Fenominal

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FenominalHPO-based text mining engine

High-performance entity recognition in Rust with Python bindings

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Python API

High Performance (Rust Core)

Built in Rust for fast and memory-safe processing of large-scale clinical text corpora.

Python Integration

Seamless bindings for use in data science and NLP pipelines via PyO3/Maturin.

Ontology-Aware (HPO)

Designed around the Human Phenotype Ontology for structured biomedical concept recognition.

Overview ​

Fenominal is a high-performance Human Phenotype Ontology (HPO) text mining engine designed for robust named entity recognition in clinical and biomedical text.

It implements and extends the algorithm described in:

Groza T, et al. (2023)
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts
Bioinformatics 39(12): btad716
https://pubmed.ncbi.nlm.nih.gov/38001031/

Key Capabilities ​

  • Extracts HPO terms from noisy clinical narratives
  • Optimized Rust backend for performance-critical workloads
  • Python bindings for ML/NLP pipelines
  • Designed for reproducible biomedical text mining

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Released under the MIT License.

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