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Year Number of Results
2010 5
2011 4
2012 7
2013 5
2014 9
2015 5
2016 16
2017 10
2018 4
2019 10
2020 4
2021 4
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Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project.
Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y; Kidney Precision Medicine Project. Ong E, et al. Among authors: he y. Nat Rev Nephrol. 2020 Nov;16(11):686-696. doi: 10.1038/s41581-020-00335-w. Epub 2020 Sep 16. Nat Rev Nephrol. 2020. PMID: 32939051 Free PMC article. Review.
Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient's phenotype. The development of two new onto …
Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinic …
The Human Phenotype Ontology in 2021.
Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, Callahan TJ, Chute CG, Est JL, Galer PD, Ganesan S, Griese M, Haimel M, Pazmandi J, Hanauer M, Harris NL, Hartnett MJ, Hastreiter M, Hauck F, He Y, Jeske T, Kearney H, Kindle G, Klein C, Knoflach K, Krause R, Lagorce D, McMurry JA, Miller JA, Munoz-Torres MC, Peters RL, Rapp CK, Rath AM, Rind SA, Rosenberg AZ, Segal MM, Seidel MG, Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. Köhler S, et al. Among authors: he y. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217. doi: 10.1093/nar/gkaa1043. Nucleic Acids Res. 2021. PMID: 33264411 Free PMC article.
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. ...We present new efforts to harmonize computational definition …
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe …
Ontology-Based Vaccine Adverse Event Representation and Analysis.
Xie J, He Y. Xie J, et al. Among authors: he y. Adv Exp Med Biol. 2017;1028:89-103. doi: 10.1007/978-981-10-6041-0_6. Adv Exp Med Biol. 2017. PMID: 29058218 Review.
To represent and analyze vaccine adverse events (VAEs), our research group has initiated and led the development of a community-based ontology: the Ontology of Adverse Events (OAE) (He et al., J Biomed Semant 5:29, 2014). The OAE has been found to have advantages to …
To represent and analyze vaccine adverse events (VAEs), our research group has initiated and led the development of a community-based ont …
Architecture and usability of OntoKeeper, an ontology evaluation tool.
Amith M, Manion F, Liang C, Harris M, Wang D, He Y, Tao C. Amith M, et al. Among authors: he y. BMC Med Inform Decis Mak. 2019 Aug 8;19(Suppl 4):152. doi: 10.1186/s12911-019-0859-z. BMC Med Inform Decis Mak. 2019. PMID: 31391056 Free PMC article.
Automated tools may help to ease the ontology construction, maintenance, assessment and quality assurance processes. ...RESULTS: In this paper, we present usability results from 5 ontologists revealing high system usability of OntoKeeper, and use-cases that demonstrate its …
Automated tools may help to ease the ontology construction, maintenance, assessment and quality assurance processes. ...RESULTS: In t …
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.
He Y, Xiang Z, Zheng J, Lin Y, Overton JA, Ong E. He Y, et al. J Biomed Semantics. 2018 Jan 12;9(1):3. doi: 10.1186/s13326-017-0169-2. J Biomed Semantics. 2018. PMID: 29329592 Free PMC article. Review.
With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. ...These XOD principles reuse existing …
With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability an …
OHMI: the ontology of host-microbiome interactions.
He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Liu K, Wu J, Curtis JL, Smith B, Alekseyenko AV, Obeid JS. He Y, et al. J Biomed Semantics. 2019 Dec 30;10(1):25. doi: 10.1186/s13326-019-0217-1. J Biomed Semantics. 2019. PMID: 31888755 Free PMC article.
METHODS: Through a multi-institutional collaboration, a community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the Open Biological/Biomedical Ontologies (OBO) Foundry principles. ...RESULTS: Aligned with the Basic Formal Ontology …
METHODS: Through a multi-institutional collaboration, a community-based Ontology of Host-Microbiome Interactions (OHMI) was developed …
Vaccine and Drug Ontology Studies (VDOS 2014).
Tao C, He Y, Arabandi S. Tao C, et al. Among authors: he y. J Biomed Semantics. 2016 Feb 25;7:6. doi: 10.1186/s13326-015-0039-8. eCollection 2016. J Biomed Semantics. 2016. PMID: 26918107 Free PMC article.
The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. ...The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/dr …
The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology mod …
Ontology-supported research on vaccine efficacy, safety and integrative biological networks.
He Y. He Y. Expert Rev Vaccines. 2014 Jul;13(7):825-41. doi: 10.1586/14760584.2014.923762. Epub 2014 Jun 7. Expert Rev Vaccines. 2014. PMID: 24909153 Free PMC article. Review.
Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature min …
Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vacci …
The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. Bandrowski A, et al. Among authors: he y. PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016. PLoS One. 2016. PMID: 27128319 Free PMC article.
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. ...OBI is being used in a wide range of projects co …
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describ …
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.
Sarntivijai S, He Y, Diehl AD. Sarntivijai S, et al. Among authors: he y. BMC Bioinformatics. 2019 Apr 25;20(Suppl 5):183. doi: 10.1186/s12859-019-2721-9. BMC Bioinformatics. 2019. PMID: 31272374 Free PMC article.
This workshop included five oral presentations and a general discussion session. Two new ontologies, including the Cancer Cell Ontology (CCL) and the Ontology for Stem Cell Investigations (OSCI), were reported in the workshop. ...The general discussion sessio …
This workshop included five oral presentations and a general discussion session. Two new ontologies, including the Cancer Cell Ont …
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