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Items: 1 to 20 of 45


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.

J Biomed Semantics. 2018 Jan 12;9(1):3. doi: 10.1186/s13326-017-0169-2. Review.


Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design.

Ong E, Wong MU, He Y.

Front Immunol. 2017 Oct 26;8:1382. doi: 10.3389/fimmu.2017.01382. eCollection 2017.


Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology.

Ni Z, Chen Y, Ong E, He Y.

Int J Mol Sci. 2017 Feb 21;18(2). pii: E458. doi: 10.3390/ijms18020458.


Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches.

He Y, Ong E, Xie J.

Glob Vaccines Immunol. 2016 Jun;1(2):37-39. doi: 10.15761/GVI.1000110. Epub 2016 May 23. No abstract available.


Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y.

Nucleic Acids Res. 2017 Jan 4;45(D1):D347-D352. doi: 10.1093/nar/gkw918. Epub 2016 Oct 12.


The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y.

J Biomed Semantics. 2016 Sep 14;7(1):53. doi: 10.1186/s13326-016-0100-2.


The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ.

J Biomed Semantics. 2016 Jul 4;7(1):44. doi: 10.1186/s13326-016-0088-7.


Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events.

Guo A, Racz R, Hur J, Lin Y, Xiang Z, Zhao L, Rinder J, Jiang G, Zhu Q, He Y.

J Biomed Semantics. 2016 May 21;7:29. doi: 10.1186/s13326-016-0069-x. eCollection 2016.


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.

PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.


Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.

Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR.

Drug Saf. 2016 Jul;39(7):697-707. doi: 10.1007/s40264-016-0414-0.


Literature Mining and Ontology based Analysis of Host-Brucella Gene-Gene Interaction Network.

Karadeniz İ, Hur J, He Y, Özgür A.

Front Microbiol. 2015 Dec 9;6:1386. doi: 10.3389/fmicb.2015.01386. eCollection 2015.


Ontology-based representation and analysis of host-Brucella interactions.

Lin Y, Xiang Z, He Y.

J Biomed Semantics. 2015 Oct 5;6:37. doi: 10.1186/s13326-015-0036-y. eCollection 2015.


Vaxvec: The first web-based recombinant vaccine vector database and its data analysis.

Deng S, Martin C, Patil R, Zhu F, Zhao B, Xiang Z, He Y.

Vaccine. 2015 Nov 27;33(48):6938-46. doi: 10.1016/j.vaccine.2015.07.113. Epub 2015 Sep 25.


Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Xiang Z, Zheng J, Lin Y, He Y.

J Biomed Semantics. 2015 Jan 9;6:4. doi: 10.1186/2041-1480-6-4. eCollection 2015.


Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

Hur J, Özgür A, Xiang Z, He Y.

J Biomed Semantics. 2015 Jan 6;6:2. doi: 10.1186/2041-1480-6-2. eCollection 2015.

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