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Project 15: Enhancing interoperability of biomedical resources using ontologies.

Abstract

In Japan, there are two medical expense subsidy systems, “specific chronic pediatric disease system” and “designated intractable disease system”, for some rare diseases called “Nanbyo”. With these medical subsidies, many medical examinations and researches have been conducted on patients with Nanbyo diseases, and various databases have been constructed to summarize those results. However, there has been no systematic investigation of the correspondence between Nanbyo diseases and diseases in international rare genetic disease databases so far.

This makes it difficult to share biomedical data on Nanbyo diseases with the rest of the world. To address this problem, we have developed a Nanbyo Disease Ontology (NANDO) with over 2700 entities which represent individual Nanbyo diseases in the two medical expense subsidy systems https://rdfportal.org/dataset/nando. Furthermore, using this first ontology of Nanbyo diseases in Japan, we constructed NanbyoData http://nanbyodata.jp, which integrates biomedical data such as variants, genetic tests, bio-resources, and patient numbers on Nanbyo diseases in Japan.

In this hackathon, we will try to map NANDO entities to Orphanet Rare Disease Ontology (ORDO) entities and Monarch Disease Ontology entities by using a semi-automatic approach. We believe that this will enhance interoperability of biomedical resources related to rare diseases between Europe, US, and Japan.

Lead(s)

  • Toyofumi Fujiwara
  • David Lagorce

Members

  • Terue Takatsuki

Achievements/Outcomes

By integrating the rare disease ontologies provided by the following organizations into a cross-referenced database, we aim to enhance the interoperability of the biomedical resources maintained by each organization.

  • ORDO - Orphanet Rare Disease ontology
    Provided by: Orphanet

    • Total Number of Entities: 9,622 - Version 4.5

  • Mondo - Mondo Disease Ontology
    Provided by: Monarch Initiative

    • Total Number of Entities: 29,392 - releases/2024-09-03

  • NANDO - Nanbyo Disease Ontology
    Provided by: DBCLS

    • Total Number of Entities: 2,784 - releases/2023-11-27

The mapping results for each ontology have been created in SSSOM format:

  • Mapping between ORDO and Mondo: SSSOM_ORDO_MONDO_20241107

    • Machine-generated mappings were manually curated.
    • Number of Mappings: 8,053
      • Number of Mapped ORDO Entities: 8,053
      • Number of Mapped Mondo Entities: 8,039

  • Mapping between NANDO and Mondo: SSSOM_NANDO_MONDO_20241107

    • Machine-generated mappings were manually curated.
    • Number of Mappings: 2,187
      • Number of Mapped NANDO Entities: 2,036
      • Number of Mapped Mondo Entities: 1,549

  • Mapping between ORDO and NANDO: SSSOM_ORDO_NANDO_20241107

    • Mapped through Mondo by leveraging the mapping results of ORDO to Mondo and NANDO to Mondo.
    • Number of Mappings: 1,658
      • Number of Mapped ORDO Entities: 1,130
      • Number of Mapped NANDO Entities: 1,616

Future plans

In this BioHackathon, we mapped entities with similar notations and manually curated them. Going forward, we will attempt to map entities that were not covered in this BioHackathon.

  • Number of NANDO entities not mapped to ORDO in this BioHakcathon: 1,168
  • Number of NANDO entities not mapped to Mondo in this BioHackathon: 748

Acknowledgement

  • Orphanet
  • Monarch Initiative
  • DBCLS