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VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.
Lin Y, Zheng J, He Y. Lin Y, et al. Among authors: zheng j. J Biomed Semantics. 2016 Apr 19;7:20. doi: 10.1186/s13326-016-0062-4. eCollection 2016. J Biomed Semantics. 2016. PMID: 27099700 Free PMC article.
Modeling biomedical experimental processes with OBI.
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 Jr, Turner JA, Zheng J; OBI consortium. Brinkman RR, et al. Among authors: zheng j. J Biomed Semantics. 2010 Jun 22;1 Suppl 1(Suppl 1):S7. doi: 10.1186/2041-1480-1-S1-S7. J Biomed Semantics. 2010. PMID: 20626927 Free PMC article.
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.
Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr. Zheng J, et al. Database (Oxford). 2011 Dec 21;2011:bar045. doi: 10.1093/database/bar045. Print 2011. Database (Oxford). 2011. PMID: 22190598 Free PMC article.
The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.
Parikh PP, Zheng J, Logan-Klumpler F, Stoeckert CJ Jr, Louis C, Topalis P, Protasio AV, Sheth AP, Carrington M, Berriman M, Sahoo SS. Parikh PP, et al. Among authors: zheng j. J Biomed Semantics. 2012 May 23;3(1):5. doi: 10.1186/2041-1480-3-5. J Biomed Semantics. 2012. PMID: 22621763 Free PMC article.
Ontodog: a web-based ontology community view generation tool.
Zheng J, Xiang Z, Stoeckert CJ Jr, He Y. Zheng J, et al. Bioinformatics. 2014 May 1;30(9):1340-2. doi: 10.1093/bioinformatics/btu008. Epub 2014 Jan 9. Bioinformatics. 2014. PMID: 24413522 Free PMC article.
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.
Xiang Z, Zheng J, Lin Y, He Y. Xiang Z, et al. Among authors: zheng j. J Biomed Semantics. 2015 Jan 9;6:4. doi: 10.1186/2041-1480-6-4. eCollection 2015. J Biomed Semantics. 2015. PMID: 25785185 Free PMC article.
CLO: The cell line ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. Sarntivijai S, et al. Among authors: zheng j. J Biomed Semantics. 2014 Aug 13;5:37. doi: 10.1186/2041-1480-5-37. eCollection 2014. J Biomed Semantics. 2014. PMID: 25852852 Free PMC article.
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: zheng j. PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016. PLoS One. 2016. PMID: 27128319 Free PMC article.
OBIB-a novel ontology for biobanking.
Brochhausen M, Zheng J, Birtwell D, Williams H, Masci AM, Ellis HJ, Stoeckert CJ Jr. Brochhausen M, et al. Among authors: zheng j. J Biomed Semantics. 2016 May 2;7:23. doi: 10.1186/s13326-016-0068-y. eCollection 2016. J Biomed Semantics. 2016. PMID: 27148435 Free PMC article.
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. Zheng J, et al. J Biomed Semantics. 2016 Sep 14;7(1):53. doi: 10.1186/s13326-016-0100-2. J Biomed Semantics. 2016. PMID: 27627881 Free PMC article.
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