The effects of shared information on semantic calculations in the gene ontology
The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2017-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037016300861 |
| _version_ | 1818153549323829248 |
|---|---|
| author | Paul W. Bible Hong-Wei Sun Maria I. Morasso Rasiah Loganantharaj Lai Wei |
| author_facet | Paul W. Bible Hong-Wei Sun Maria I. Morasso Rasiah Loganantharaj Lai Wei |
| author_sort | Paul W. Bible |
| collection | DOAJ |
| description | The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures. No thorough investigation has been made into the behavior, complexity, and performance of semantic methods derived from distinct SI approaches. We apply bootstrapping to compare the generalized performance of 57 gene-to-gene semantic measures across six benchmarks. Considering the number of measures, we additionally evaluate whether these methods can be leveraged through ensemble machine learning to improve prediction performance. Results showed that the choice of ontology type most strongly influenced performance across all evaluations. Combining measures into an ensemble classifier reduces cross-validation error beyond any individual measure for protein interaction prediction. This improvement resulted from information gained through the combination of ontology types as ensemble methods within each GO type offered no improvement. These results demonstrate that multiple SI measures can be leveraged for machine learning tasks such as automated gene function prediction by incorporating methods from across the ontologies. To facilitate future research in this area, we developed the GO Graph Tool Kit (GGTK), an open source C++ library with Python interface (github.com/paulbible/ggtk). Keywords: Semantic similarity, Gene ontology, Function prediction, Machine learning, Protein–protein interaction, Gene expression |
| first_indexed | 2024-12-11T14:12:23Z |
| format | Article |
| id | doaj.art-cf978c9158a84c4b84660e06ff8dc1ef |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-11T14:12:23Z |
| publishDate | 2017-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-cf978c9158a84c4b84660e06ff8dc1ef2022-12-22T01:03:22ZengElsevierComputational and Structural Biotechnology Journal2001-03702017-01-0115195211The effects of shared information on semantic calculations in the gene ontologyPaul W. Bible0Hong-Wei Sun1Maria I. Morasso2Rasiah Loganantharaj3Lai Wei4State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Corresponding authors.Biodata Mining and Discovery Section, Office of Science and Technology, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MarylandLaboratory of Skin Biology, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MarylandLaboratory of Bioinformatics, Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LouisianaState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Corresponding authors.The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures. No thorough investigation has been made into the behavior, complexity, and performance of semantic methods derived from distinct SI approaches. We apply bootstrapping to compare the generalized performance of 57 gene-to-gene semantic measures across six benchmarks. Considering the number of measures, we additionally evaluate whether these methods can be leveraged through ensemble machine learning to improve prediction performance. Results showed that the choice of ontology type most strongly influenced performance across all evaluations. Combining measures into an ensemble classifier reduces cross-validation error beyond any individual measure for protein interaction prediction. This improvement resulted from information gained through the combination of ontology types as ensemble methods within each GO type offered no improvement. These results demonstrate that multiple SI measures can be leveraged for machine learning tasks such as automated gene function prediction by incorporating methods from across the ontologies. To facilitate future research in this area, we developed the GO Graph Tool Kit (GGTK), an open source C++ library with Python interface (github.com/paulbible/ggtk). Keywords: Semantic similarity, Gene ontology, Function prediction, Machine learning, Protein–protein interaction, Gene expressionhttp://www.sciencedirect.com/science/article/pii/S2001037016300861 |
| spellingShingle | Paul W. Bible Hong-Wei Sun Maria I. Morasso Rasiah Loganantharaj Lai Wei The effects of shared information on semantic calculations in the gene ontology Computational and Structural Biotechnology Journal |
| title | The effects of shared information on semantic calculations in the gene ontology |
| title_full | The effects of shared information on semantic calculations in the gene ontology |
| title_fullStr | The effects of shared information on semantic calculations in the gene ontology |
| title_full_unstemmed | The effects of shared information on semantic calculations in the gene ontology |
| title_short | The effects of shared information on semantic calculations in the gene ontology |
| title_sort | effects of shared information on semantic calculations in the gene ontology |
| url | http://www.sciencedirect.com/science/article/pii/S2001037016300861 |
| work_keys_str_mv | AT paulwbible theeffectsofsharedinformationonsemanticcalculationsinthegeneontology AT hongweisun theeffectsofsharedinformationonsemanticcalculationsinthegeneontology AT mariaimorasso theeffectsofsharedinformationonsemanticcalculationsinthegeneontology AT rasiahloganantharaj theeffectsofsharedinformationonsemanticcalculationsinthegeneontology AT laiwei theeffectsofsharedinformationonsemanticcalculationsinthegeneontology AT paulwbible effectsofsharedinformationonsemanticcalculationsinthegeneontology AT hongweisun effectsofsharedinformationonsemanticcalculationsinthegeneontology AT mariaimorasso effectsofsharedinformationonsemanticcalculationsinthegeneontology AT rasiahloganantharaj effectsofsharedinformationonsemanticcalculationsinthegeneontology AT laiwei effectsofsharedinformationonsemanticcalculationsinthegeneontology |