Improving integrative searching of systems chemical biology data using semantic annotation

Journal of Cheminformatics

Volumn 4, Issue 3, 2012, Pages

  Chen, Bin ^a   Ding, Ying ^b   Wild, David J ^a  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84862637212     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-4-6     Document Type: Article

References (48)

1. Belleau F, et al: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008, 41(5):706-716.
2. Jentzsch A, et al: Linking open drug data. Triplification Challenge of the International Conference on Semantic Systems 2009.
3. Chen B, et al: Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics 2010, 11:255, doi:10.1186/1471-2105-11-255.
4. Linked Open Data. [http://linkeddata.org/].
5. SPARQL query language. [http://www.w3.org/TR/rdf-sparql-query/].
6. Philipp Heim SL, Stegemann T: Interactive relationship discovery via the semantic web. Lecture Notes Comput Sci 2010, 6088:303-317.
7. Aleman-Meza B, et al: Ranking complex relationships on the semantic web. IEEE Internet Comput 2005, 9(9):37-44. (Pubitemid 40871234)
8. Dong X, et al: Chem2Bio2RDF Dashboard: Ranking Semantic Associations in Systems Chemical Biology Space. Future of the Web in Collaboratice Science (FWCS), WWW2010 Raleigh NC; 2010.
9. Ashburner M, et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29, doi:10.1038/75556. (Pubitemid 30257031)
10. Eilbeck K, et al: The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol 2005, 6(5):44, doi:10.1186/gb-2005-6-5-r44.
11. Natale DA, et al: Framework for a protein ontology. BMC Bioinformatics 2007, 8(9):1, doi:10.1186/1471-2105-8-S9-S1.
12. Degtyarenko K, et al: ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 2008, 36:344-350, doi:10.1093/nar/gkm791. (Pubitemid 351149747)
13. Warren A, et al: Disease Ontology. Disease Ontology 2006.
14. Dumontier M, Villanueva-Rosales N: Towards pharmacogenomics knowledge discovery with the semantic web. Brief Bioinform 2009, 10(2):153-163, doi:10.1093/bib/bbn056.
15. Choi J, et al: A semantic web ontology for small molecules and their biological targets. J Chem Inf Model 2010, 50(5):732-741, doi:10.1021/ci900461j.
16. Ivchenko O, et al: PLIO: an ontology for formal description of protein-ligand interactions. Bioinformatics 2011 [http://dx.doi.org/10.1093/ bioinformatics/btr256].
17. Qu XA, et al: Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. BMC Bioinf 2009, 10(5):4, doi:10.1186/1471-2105-10-S5-S4.
18. Demir E, et al: The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010, 28(9):935-942, doi:10.1038/nbt.1666.
19. Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M: The translational medicine ontology and knowledge base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics 2011, 2(2):1, doi:10.1186/2041-1480-2-S2-S1.
20. Ciccarese P, et al: The SWAN biomedical discourse ontology. J Biomed Inform 2008, 41(5):739-751, doi:10.1016/j.jbi.2008.04.010.
21. Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Piparo EL, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J: Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov 2011, 10(9):661-669, doi:10.1038/nrd3503.
22. Visser U, Abeyruwan S, Vempati U, Smith RP, Lemmon V, Schurer SC: BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. BMC Bioinformatics 2011, 12:257, doi:10.1186/1471-2105-12- 257.
23. Qi D, King RD, Hopkins AL, Bickerton GRJ, Soldatova LN: An ontology for description of drug discovery investigations. J Integr Bioinform 2010, 7(3), doi:10.2390/biecoll-jib-2010-126.
24. 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, Turner JA, Zheng J, consortium OBI: Modeling biomedical experimental processes with OBI. J Biomed Semantics 2010, 1(1):7.
25. Basic Formal Ontology. [http://www.ifomis.org/bfo/].
26. Smith B, et al: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255, doi:10.1038/nbt1346. (Pubitemid 350076511)
27. Noy NF, et al: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 2009, 37:170-173, doi:10.1093/nar/gkp440.
28. Baitaluk M, Ponomarenko J: Semantic integration of data on transcriptional regulation. Bioinformatics 2010, 13:1651-1661, doi:10.1093/bioinformatics/btq231.
29. Holford ME, et al: Using semantic web rules to reason on an ontology of pseudogenes. Bioinformatics 2010, 26(12):71-78, doi:10.1093/bioinformatics/ btq173.
30. Oprea TI, et al: Systems chemical biology. Nat Chem Biol 2007, 3(8):447-450, doi:10.1038/nchembio0807-447. (Pubitemid 47080379)
31. Ruebenacker O, Moraru II, Schaff JC, Blinov ML: Kinetic modeling using BioPAX ontology. Proceedings (IEEE Int Conf Bioinformatics Biomed) 2007, 2007:339-348, doi:[http://dx.doi.org/10.1109/BIBM.2007.55]].
32. Chen B, et al: Chem2Bio2RDF: A Linked Open Data Portal for Systems Chemical Biology. 2010, 232-239, Web Intelligence and Intelligent Agent Technology (WI-IAT), 2010 IEEE/WIC/ACM International Conference on, Toronto.
33. Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C: Relations in biomedical ontologies. Genome Biol 2005, 6(5):46, doi:10.1186/gb-2005-6-5-r46.
34. Protege. [http://protege.stanford.edu/].
35. Harland L, Gaulton A: Drug target central. Expert Opin on Drug Discovery 2009, 4(8):857-872.
36. Davis AP, et al: The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res 2010, doi:10.1093/nar/gkq813.
37. Horridge M, et al: The OWL API: A Java API for Working with OWL 2 Ontologies. Proceedings of the OWL: Experiences and Directions 2009 Chantilly, USA, CEUR Workshop Proceedings; 2009.
38. Sirin E, et al: Pellet: a practical OWL-DL reasoner. J Web Semantics 2007, 5(2):51-53. (Pubitemid 46856283)
39. Virtuoso triple store. [http://virtuoso.openlinksw.com/].
40. Funk C, Ponelle C, Scheuermann G, Pantze M: Cholestatic potential of troglitazone as a possible factor contributing to troglitazone-induced hepatotoxicity: in vivo and in vitro interaction at the canalicular bile salt export pump (Bsep) in the rat. Mol Pharmacol 2001, 59(3):627-635. (Pubitemid 32179943)
41. Ekins S, et al: Human pregnane × receptor antagonists and agonists define molecular requirements for different binding sites. Mol Pharmacol 2007, 72(3):592-603, doi:10.1124/mol.107.038398. (Pubitemid 47347294)
42. Cohen JS: Risks of troglitazone apparent before approval in USA. Diabetologia 2006, 49(6):1454-1455, doi:10.1007/s00125-006-0245-0.
43. Ajjan RA, Grant PJ: The cardiovascular safety of rosiglitazone. Expert Opin Drug Saf 2008, 7(4):367-376, doi:10.1517/14740338.7.4.367.
44. Xie L, et al: Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol 2009, 5(5):1000387, doi:10.1371/journal. pcbi.1000387.
45. Lessard E, et al: Influence of CYP2D6 activity on the disposition and cardiovascular toxicity of the antidepressant agent venlafaxine in humans. Pharmacogenetics 1999, 9(4):435-443. (Pubitemid 29419562)
46. Chen H, et al: Semantic web for integrated network analysis in biomedicine. Brief Bioinform 2009, 10(2):177-192, doi:10.1093/bib/bbp002.
47. Wang H, et al: Finding complex biological relationships in recent PubMed articles using Bio-LDA. PLoS One 2011, 6(3):e17243.
48. He B, Tang J, Ding Y, Wang H, Sun Y, Shin JH, Chen B, Moorthy G, Qiu J, Desai P, Wild DJ: Mining relational paths in integrated biomedical data. PLoS One 2011, 6(12):e27506, doi: [http://dx.doi.org/10.1371/journal. pone.0027506].