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Showing 1 to 12 of 19 entries
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Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

Journal of biomedical semantics

Hur J, Özgür A, Xiang Z, He Y.
PMID: 25785184
J Biomed Semantics. 2015 Jan 06;6:2. doi: 10.1186/2041-1480-6-2. eCollection 2015.

BACKGROUND: Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords.METHODS: In this study, we report the development...

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Hur J, Özgür A, Xiang Z, et al. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J Biomed Semantics. 2015;6:2doi: 10.1186/2041-1480-6-2.
Hur, J., Özgür, A., Xiang, Z., & He, Y. (2015). Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. Journal of biomedical semantics, 62. https://doi.org/10.1186/2041-1480-6-2
Hur, Junguk, et al. "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions." Journal of biomedical semantics vol. 6 (2015): 2. doi: https://doi.org/10.1186/2041-1480-6-2
Hur J, Özgür A, Xiang Z, He Y. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J Biomed Semantics. 2015 Jan 06;6:2. doi: 10.1186/2041-1480-6-2. eCollection 2015. PMID: 25785184; PMCID: PMC4362819.
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Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Journal of biomedical semantics

Xiang Z, Zheng J, Lin Y, He Y.
PMID: 25785185
J Biomed Semantics. 2015 Jan 09;6:4. doi: 10.1186/2041-1480-6-4. eCollection 2015.

BACKGROUND: It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in...

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Xiang Z, Zheng J, Lin Y, et al. Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J Biomed Semantics. 2015;6:4doi: 10.1186/2041-1480-6-4.
Xiang, Z., Zheng, J., Lin, Y., & He, Y. (2015). Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. Journal of biomedical semantics, 64. https://doi.org/10.1186/2041-1480-6-4
Xiang, Zuoshuang, et al. "Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns." Journal of biomedical semantics vol. 6 (2015): 4. doi: https://doi.org/10.1186/2041-1480-6-4
Xiang Z, Zheng J, Lin Y, He Y. Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J Biomed Semantics. 2015 Jan 09;6:4. doi: 10.1186/2041-1480-6-4. eCollection 2015. PMID: 25785185; PMCID: PMC4362828.
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Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design.

Frontiers in immunology

Ong E, Wong MU, He Y.
PMID: 29123525
Front Immunol. 2017 Oct 26;8:1382. doi: 10.3389/fimmu.2017.01382. eCollection 2017.

With many protective vaccine antigens reported in the literature and verified experimentally, how to use the knowledge mined from these antigens to support rational vaccine design and study underlying design mechanism remains unclear. In order to address the problem,...

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Ong E, Wong MU, He Y. Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. Front Immunol. 2017;8:1382doi: 10.3389/fimmu.2017.01382.
Ong, E., Wong, M. U., & He, Y. (2017). Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. Frontiers in immunology, 81382. https://doi.org/10.3389/fimmu.2017.01382
Ong, Edison, et al. "Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design." Frontiers in immunology vol. 8 (2017): 1382. doi: https://doi.org/10.3389/fimmu.2017.01382
Ong E, Wong MU, He Y. Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. Front Immunol. 2017 Oct 26;8:1382. doi: 10.3389/fimmu.2017.01382. eCollection 2017. PMID: 29123525; PMCID: PMC5662880.
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Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches.

Global vaccines and immunology

He Y, Ong E, Xie J.
PMID: 27868103
Glob Vaccines Immunol. 2016 Jun;1(2):37-39. doi: 10.15761/GVI.1000110. Epub 2016 May 23.

No abstract available.

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He Y, Ong E, Xie J. Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches. Glob Vaccines Immunol. 2016;1(2):37-39doi: 10.15761/GVI.1000110.
He, Y., Ong, E., & Xie, J. (2016). Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches. Global vaccines and immunology, 1(2), 37-39. https://doi.org/10.15761/GVI.1000110
He, Yongqun, et al. "Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches." Global vaccines and immunology vol. 1,2 (2016): 37-39. doi: https://doi.org/10.15761/GVI.1000110
He Y, Ong E, Xie J. Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches. Glob Vaccines Immunol. 2016 Jun;1(2):37-39. doi: 10.15761/GVI.1000110. Epub 2016 May 23. PMID: 27868103; PMCID: PMC5111632.
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Ontology-based representation and analysis of host-Brucella interactions.

Journal of biomedical semantics

Lin Y, Xiang Z, He Y.
PMID: 26445639
J Biomed Semantics. 2015 Oct 05;6:37. doi: 10.1186/s13326-015-0036-y. eCollection 2015.

BACKGROUND: Biomedical ontologies are representations of classes of entities in the biomedical domain and how these classes are related in computer- and human-interpretable formats. Ontologies support data standardization and exchange and provide a basis for computer-assisted automated reasoning. IDOBRU...

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Lin Y, Xiang Z, He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015;6:37doi: 10.1186/s13326-015-0036-y.
Lin, Y., Xiang, Z., & He, Y. (2015). Ontology-based representation and analysis of host-Brucella interactions. Journal of biomedical semantics, 637. https://doi.org/10.1186/s13326-015-0036-y
Lin, Yu, et al. "Ontology-based representation and analysis of host-Brucella interactions." Journal of biomedical semantics vol. 6 (2015): 37. doi: https://doi.org/10.1186/s13326-015-0036-y
Lin Y, Xiang Z, He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015 Oct 05;6:37. doi: 10.1186/s13326-015-0036-y. eCollection 2015. PMID: 26445639; PMCID: PMC4594885.
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Ontodog: a web-based ontology community view generation tool.

Bioinformatics (Oxford, England)

Zheng J, Xiang Z, Stoeckert CJ, He Y.
PMID: 24413522
Bioinformatics. 2014 May 01;30(9):1340-2. doi: 10.1093/bioinformatics/btu008. Epub 2014 Jan 09.

Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated...

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Zheng J, Xiang Z, Stoeckert CJ, et al. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014;30(9):1340-2doi: 10.1093/bioinformatics/btu008.
Zheng, J., Xiang, Z., Stoeckert, C. J., & He, Y. (2014). Ontodog: a web-based ontology community view generation tool. Bioinformatics (Oxford, England), 30(9), 1340-2. https://doi.org/10.1093/bioinformatics/btu008
Zheng, Jie, et al. "Ontodog: a web-based ontology community view generation tool." Bioinformatics (Oxford, England) vol. 30,9 (2014): 1340-2. doi: https://doi.org/10.1093/bioinformatics/btu008
Zheng J, Xiang Z, Stoeckert CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014 May 01;30(9):1340-2. doi: 10.1093/bioinformatics/btu008. Epub 2014 Jan 09. PMID: 24413522; PMCID: PMC3998133.
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Modeling biomedical experimental processes with OBI.

Journal of biomedical semantics

Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J.
PMID: 20626927
J Biomed Semantics. 2010 Jun 22;1:S7. doi: 10.1186/2041-1480-1-S1-S7.

BACKGROUND: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval.RESULTS: The Ontology for Biomedical Investigations (OBI), developed as a...

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Brinkman RR, Courtot M, Derom D, et al. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010;1:S7doi: 10.1186/2041-1480-1-S1-S7.
Brinkman, R. R., Courtot, M., Derom, D., Fostel, J. M., He, Y., Lord, P., Malone, J., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Soldatova, L. N., Stoeckert, C. J., Turner, J. A., Zheng, J. (2010). Modeling biomedical experimental processes with OBI. Journal of biomedical semantics, 1S7. https://doi.org/10.1186/2041-1480-1-S1-S7
Brinkman, Ryan R, et al. "Modeling biomedical experimental processes with OBI." Journal of biomedical semantics vol. 1 (2010): S7. doi: https://doi.org/10.1186/2041-1480-1-S1-S7
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1:S7. doi: 10.1186/2041-1480-1-S1-S7. PMID: 20626927; PMCID: PMC2903726.
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Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

Immunome research

He Y, Xiang Z.
PMID: 20875156
Immunome Res. 2010 Sep 27;6:S5. doi: 10.1186/1745-7580-6-S1-S5.

BACKGROUND: Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe...

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He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res. 2010;6:S5doi: 10.1186/1745-7580-6-S1-S5.
He, Y., & Xiang, Z. (2010). Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome research, 6S5. https://doi.org/10.1186/1745-7580-6-S1-S5
He, Yongqun, and Xiang, Zuoshuang. "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN." Immunome research vol. 6 (2010): S5. doi: https://doi.org/10.1186/1745-7580-6-S1-S5
He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res. 2010 Sep 27;6:S5. doi: 10.1186/1745-7580-6-S1-S5. PMID: 20875156; PMCID: PMC2946783.
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OntoFox: web-based support for ontology reuse.

BMC research notes

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y.
PMID: 20569493
BMC Res Notes. 2010 Jun 22;3:175. doi: 10.1186/1756-0500-3-175.

BACKGROUND: Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of...

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Xiang Z, Courtot M, Brinkman RR, et al. OntoFox: web-based support for ontology reuse. BMC Res Notes. 2010;3:175doi: 10.1186/1756-0500-3-175.
Xiang, Z., Courtot, M., Brinkman, R. R., Ruttenberg, A., & He, Y. (2010). OntoFox: web-based support for ontology reuse. BMC research notes, 3175. https://doi.org/10.1186/1756-0500-3-175
Xiang, Zuoshuang, et al. "OntoFox: web-based support for ontology reuse." BMC research notes vol. 3 (2010): 175. doi: https://doi.org/10.1186/1756-0500-3-175
Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Res Notes. 2010 Jun 22;3:175. doi: 10.1186/1756-0500-3-175. PMID: 20569493; PMCID: PMC2911465.
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Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291.

Environmental microbiology

Zhu D, Patabendige HMLW, Tomlinson BR, Wang S, Hussain S, Flores D, He Y, Shaw LN, Sun X.
PMID: 33893759
Environ Microbiol. 2021 Sep;23(9):5222-5238. doi: 10.1111/1462-2920.15529. Epub 2021 Apr 24.

Clostridioides difficile is a Gram-positive, spore-forming, toxin-producing anaerobe that can cause nosocomial antibiotic-associated intestinal disease. Although the production of toxin A (TcdA) and toxin B (TcdB) contribute to the main pathogenesis of C. difficile, the mechanism of TcdA and...

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Zhu D, Patabendige HMLW, Tomlinson BR, et al. Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291. Environ Microbiol. 2021;23(9):5222-5238doi: 10.1111/1462-2920.15529.
Zhu, D., Patabendige, H. M. L. W., Tomlinson, B. R., Wang, S., Hussain, S., Flores, D., He, Y., Shaw, L. N., & Sun, X. (2021). Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291. Environmental microbiology, 23(9), 5222-5238. https://doi.org/10.1111/1462-2920.15529
Zhu, Duolong, et al. "Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291." Environmental microbiology vol. 23,9 (2021): 5222-5238. doi: https://doi.org/10.1111/1462-2920.15529
Zhu D, Patabendige HMLW, Tomlinson BR, Wang S, Hussain S, Flores D, He Y, Shaw LN, Sun X. Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291. Environ Microbiol. 2021 Sep;23(9):5222-5238. doi: 10.1111/1462-2920.15529. Epub 2021 Apr 24. PMID: 33893759.
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The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines.

Quantitative biology (Beijing, China)

Zheng J, Li H, Liu Q, He Y.
PMID: 30034908
Quant Biol. 2017 Dec;5(4):291-301. Epub 2017 Nov 12.

BACKGROUND: The community-based Ontology of Biological and Clinical Statistics (OBCS) represents and standardizes biological and clinical data and statistical methods.METHODS: Both OBCS and the Vaccine Ontology (VO) were used to ontologically model various components and relations in a typical...

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Zheng J, Li H, Liu Q, et al. The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. Quant Biol. 2017;5(4):291-301
Zheng, J., Li, H., Liu, Q., & He, Y. (2017). The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. Quantitative biology (Beijing, China), 5(4), 291-301.
Zheng, Jie, et al. "The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines." Quantitative biology (Beijing, China) vol. 5,4 (2017): 291-301.
Zheng J, Li H, Liu Q, He Y. The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. Quant Biol. 2017 Dec;5(4):291-301. Epub 2017 Nov 12. PMID: 30034908; PMCID: PMC6054478.
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Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella pneumophila.

Genome announcements

Ma J, He Y, Hu B, Luo ZQ.
PMID: 23792742
Genome Announc. 2013 Jun 27;1(3). doi: 10.1128/genomeA.00320-13.

We report here the genomic sequence of Legionella pneumophila strain LPE509 from the water distribution system of a hospital in Shanghai, China. This is the first complete genome sequence of an environmental L. pneumophila isolate. Genomic analyses identified approximately...

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Ma J, He Y, Hu B, et al. Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella pneumophila. Genome Announc. 2013;1(3)doi: 10.1128/genomeA.00320-13.
Ma, J., He, Y., Hu, B., & Luo, Z. Q. (2013). Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella pneumophila. Genome announcements, 1(3), . https://doi.org/10.1128/genomeA.00320-13
Ma, Jian, et al. "Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella pneumophila." Genome announcements vol. 1,3 (2013). doi: https://doi.org/10.1128/genomeA.00320-13
Ma J, He Y, Hu B, Luo ZQ. Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella pneumophila. Genome Announc. 2013 Jun 27;1(3). doi: 10.1128/genomeA.00320-13. PMID: 23792742; PMCID: PMC3675512.
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Showing 1 to 12 of 19 entries