Login

Join for Free!
119221 members
table of contents table of contents

The numerous public data resources make integrative bioinformatics experimentation increasingly important in …


Biology Articles » Bioinformatics » A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data » References

References
- A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data

  

Ashburner M, et al. Gene Ontology: tool for the unification of biology. Nat. Genet., ( (2000) ) 25, : 25–29.

Birkland A, Yona G. BIOZON: a hub of heterogeneous biological data. Nucleic Acids Res., ( (2006) ) 34, : D235–D242.

Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform., ( (2006) ) 7, : 256–274.

Caragea D, et al. Algorithms and software for collaborative discovery from autonomous, semantically heterogeneous, distributed information sources. Discov. Sci. Proc., ( (2005) ) 3735, : 14.

Carroll JS, et al. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet., ( (2006) ) 38, : 1289–1297.

Cheung KH, et al. YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioinformatics, ( (2005) ) 21, (Suppl. 1): i85–i96.

Eckman B, et al. Data management in molecular and cell biology: vision and recommendations. Omics, ( (2003) ) 7, : 93–97.

Euzenat J, Valtchev P. An integrative proximity measure for ontology alignment. In:. Doan A, et al, eds. ( (2003) ) Proceedings of the Semantic Integration Workshop at ISWC-03. CEUR-WS..

Felsenfeld G, Groudine M. Controlling the double helix. Nature, ( (2003) ) 421, : 448–453.

Goble C, et al. The semantic web and knowledge grids. Drug Discov. Today: Technol., ( (2005) ) 2, : 225–233.

Good BM, Wilkinson MD. The life sciences semantic web is full of creeps! Brief Bioinform., ( (2006) ) 7, : 275–286.

Grenon P, et al. Biodynamic ontology: applying BFO in the biomedical domain. Stud. Health Technol. Inform., ( (2004) ) 102, : 20–38.

Gudivada RC. A genome – phenome integrated approach for mining disease-causal genes using semantic web. ( (2007) ) Health Care and Life Sciences Data Integration for the Semantic Web, Sixteenth International World Wide Web Conference (WWW2007) Workshops..

Heintzman ND, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., ( (2007) ) 39, : 311–318.

Lein ES, et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature, ( (2007) ) 445, : 168–176.

Marshall MS, et al. Using semantic web tools to integrate experimental measurement data on our own terms. In: Meersman,R. et al. (eds) Workshop on Knowledge Systems in Bioinformatics (KSinBIT'06), ( (2006) ) Springer Verlag LNCS 4277. 679–688..

Matys V, et al. TRANSFAC(R): transcriptional regulation, from patterns to profiles. Nucleic Acids Res., ( (2003) ) 31, : 374–378.

Miled ZB, et al. An efficient implementation of a drug candidate database. J. Chem. Inf. Comput. Sci., ( (2003) ) 43, : 25–35.

Mork P, et al. The multiple roles of ontologies in the biomediator data integration system. Data Integration Life Sci. Proc., ( (2005) ) 3615, : 96–104..

Peterson CL, Laniel M.-A. Histones and histone modifications. Curr. Biol., ( (2004) ) 14, : R546–R551.

Rauwerda H, et al. The promise of a virtual lab in drug discovery. Drug Discov. Today, ( (2006) ) 11, : 228–236.

Rector AL, Rogers J. Patterns, properties and minimizing commitment: reconstruction of the GALEN upper ontology in OWL. In. Gangemi A, Borgo S, eds. ( (2004) ) Proceedings of the EKAW*04 Workshop on Core Ontologies in Ontology Engineering (CORONT). CEUR-WS, Northamptonshire..

Ritter O, et al. Prototype implementation of the integrated genomic database. Comput. Biomed. Res., ( (1994) ) 27, : 97–115.

Roos M, et al. Future application of ontologies in e-Bioscience. ( (2004) ) Position paper W3C Workshop on Semantic Web for Life Sciences..

Ruttenberg A, et al. Advancing translational research with the Semantic Web. BMC Bioinformatics, ( (2007) ) 8, : S2..

Schneider R, et al. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol., ( (2004) ) 6, : 73–77.

Schulz S, et al. Towards an upper level ontology for molecular biology. AMIA Annu. Symp. Proc., ( (2006) ) pp. 694–698..

Searls DB. Data integration: challenges for drug discovery. Nat. Rev. Drug Discov., ( (2005) ) 4, : 45–58.

Souchelnytskyi S. Bridging proteomics and systems biology: what are the roads to be traveled? Proteomics, ( (2005) ) 5, : 4123–4137.

Spellman PT, et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, ( (1998) ) 9, : 3273–3297.

Stein LD. Integrating biological databases. Nat. Rev. Genet., ( (2003) ) 4, : 337–345.

Stevens R, et al. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics, ( (2000) ) 16, : 184–186.

Strahl BD, Allis CD. The language of covalent histone modifications. Nature, ( (2000) ) 403, : 41–45.

Strizh IG. Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. Bioessays, ( (2006) ) 28, : 199–210.

The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) project. Science, ( (2004) ) 306, : 636–640.

Turner BM. Reading signals on the nucleosome with a new nomenclature for modified histones. Nat. Struct. Mol. Biol., ( (2005) ) 12, : 110–112.

van Steensel B. Mapping of genetic and epigenetic regulatory networks using microarrays. Nat. Genet., ( (2005) ) 37, : S18–S24.

Wilkinson M, et al. BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case. Plant Physiol., ( (2005) ) 138, : 5–17.

Wolstencroft K, et al. Protein classification using ontology classification. Bioinformatics, ( (2006) ) 22, : e530–e538.

Zdobnov EM, et al. The EBI SRS server-new features. Bioinformatics, ( (2002) ) 18, : 1149–1150.


rating: 1.00 from 3 votes | updated on: 1 Dec 2007 | views: 9209 |

Rate article:







excellent!bad…