Databases as Ontologies Part 2 - A Case Study with HGNC

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This is a Experimental Study study.

Charles Tapley Hoyt

doi:10.59350/3g3h8-r3h59

October 14, 2025Open Access

Databases as Ontologies Part 2 - A Case Study with HGNC

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Key Points

The case study demonstrates how the HGNC database can be effectively encoded as an ontology using specialized software tools.
By incorporating ontologies, the design approach aims to enhance the understanding and usability of genomic data for researchers.
The use of PyOBO as a framework informs the methodology for translating database structures into ontological representations.
Encoding databases as ontologies may enable better data interoperability and richer semantic connections between biological concepts.

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Implication

This case study reveals the design and methodology for encoding the HGNC database as an ontology, indicating the role of ontologies in data representation.

Abstract

This is the second of a two-part post about encoding databases as ontologies. In the first part, I gave a background on how I started working on this problem and the software stack I developed along the way. In this post, I explain the philosophy and design about how I encoded the HGNC (HUGO Gene Nomenclature Committee) database as an ontology using PyOBO.

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Cite This Study

Charles Tapley Hoyt (2025) studied this question.

synapsesocial.com/papers/68f199ccde32064e504dd375 https://doi.org/10.59350/3g3h8-r3h59

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Databases as Ontologies Part 2 - A Case Study with HGNC

Key Points

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Implication

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Databases as Ontologies Part 2 - A Case Study with HGNC

Key Points

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Implication

Abstract

Discussion

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