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OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B. Jackson R, et al. Among authors: zheng j. Database (Oxford). 2021 Oct 26;2021:baab069. doi: 10.1093/database/baab069. Database (Oxford). 2021. PMID: 34697637 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.
Standardized metadata for human pathogen/vector genomic sequences.
Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Dugan VG, et al. Among authors: zheng j. PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014. PLoS One. 2014. PMID: 24936976 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.
A Framework for Global Collaborative Data Management for Malaria Research.
Gutierrez JB, Harb OS, Zheng J, Tisch DJ, Charlebois ED, Stoeckert CJ, Sullivan SA. Gutierrez JB, et al. Among authors: zheng j. Am J Trop Med Hyg. 2015 Sep;93(3 Suppl):124-132. doi: 10.4269/ajtmh.15-0003. Epub 2015 Aug 10. Am J Trop Med Hyg. 2015. PMID: 26259944 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.
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