Building Bio-Ontology Graphs from Data Using Logic and NLP
In this age of big data and natural language processing, to what extent can we leverage new technologies and new tools to make progress in organizing disparate biomedical data sources? Imagine a system in which one could bring together sequencing data with phenotypes, gene expression data, and clini...
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MDPI AG
2024-10-01
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| author | Theresa Gasser Erick Chastain |
| author_facet | Theresa Gasser Erick Chastain |
| author_sort | Theresa Gasser |
| collection | DOAJ |
| description | In this age of big data and natural language processing, to what extent can we leverage new technologies and new tools to make progress in organizing disparate biomedical data sources? Imagine a system in which one could bring together sequencing data with phenotypes, gene expression data, and clinical information all under the same conceptual heading where applicable. Bio-ontologies seek to carry this out by organizing the relations between concepts and attaching the data to their corresponding concept. However, to accomplish this, we need considerable time and human input. Instead of resorting to human input alone, we describe a novel approach to obtaining the foundation for bio-ontologies: obtaining propositions (links between concepts) from biomedical text so as to fill the ontology. The heart of our approach is applying logic rules from Aristotelian logic and natural logic to biomedical information to derive propositions so that we can have material to organize knowledge bases (ontologies) for biomedical research. We demonstrate this approach by constructing a proof-of-principle bio-ontology for COVID-19 and related diseases. |
| format | Article |
| id | doaj-art-24feeeb5ac214a95b37a81f28d89a521 |
| institution | Kabale University |
| issn | 2078-2489 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Information |
| spelling | doaj-art-24feeeb5ac214a95b37a81f28d89a5212024-11-26T18:06:31ZengMDPI AGInformation2078-24892024-10-01151166910.3390/info15110669Building Bio-Ontology Graphs from Data Using Logic and NLPTheresa Gasser0Erick Chastain1Department of Mathematics, University of Dallas, Irving, TX 75062, USADepartment of Mathematics, University of Dallas, Irving, TX 75062, USAIn this age of big data and natural language processing, to what extent can we leverage new technologies and new tools to make progress in organizing disparate biomedical data sources? Imagine a system in which one could bring together sequencing data with phenotypes, gene expression data, and clinical information all under the same conceptual heading where applicable. Bio-ontologies seek to carry this out by organizing the relations between concepts and attaching the data to their corresponding concept. However, to accomplish this, we need considerable time and human input. Instead of resorting to human input alone, we describe a novel approach to obtaining the foundation for bio-ontologies: obtaining propositions (links between concepts) from biomedical text so as to fill the ontology. The heart of our approach is applying logic rules from Aristotelian logic and natural logic to biomedical information to derive propositions so that we can have material to organize knowledge bases (ontologies) for biomedical research. We demonstrate this approach by constructing a proof-of-principle bio-ontology for COVID-19 and related diseases.https://www.mdpi.com/2078-2489/15/11/669natural language processingnatural logicontologyknowledge graphsrelation extraction |
| spellingShingle | Theresa Gasser Erick Chastain Building Bio-Ontology Graphs from Data Using Logic and NLP Information natural language processing natural logic ontology knowledge graphs relation extraction |
| title | Building Bio-Ontology Graphs from Data Using Logic and NLP |
| title_full | Building Bio-Ontology Graphs from Data Using Logic and NLP |
| title_fullStr | Building Bio-Ontology Graphs from Data Using Logic and NLP |
| title_full_unstemmed | Building Bio-Ontology Graphs from Data Using Logic and NLP |
| title_short | Building Bio-Ontology Graphs from Data Using Logic and NLP |
| title_sort | building bio ontology graphs from data using logic and nlp |
| topic | natural language processing natural logic ontology knowledge graphs relation extraction |
| url | https://www.mdpi.com/2078-2489/15/11/669 |
| work_keys_str_mv | AT theresagasser buildingbioontologygraphsfromdatausinglogicandnlp AT erickchastain buildingbioontologygraphsfromdatausinglogicandnlp |