John Beverley, Shane Babcock, Carter Benson, Giacomo De Colle, Sydney Cohen, Alexander D Diehl, Ram A N R Challa, Rachel A Mavrovich, Joshua Billig, Anthony Huffman, Yongqun He
{"title":"四层病原体参考本体套件。","authors":"John Beverley, Shane Babcock, Carter Benson, Giacomo De Colle, Sydney Cohen, Alexander D Diehl, Ram A N R Challa, Rachel A Mavrovich, Joshua Billig, Anthony Huffman, Yongqun He","doi":"10.1186/s13326-025-00333-6","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases.</p><p><strong>Methods: </strong>The \"hub-and-spoke\" methodology is adopted to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO).</p><p><strong>Results: </strong>IDO is introduced before reporting on the scopes, major classes and relations, applications and extensions of IDO to VIDO, BIDO, MIDO, and PIDO.</p><p><strong>Conclusions: </strong>The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease ontologies within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing, quality, and analysis.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"16 1","pages":"12"},"PeriodicalIF":1.6000,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A fourfold pathogen reference ontology suite.\",\"authors\":\"John Beverley, Shane Babcock, Carter Benson, Giacomo De Colle, Sydney Cohen, Alexander D Diehl, Ram A N R Challa, Rachel A Mavrovich, Joshua Billig, Anthony Huffman, Yongqun He\",\"doi\":\"10.1186/s13326-025-00333-6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases.</p><p><strong>Methods: </strong>The \\\"hub-and-spoke\\\" methodology is adopted to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO).</p><p><strong>Results: </strong>IDO is introduced before reporting on the scopes, major classes and relations, applications and extensions of IDO to VIDO, BIDO, MIDO, and PIDO.</p><p><strong>Conclusions: </strong>The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease ontologies within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing, quality, and analysis.</p>\",\"PeriodicalId\":15055,\"journal\":{\"name\":\"Journal of Biomedical Semantics\",\"volume\":\"16 1\",\"pages\":\"12\"},\"PeriodicalIF\":1.6000,\"publicationDate\":\"2025-07-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Biomedical Semantics\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://doi.org/10.1186/s13326-025-00333-6\",\"RegionNum\":3,\"RegionCategory\":\"工程技术\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Biomedical Semantics","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1186/s13326-025-00333-6","RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
Background: Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases.
Methods: The "hub-and-spoke" methodology is adopted to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO).
Results: IDO is introduced before reporting on the scopes, major classes and relations, applications and extensions of IDO to VIDO, BIDO, MIDO, and PIDO.
Conclusions: The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease ontologies within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing, quality, and analysis.
期刊介绍：
Journal of Biomedical Semantics addresses issues of semantic enrichment and semantic processing in the biomedical domain. The scope of the journal covers two main areas:
Infrastructure for biomedical semantics: focusing on semantic resources and repositories, meta-data management and resource description, knowledge representation and semantic frameworks, the Biomedical Semantic Web, and semantic interoperability.
Semantic mining, annotation, and analysis: focusing on approaches and applications of semantic resources; and tools for investigation, reasoning, prediction, and discoveries in biomedicine.
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