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A semantic proteomics dashboard (SemPoD) for data management in translational research.

Jayapandian CP, Zhao M, Ewing RM, Zhang GQ, Sahoo SS.

BMC Syst Biol. 2012;6 Suppl 3:S20. doi: 10.1186/1752-0509-6-S3-S20.


LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.

Smith AK, Cheung KH, Yip KY, Schultz M, Gerstein MK.

BMC Bioinformatics. 2007 May 9;8 Suppl 3:S5. Review.


Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification.

Wolahan SM, Hirt D, Glenn TC.

In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25.


Techniques for optimization of queries on integrated biological resources.

Lacroix Z, Raschid L, Eckman BA.

J Bioinform Comput Biol. 2004 Jun;2(2):375-411. Review.


Advancing translational research with the Semantic Web.

Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH.

BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2. Review.


Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Review.


Accelerating cancer systems biology research through Semantic Web technology.

Wang Z, Sagotsky J, Taylor T, Shironoshita P, Deisboeck TS.

Wiley Interdiscip Rev Syst Biol Med. 2013 Mar-Apr;5(2):135-51. doi: 10.1002/wsbm.1200. Review.


The ontology of craniofacial development and malformation for translational craniofacial research.

Brinkley JF, Borromeo C, Clarkson M, Cox TC, Cunningham MJ, Detwiler LT, Heike CL, Hochheiser H, Mejino JL, Travillian RS, Shapiro LG.

Am J Med Genet C Semin Med Genet. 2013 Nov;163C(4):232-45. doi: 10.1002/ajmg.c.31377. Review.


Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned.

Sullivan DE, Gabbard JL Jr, Shukla M, Sobral B.

Chem Biodivers. 2010 May;7(5):1124-41. doi: 10.1002/cbdv.200900317. Review.


Data management in structural genomics: an overview.

Haquin S, Oeuillet E, Pajon A, Harris M, Jones AT, van Tilbeurgh H, Markley JL, Zolnai Z, Poupon A.

Methods Mol Biol. 2008;426:49-79. doi: 10.1007/978-1-60327-058-8_4. Review.


Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.

Proteomics. 2015 Mar;15(5-6):930-49. doi: 10.1002/pmic.201400302. Review.


An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines.

de Souza A, Bittker JA, Lahr DL, Brudz S, Chatwin S, Oprea TI, Waller A, Yang JJ, Southall N, Guha R, Schürer SC, Vempati UD, Southern MR, Dawson ES, Clemons PA, Chung TD.

J Biomol Screen. 2014 Jun;19(5):614-27. doi: 10.1177/1087057113517139. Review.


Epilepsy informatics and an ontology-driven infrastructure for large database research and patient care in epilepsy.

Sahoo SS, Zhang GQ, Lhatoo SD.

Epilepsia. 2013 Aug;54(8):1335-41. doi: 10.1111/epi.12211. Review.


Parasites, proteomes and systems: has Descartes' clock run out of time?

Wastling JM, Armstrong SD, Krishna R, Xia D.

Parasitology. 2012 Aug;139(9):1103-18. doi: 10.1017/S0031182012000716. Review.


Proteomics: from single molecules to biological pathways.

Langley SR, Dwyer J, Drozdov I, Yin X, Mayr M.

Cardiovasc Res. 2013 Mar 15;97(4):612-22. doi: 10.1093/cvr/cvs346. Review.


Integration of proteomics into systems biology of cancer.

Hanash S, Schliekelman M, Zhang Q, Taguchi A.

Wiley Interdiscip Rev Syst Biol Med. 2012 Jul-Aug;4(4):327-37. doi: 10.1002/wsbm.1169. Review.


Proteomics and systems biology for understanding diabetic nephropathy.

Starkey JM, Tilton RG.

J Cardiovasc Transl Res. 2012 Aug;5(4):479-90. doi: 10.1007/s12265-012-9372-9. Review.


Applications of targeted proteomics in systems biology and translational medicine.

Ebhardt HA, Root A, Sander C, Aebersold R.

Proteomics. 2015 Sep;15(18):3193-208. doi: 10.1002/pmic.201500004. Review.


Development and Applications of the Bioassay Ontology (BAO) to Describe and Categorize High-Throughput Assays.

Vempati UD, Schürer SC.

In: Sittampalam GS, Coussens NP, Brimacombe K, Grossman A, Arkin M, Auld D, Austin C, Bejcek B, Glicksman M, Inglese J, Iversen PW, Li Z, McGee J, McManus O, Minor L, Napper A, Peltier JM, Riss T, Trask OJ Jr., Weidner J, editors. Assay Guidance Manual [Internet]. Bethesda (MD): Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2004-.
2012 May 1 [updated 2012 Oct 1].


[Chemical probe in the proteomics].

Hao YW, Jiang Y, He FC.

Yi Chuan. 2007 Jul;29(7):779-84. Review. Chinese.

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