K
---
# CellTissue-dict
<!-- Provide a quick summary of the dataset. -->
This dictionary is comprised of a merge of two source dictionaries (from Bioportal and ChEMBL), used to tag cell and tissue descriptions in text.
## Dataset Details
### Dataset Description
- **Curated by:** Christine Withers
- **Funded by:** Open Targets
- **Shared by:** Christine Withers
- **Language(s) (NLP):** English
- **License:** MIT
### Dataset Sources
<!-- Provide the basic links for the dataset. -->
This dictionary was produced by a combination of quick data sourcing, followed by partial manual categorising of terms.
- **Repository:** _https://github.com/ML4LitS/OTAR3088_
### Direct Use
<!-- This section describes suitable use cases for the dataset. -->
This data may be used to tag phrases in natural language, categorising them into broad bins _'CELL'_ and _'TISSUE'_.
### Out-of-Scope Use
<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
This dictionary is by no means an exhaustive list of cell and tissue terms, the dictionary too does not ground terms to unique identifiers.
## Dataset Structure
<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
The _'term : label'_ entires here describe _'cell/tissue phrase' : 'CELL | TISSUE label'_
E.g. _'HeLa' : 'CELL'_
## Dataset Creation
### Curation Rationale
<!-- Motivation for the creation of this dataset. -->
This data was used as a screen to quickly annotate texts, with the intention of these pre-annotated texts then being manually curated.
Curated data were then used in a production pipeline for the creation of the CeLLaTe NER model.
### Source Data
<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->
Source data was comprised of the ChEMBL cell dictionary, and a flattened dictionary of the BRENDA Tissue and Enzyme source ontology.
Queries relating to ChEMBL dictionary extraction are located here: _https://github.com/ML4LitS/OTAR3088/blob/main/Data_mining/chembl_sql/cell_line/cell_line_chembl_extraction.py_
BRENDA dictionary was sourced here: _https://bioportal.bioontology.org/ontologies/BTO_
#### Data Collection and Processing
<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. -->
The BRENDA dictionary, on downloading, was manually organised, labelling terms as either _'CELL'_ or _'TISSUE'_.
Dictionaries were concatenated in _https://github.com/ML4LitS/OTAR3088/blob/main/Data_mining/labelstudio_e2e/labelstudio_e2e.py_
#### Who are the source data producers?
<!-- This section describes the people or systems who originally created the data. It should also include self-reported demographic or identity information for the source data creators if this information is available. -->
Bioportal sourced the BRENDA dictionary, and ChEMBL the cell dictionary.
#### Citations:
- **ChEMBL:** _Zdrazil B, Felix E, Hunter F, Manners EJ, Blackshaw J, Corbett S, de Veij M, Ioannidis H, Lopez DM, Mosquera JF, Magarinos MP, Bosc N, Arcila R, Kizilören T, Gaulton A, Bento AP, Adasme MF, Monecke P, Landrum GA, Leach AR. The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. Nucleic Acids Res. 2024 Jan 5;52(D1):D1180-D1192._
- **Bioportal (BRENDA):** _Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Goncalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. Nucleic Acids Research, Volume 53, Issue W1, 7 July 2025, Pages W84-W94, https://academic.oup.com/nar/article/53/W1/W84/8129374._
## Dataset Card Authors
Christine Withers - _https://huggingface.co/christine-withers_
## Dataset Card Contact
Christine Withers - _https://huggingface.co/christine-withers_
withers@ebi.ac.uk |