Source: https://docs.nygen.io/CyteOnto/support/citing/
Revision: cb82698da3fc9e2bc385eb9a70e07f9304835eba
Structured page: https://docs.nygen.io/CyteOnto/support.citing.json

Cite CyteOnto

CyteOnto is part of CyteType <https://docs.nygen.io/CyteType/>. If you use CyteOnto in your work, please cite the CyteType preprint:

Ahuja G, Antill A, Su Y, Dall’Olio GM, Basnayake S, Karlsson G, Dhapola P. Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics. bioRxiv 2025. doi:Ahuja et al. (2025) <https://doi.org/10.1101/2025.11.06.686964>

BibTeX:

@article{cytetype2025,
  title   = {Multi-agent {AI} enables evidence-based cell annotation in single-cell transcriptomics},
  author  = {Ahuja, Gautam and Antill, Alex and Su, Yi and Dall'Olio, Giovanni Marco and Basnayake, Sukhitha and Karlsson, G{\"o}ran and Dhapola, Parashar},
  journal = {bioRxiv},
  year    = {2025},
  doi     = {10.1101/2025.11.06.686964},
  url     = {https://www.biorxiv.org/content/10.1101/2025.11.06.686964v1}
}

Record what you ran

The scores depend on the models and the options of the comparison, and the LLM’s descriptions can differ between runs. Record these items for each comparison you report:

Item	Where to find it

CyteOnto version	cyteonto.__version__, and the commit you installed

Model pair	The provider and model of LlmConfig and EmbdConfig, or of the request to the hosted API

Fallback use	cyto.model_pair_usage.to_status_dict(), or the modelPairUsage of the job’s status. When a tier is not primary, it names the fallback model; in Python, the fallback LLM only if you passed fallback_llm

Options	metric, metric_params, min_match_similarity and compound_scoring, or the request body without its API keys

Run ID	The run_id column of the results

Results	The result DataFrame or file, with the label pairs, the matched terms and the scores

Keep the files behind the scores: the run caches in user_dir, which hold the descriptions and embeddings of your labels, and the ontology files of the model pair in data_dir, against which the labels were matched and scored. See Caching and runs <https://docs.nygen.io/CyteOnto/guides/caching>.

License

The cyteonto package is released under the MIT license <https://github.com/NygenAnalytics/CyteOnto/blob/master/LICENSE>. The Cell Ontology is published by the OBO Foundry <https://obofoundry.org/ontology/cl.html> under its own license.

References¶ <https://docs.nygen.io/CyteOnto/support/citing/#references>

Ahuja, G., Antill, A., Su, Y., Dall’Olio, G. M., Basnayake, S., Karlsson, G., & Dhapola, P. (2025). Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics. 10.1101/2025.11.06.686964 <https://doi.org/10.1101/2025.11.06.686964>