# A general strategy for generating expert-guided, simplified views of ontologies

## TL;DR

This paper introduces tools to simplify complex biomedical ontologies for specific applications, using expert guidance to ensure compatibility and ease of use.

## Contribution

The paper introduces tools for validating expert-curated term hierarchies against ontology structures to simplify and adapt ontologies for specific use cases.

## Key findings

- Tools were developed to validate curated term hierarchies against ontology structures.
- The approach was validated using the HuBMAP Human Reference Atlas and the Human Developmental Cell Atlas as use cases.
- The tools provide statistical and graphical outputs to aid in conflict resolution and discussion.

## Abstract

Annotation of biomedical entities with widely used, well-structured ontologies and ontology-aware tools ensures data and analyses are Findable, Accessible, Interoperable, and Reusable (FAIR). Standardized terms with synonyms support lexical search, while ontology structure enables biologically meaningful grouping of annotations, such as by location and type. However, ontologies serving diverse communities are often more complex than needed for specific applications, creating barriers to adoption by researchers and resource developers. For example, cell atlases often attempt simplifications by manually building term hierarchies linking to cell type and anatomy ontologies, but these may include relationship types unsuitable for grouping annotations. We present tools for validating human expert curated term hierarchies, developed in two human reference atlas projects, against ontology structures. The tools provide tabular statistics plus graphical views of matching and non-matching terms and relationships to support discussion and conflict resolution. The HuBMAP Human Reference Atlas (HRA) effort is used to validate the approach and tools, and the Human Developmental Cell Atlas is featured as a use case.