Datasets:

imageomics
/

char-sim-data

license: cc0-1.0
language:
  - en
pretty_name: Character Similarity Dataset
description: >-
  Collection of textual trait descriptions of fish along with the corresponding
  ontology based similarity measures between trait description pairs. The
  distance is estimated using the Phenoscape Knowledgebase as the ontology.
task_categories:
  - feature-extraction
tags:
  - biology
  - organism
  - animals
  - fish
  - traits
  - ontology
  - phenoscape
size_categories: 10K<n<100K
configs:
  - config_name: full_data
    data_files:
      - split: train
        path: all/*_TRAINING.tsv.gz
      - split: test
        path: all/*_ALL_NON_TRAIN.tsv.gz
    default: true
  - config_name: characiformes
    data_files:
      - split: train
        path: characiformes/*_TRAINING.tsv.gz
      - split: test
        path: characiformes/*_ALL_NON_TRAIN.tsv.gz
  - config_name: cypriniformes
    data_files:
      - split: train
        path: cypriniformes/*_TRAINING.tsv.gz
      - split: test
        path: cypriniformes/*_ALL_NON_TRAIN.tsv.gz
  - config_name: gymnotiformes
    data_files:
      - split: train
        path: gymnotiformes/*_TRAINING.tsv.gz
      - split: test
        path: gymnotiformes/*_ALL_NON_TRAIN.tsv.gz
  - config_name: siruliformes
    data_files:
      - split: train
        path: siruliformes/*_TRAINING.tsv.gz
      - split: test
        path: siruliformes/*_ALL_NON_TRAIN.tsv.gz

Dataset Card for Character Similarity Dataset

Dataset Details

The Character Similarity Dataset is a collection of textual trait descriptions along with the corresponding ontology based similarity measures between trait description pairs. The distance is estimated using the Phenoscape Knowledgebase as the ontology.

Dataset Description

Curated by: Jim Balhoff, Soumyashree Kar, Juan Garcia, Hilmar Lapp
Language(s) (NLP): English
Repository: Imageomics/char-sim
Paper: Coming soon!

The Character Similarity Dataset is a collection of 19K textual trait descriptions of fish collected from the Phenoscape Knowledgebase. The dataset also contains the corresponding pairwise similarity measures between trait descriptors (i.e., maxIC, Jaccard, SimGIC). These metrics estimate semantic similarity between the ontological representation of the traits descriptions per the Phenoscape Knowledgebase. The goal is to use this pairwise similarities to inform an embedding space that preserves the structure of the underlying ontology.

Supported Tasks and Leaderboards

Task: Aligned feature extraction. Metric: Spearman's correlation coefficient.

Model	Test set
Trait2Vec	0.7057

Dataset Structure

raw-source/
    phenex-data-merged.ofn.gz
    phenoscape-kb-tbox-classified.ttl.gz
processed-data/
    all/
        data_{percentage}p_TRAINING.tsv.gz
        data_{percentage}p_ALL_NON_TRAIN.tsv.gz
        data_{percentage}p_NON_OVERLAP.tsv.gz
    characiformes/
        data_{percentage}p_TRAINING.tsv.gz
        data_{percentage}p_ALL_NON_TRAIN.tsv.gz
        data_{percentage}p_NON_OVERLAP.tsv.gz
    cypriniformes/
        data_{percentage}p_TRAINING.tsv.gz
        data_{percentage}p_ALL_NON_TRAIN.tsv.gz
        data_{percentage}p_NON_OVERLAP.tsv.gz
    gymnotiformes/
        data_{percentage}p_TRAINING.tsv.gz
        data_{percentage}p_ALL_NON_TRAIN.tsv.gz
        data_{percentage}p_NON_OVERLAP.tsv.gz
    siruliformes/
        data_{percentage}p_TRAINING.tsv.gz
        data_{percentage}p_ALL_NON_TRAIN.tsv.gz
        data_{percentage}p_NON_OVERLAP.tsv.gz

phenex-data-merged.ofn.gz and phenoscape-kb-tbox-classified.ttl.gz contain URLs to access the trait data from Phenoscape Knowledgebase. Running the processing script creates the four subset folders (characiformes/, cypriniformes/, gymnotiformes/, and siruliformes/, each an order of fish), then combines their data into the all/ directory to create the training and test datasets.

Note: percentage is the parameter passed for the percentage of the data to use for training; in this case, percentage = 80.

Data Instances

Percentage is the proportion of data that will be used for training (i.e. data_{percentage}p_TRAINING.tsv.gz). In case the percentage is smaller than 100, the remaining proportion of the dataset is stored in data{percentage}p_ALL_NON_TRAIN.tsv.gz and a subset of this in data_{percentage}p_NON_OVERLAP.tsv.gz. Each of this files corresponds to a

Data Fields

data_{percentage}p_TRAINING.tsv.gz: [ADD SUMMARY HERE + descriptions of columns below]

id_1:
id_2:
maxIC: Ontology based measure
jaccard: Ontology based measure
simGIC: Ontology based measure
order: Pairwise score indices
character_1:
desc_1: Textual trait description.
character_2:
desc_2: Textual trait description. [More Information Needed]
Source Data

Data was collected from the Phenoscape Knowledgebase.

Data Collection and Processing

Who are the source data producers?

[More Information Needed]

Annotations

Annotation process

[More Information Needed]

Who are the annotators?

[More Information Needed]

Personal and Sensitive Information

None

Considerations for Using the Data

The distribution of SimGIC scores is skewed towards smaller values. This imbalance may cause the similarity of embeddings to follow the same bias. Consider subsampling to ensure uniform representation of distances.

Bias, Risks, and Limitations

This dataset has the biases of the Phenoscape ontology. This means the estimated models embeddings will inherit the ontology's inductive biases, coverage gaps, and evolving definitions. Biological conclusions may differ under alternative metrics (e.g., [Resnik](ADD LINK)) or other phenotype ontologies.

Licensing Information

This dataset is dedicated to the public domain for the benefit of scientific pursuits. We ask that you cite the dataset and original source data using the below citations if you make use of it in your research.

[CHECK THIS]

Citation

We ask that you cite the dataset and original source data using the below citations if you make use of it in your research.

Data
```
@misc{char-sim-data-2025,
  author = {Jim Balhoff and Soumyashree Kar and Juan Garcia and Hilmar Lapp},
  title = {Character Similarity Dataset},
  year = {2025},
  url = {https://huggingface.co/datasets/imageomics/char-sim-data},
  doi = {<doi once generated>},
  publisher = {Hugging Face}
}
```
Please be sure to also cite the original data source:
```
ADD Phenoscape Knowledgebase citation HERE
```
Acknowledgements

This work was supported by the Imageomics Institute, which is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Dataset Card Authors

Juan Garcia, Jim Balhoff, and Elizabeth Campolongo

Dataset Card Contact

Please open a Discussion on the Community Tab with any questions on the dataset.

Dataset Card for Character Similarity Dataset

Dataset Details

Dataset Description

Supported Tasks and Leaderboards

Dataset Structure

Data Instances

Data Fields

Source Data

Data Collection and Processing

Who are the source data producers?

Annotations

Annotation process

Who are the annotators?

Personal and Sensitive Information

Considerations for Using the Data

Bias, Risks, and Limitations

Licensing Information

Citation

Acknowledgements

Dataset Card Authors

Dataset Card Contact