The use of foundational ontologies in biomedical research
Abstract Background The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data and metadata concepts. Ontologies are currently modelled following different approaches, sometimes describing conflicting definitions of the same concepts, which can affect intero...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | Journal of Biomedical Semantics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13326-023-00300-z |
| _version_ | 1797388011693932544 |
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| author | César H. Bernabé Núria Queralt-Rosinach Vítor E. Silva Souza Luiz Olavo Bonino da Silva Santos Barend Mons Annika Jacobsen Marco Roos |
| author_facet | César H. Bernabé Núria Queralt-Rosinach Vítor E. Silva Souza Luiz Olavo Bonino da Silva Santos Barend Mons Annika Jacobsen Marco Roos |
| author_sort | César H. Bernabé |
| collection | DOAJ |
| description | Abstract Background The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data and metadata concepts. Ontologies are currently modelled following different approaches, sometimes describing conflicting definitions of the same concepts, which can affect interoperability. To cope with that, prior literature suggests organising ontologies in levels, where domain specific (low-level) ontologies are grounded in domain independent high-level ontologies (i.e., foundational ontologies). In this level-based organisation, foundational ontologies work as translators of intended meaning, thus improving interoperability. Despite their considerable acceptance in biomedical research, there are very few studies testing foundational ontologies. This paper describes a systematic literature mapping that was conducted to understand how foundational ontologies are used in biomedical research and to find empirical evidence supporting their claimed (dis)advantages. Results From a set of 79 selected papers, we identified that foundational ontologies are used for several purposes: ontology construction, repair, mapping, and ontology-based data analysis. Foundational ontologies are claimed to improve interoperability, enhance reasoning, speed up ontology development and facilitate maintainability. The complexity of using foundational ontologies is the most commonly cited downside. Despite being used for several purposes, there were hardly any experiments (1 paper) testing the claims for or against the use of foundational ontologies. In the subset of 49 papers that describe the development of an ontology, it was observed a low adherence to ontology construction (16 papers) and ontology evaluation formal methods (4 papers). Conclusion Our findings have two main implications. First, the lack of empirical evidence about the use of foundational ontologies indicates a need for evaluating the use of such artefacts in biomedical research. Second, the low adherence to formal methods illustrates how the field could benefit from a more systematic approach when dealing with the development and evaluation of ontologies. The understanding of how foundational ontologies are used in the biomedical field can drive future research towards the improvement of ontologies and, consequently, data FAIRness. The adoption of formal methods can impact the quality and sustainability of ontologies, and reusing these methods from other fields is encouraged. |
| first_indexed | 2024-03-08T22:34:31Z |
| format | Article |
| id | doaj.art-a685d807047649c9870c6549288cfcbf |
| institution | Directory Open Access Journal |
| issn | 2041-1480 |
| language | English |
| last_indexed | 2024-03-08T22:34:31Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Semantics |
| spelling | doaj.art-a685d807047649c9870c6549288cfcbf2023-12-17T12:34:06ZengBMCJournal of Biomedical Semantics2041-14802023-12-0114111410.1186/s13326-023-00300-zThe use of foundational ontologies in biomedical researchCésar H. Bernabé0Núria Queralt-Rosinach1Vítor E. Silva Souza2Luiz Olavo Bonino da Silva Santos3Barend Mons4Annika Jacobsen5Marco Roos6Department of Human Genetics, Leiden University Medical CenterDepartment of Human Genetics, Leiden University Medical CenterFederal University of Espírito SantoDepartment of Human Genetics, Leiden University Medical CenterDepartment of Human Genetics, Leiden University Medical CenterDepartment of Human Genetics, Leiden University Medical CenterDepartment of Human Genetics, Leiden University Medical CenterAbstract Background The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data and metadata concepts. Ontologies are currently modelled following different approaches, sometimes describing conflicting definitions of the same concepts, which can affect interoperability. To cope with that, prior literature suggests organising ontologies in levels, where domain specific (low-level) ontologies are grounded in domain independent high-level ontologies (i.e., foundational ontologies). In this level-based organisation, foundational ontologies work as translators of intended meaning, thus improving interoperability. Despite their considerable acceptance in biomedical research, there are very few studies testing foundational ontologies. This paper describes a systematic literature mapping that was conducted to understand how foundational ontologies are used in biomedical research and to find empirical evidence supporting their claimed (dis)advantages. Results From a set of 79 selected papers, we identified that foundational ontologies are used for several purposes: ontology construction, repair, mapping, and ontology-based data analysis. Foundational ontologies are claimed to improve interoperability, enhance reasoning, speed up ontology development and facilitate maintainability. The complexity of using foundational ontologies is the most commonly cited downside. Despite being used for several purposes, there were hardly any experiments (1 paper) testing the claims for or against the use of foundational ontologies. In the subset of 49 papers that describe the development of an ontology, it was observed a low adherence to ontology construction (16 papers) and ontology evaluation formal methods (4 papers). Conclusion Our findings have two main implications. First, the lack of empirical evidence about the use of foundational ontologies indicates a need for evaluating the use of such artefacts in biomedical research. Second, the low adherence to formal methods illustrates how the field could benefit from a more systematic approach when dealing with the development and evaluation of ontologies. The understanding of how foundational ontologies are used in the biomedical field can drive future research towards the improvement of ontologies and, consequently, data FAIRness. The adoption of formal methods can impact the quality and sustainability of ontologies, and reusing these methods from other fields is encouraged.https://doi.org/10.1186/s13326-023-00300-zSystematic literature mappingFoundational ontologiesFAIRBiomedical ontologies |
| spellingShingle | César H. Bernabé Núria Queralt-Rosinach Vítor E. Silva Souza Luiz Olavo Bonino da Silva Santos Barend Mons Annika Jacobsen Marco Roos The use of foundational ontologies in biomedical research Journal of Biomedical Semantics Systematic literature mapping Foundational ontologies FAIR Biomedical ontologies |
| title | The use of foundational ontologies in biomedical research |
| title_full | The use of foundational ontologies in biomedical research |
| title_fullStr | The use of foundational ontologies in biomedical research |
| title_full_unstemmed | The use of foundational ontologies in biomedical research |
| title_short | The use of foundational ontologies in biomedical research |
| title_sort | use of foundational ontologies in biomedical research |
| topic | Systematic literature mapping Foundational ontologies FAIR Biomedical ontologies |
| url | https://doi.org/10.1186/s13326-023-00300-z |
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