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Items: 1 to 20 of 92

1.

Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems).

Fostel JM.

Toxicol Appl Pharmacol. 2008 Nov 15;233(1):54-62. doi: 10.1016/j.taap.2008.06.015. Epub 2008 Jul 2.

PMID:
18680759
2.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ 3rd, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD.

Bioinformatics. 2006 Apr 1;22(7):874-82. Epub 2006 Jan 12.

PMID:
16410321
3.

CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

Waters M, Stasiewicz S, Merrick BA, Tomer K, Bushel P, Paules R, Stegman N, Nehls G, Yost KJ, Johnson CH, Gustafson SF, Xirasagar S, Xiao N, Huang CC, Boyer P, Chan DD, Pan Q, Gong H, Taylor J, Choi D, Rashid A, Ahmed A, Howle R, Selkirk J, Tennant R, Fostel J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D892-900. Epub 2007 Oct 25.

4.

CEBS object model for systems biology data, SysBio-OM.

Xirasagar S, Gustafson S, Merrick BA, Tomer KB, Stasiewicz S, Chan DD, Yost KJ 3rd, Yates JR 3rd, Sumner S, Xiao N, Waters MD.

Bioinformatics. 2004 Sep 1;20(13):2004-15. Epub 2004 Mar 25.

PMID:
15044233
5.

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.

Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR, Brown R, Bruno M, Cunningham ML, Dix D, Eastin W, Frade C, Garcia A, Heinloth A, Irwin R, Madenspacher J, Merrick BA, Papoian T, Paules R, Rocca-Serra P, Sansone AS, Stevens J, Tomer K, Yang C, Waters M.

Toxicol Sci. 2005 Dec;88(2):585-601. Epub 2005 Sep 8.

PMID:
16150882
6.

Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base.

Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R.

EHP Toxicogenomics. 2003 Jan;111(1T):15-28.

PMID:
12735106
7.

Sharing gene expression data: an array of options.

Geschwind DH.

Nat Rev Neurosci. 2001 Jun;2(6):435-8. Review.

PMID:
11389477
8.

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.

Stokes TH, Torrance JT, Li H, Wang MD.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S18. doi: 10.1186/1471-2105-9-S6-S18.

9.

CEBS: a comprehensive annotated database of toxicological data.

Lea IA, Gong H, Paleja A, Rashid A, Fostel J.

Nucleic Acids Res. 2017 Jan 4;45(D1):D964-D971. doi: 10.1093/nar/gkw1077. Epub 2016 Nov 28.

10.

Databases applicable to quantitative hazard/risk assessment--towards a predictive systems toxicology.

Waters M, Jackson M.

Toxicol Appl Pharmacol. 2008 Nov 15;233(1):34-44. doi: 10.1016/j.taap.2007.12.036. Epub 2008 Jul 2. Review.

PMID:
18675838
11.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Kuhn A, Luthi-Carter R, Delorenzi M.

BMC Bioinformatics. 2008 Jan 17;9:26. doi: 10.1186/1471-2105-9-26.

12.

The sharing of cDNA microarray data.

Becker KG.

Nat Rev Neurosci. 2001 Jun;2(6):438-40. Review.

PMID:
11389478
13.

The MGED Ontology: a resource for semantics-based description of microarray experiments.

Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.

Bioinformatics. 2006 Apr 1;22(7):866-73. Epub 2006 Jan 21.

PMID:
16428806
14.

MGED standards: work in progress.

Ball CA, Brazma A.

OMICS. 2006 Summer;10(2):138-44. Review.

PMID:
16901218
15.

Microarrays: lost in a storm of data?

Miles MF.

Nat Rev Neurosci. 2001 Jun;2(6):441-3. Review.

PMID:
11389479
16.

SEMEDA: ontology based semantic integration of biological databases.

Köhler J, Philippi S, Lange M.

Bioinformatics. 2003 Dec 12;19(18):2420-7.

PMID:
14668226
17.

JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.

Huang Y, Ni T, Zhou L, Su S.

Bioinformatics. 2003 Dec 12;19(18):2351-8.

PMID:
14668218
18.

An XML message broker framework for exchange and integration of microarray data.

Tjandra D, Wong S, Shen W, Pulliam B, Yu E, Esserman L.

Bioinformatics. 2003 Sep 22;19(14):1844-5.

PMID:
14512357
19.

Microarrays in brain research: the good, the bad and the ugly.

Mirnics K.

Nat Rev Neurosci. 2001 Jun;2(6):444-7. Review.

PMID:
11389480
20.

Integrating computing, data and collaboration grids: the RMCS tool.

Walker AM, Bruin RP, Dove MT, White TO, Kleese van Dam K, Tyer RP.

Philos Trans A Math Phys Eng Sci. 2009 Mar 13;367(1890):1047-50. doi: 10.1098/rsta.2008.0159.

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