DOSim: An R package for similarity between diseases based on Disease Ontology

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Li, Jiang ^a   Gong, Binsheng ^a   Chen, Xi ^a   Liu, Tao ^a   Wu, Chao ^a   Zhang, Fan ^a   Li, Chunquan ^a   Li, Xiang ^a   Rao, Shaoqi ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS TOOLS; DISEASE RISKS; DISEASE SIMILARITIES; GENE SIMILARITY; HIER-ARCHICAL CLUSTERING; MOLECULAR PATHOGENESIS; MULTI-LAYERED; SEMANTIC SIMILARITY MEASURES;

BIOINFORMATICS; COMPLEX NETWORKS; DISEASES; NUTRITION;

GENES;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENERAL ASPECTS OF DISEASE; GENETIC DATABASE; GENETICS; HUMAN; LINGUISTICS; METHODOLOGY; NEOPLASM; OBESITY; SEMANTICS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DISEASE; HUMANS; NEOPLASMS; OBESITY; SEMANTICS; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 79959632257     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-266     Document Type: Article

References (31)

1. Kalaria R. Similarities between Alzheimer's disease and vascular dementia. J Neurol Sci 2002, 203-204:29-34.
2. Hu G, Agarwal P. Human disease-drug network based on genomic expression profiles. PLoS One 2009, 4(8):e6536. 10.1371/journal.pone.0006536, 2715883, 19657382.
3. Wang F, Syeda-Mahmood T, Beymer D. Finding Disease Similarity by Combining ECG with Heart Auscultation Sound. Computers in Cardiology 2007, 261-264.
4. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc Natl Acad Sci USA 2007, 104(21):8685-8690. 10.1073/pnas.0701361104, 1885563, 17502601.
5. McKusick VA. Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 2007, 80(4):588-604. 10.1086/514346, 1852721, 17357067.
6. Becker KG, Barnes KC, Bright TJ, Wang SA. The genetic association database. Nat Genet 2004, 36(5):431-432. 10.1038/ng0504-431, 15118671.
7. Liu YI, Wise PH, Butte AJ. The "etiome": identification and clustering of human disease etiological factors. BMC Bioinformatics 2009, 10(Suppl 2):S14. 10.1186/1471-2105-10-S2-S14, 2762063, 19828074.
8. Fowler J, Kouramajian V, Maram S, Devadhar V. Automated MeSH indexing of the World-Wide Web. Proc Annu Symp Comput Appl Med Care 1995, 893-897.
9. Zhang SH, Wu C, Li X, Chen X, Jiang W, Gong BS, Li J, Yan YQ. From phenotype to gene: detecting disease-specific gene functional modules via a text-based human disease phenotype network construction. FEBS Lett 2010, 584(16):3635-3643. 10.1016/j.febslet.2010.07.038, 20659468.
10. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32(Database issue):D258-261. 308770, 14681407.
11. Warren A, Kibbe J, Wolf W, Smith M, Zhu L, Lin S, Chisholm R. Disease Ontology. 2006,
12. Osborne J, Flatow J, Holko M, Lin S, Kibbe W, Zhu L, Danila M, Feng G, Chisholm R. Annotating the human genome with Disease Ontology. BMC Genomics 2009, 10(Suppl 1):S6. 10.1186/1471-2164-10-S1-S6, 2788393, 19958504.
13. Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics 2009, 25(12):i63-68. 10.1093/bioinformatics/btp193, 2687947, 19478018.
14. Pesquita C, Faria D, Falcão AO, Lord P, Couto FM. Semantic Similarity in Biomedical Ontologies. PLoS Comput Biol 2009, 5(7):e1000443. 10.1371/journal.pcbi.1000443, 2712090, 19649320.
15. Resnik P. Using Information Content to Evaluate Semantic Similarity in a Taxonomy. Proceedings of the 14th International Joint Conference on Artificial Intelligence, Montreal 1995, 1:448-453.
16. Lin D. An Information-Theoretic Definition of Similarity. ICML '98: Proceedings of the Fifteenth International Conference on Machine Learning 1998, 296-304.
17. Jiang J, Conrath D. Semantic similarity based on corpus statistics and lexical taxonomy. Proceedings of the International Conference on Research in Computational Linguistics, Taiwan 1998,
18. A Schlicker FD. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006,
19. C Pesquita DF. Evaluating GO-based Semantic Similarity Measures. In: Proc 10th Annual Bio-Ontologies Meeting 2007, 37-40.
20. A Feltus B, Li JW. Effectively Integrating Information Content and Structural Relationship to Improve the GO-based Similarity Measure Between Proteins. BMC Bioinformatics 2009,
21. James Z, Wang ZD. A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 1274-1281.
22. Couto F, Silva M, Coutinho P. Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors. Conference in Information and Knowledge Management 2005,
23. Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19(10):1275-1283. 10.1093/bioinformatics/btg153, 12835272.
24. Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 2008, 24(5):719-720. 10.1093/bioinformatics/btm563, 18024473.
25. Frohlich H, Speer N, Poustka A, BeiSZbarth T. GOSim: an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 2007, 8(1):166. 10.1186/1471-2105-8-166, 1892785, 17519018.
26. Li C, Li X, Miao Y, Wang Q, Jiang W, Xu C, Li J, Han J, Zhang F, Gong B, et al. SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res 2009, 37(19):e131. 10.1093/nar/gkp667, 2770656, 19706733.
27. Tokoro Y. Cytology of malignant lymphoma. Rinsho Byori 2010, 58(11):1113-1120.
28. Iannitto E, Tripodo C. How I diagnose and treat splenic lymphomas. Blood 2010, 117(9):2585-2595.
29. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2(10):2366-2382. 10.1038/nprot.2007.324, 17947979.
30. Haslam DW, James WP. Obesity. Lancet 2005, 366(9492):1197-1209. 10.1016/S0140-6736(05)67483-1, 16198769.
31. Yu W, Clyne M, Khoury MJ, Gwinn M. Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations. Bioinformatics 2009, 26(1):145-146. 2796820, 19864262.