Scholarlink

<p>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.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月9日

查看全文
  • Anita R. Caron,
  • Aleix Puig-Barbe,
  • Ellen M. Quardokus,
  • James P. Balhoff,
  • Jasmine Belfiore,
  • Nana-Jane Chipampe,
  • Josef Hardi,
  • Bruce W. Herr II,
  • Huseyin Kir,
  • Paola Roncaglia,
  • Mark A. Musen,
  • Helen Parkinson,
  • James A. McLaughlin,
  • Katy Börner,
  • David Osumi-Sutherland

摘要

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.