Use of semantic workflows to enhance transparency and reproducibility in clinical omics

Genome Medicine

Volumn 7, Issue 1, 2015, Pages

  Zheng, Christina L ^a   Ratnakar, Varun ^b   Gil, Yolanda ^b   McWeeney, Shannon K ^a  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; COMPUTER PROGRAM; DATA MINING; DNA SEQUENCE; INFORMATION PROCESSING; MOLECULAR GENETICS; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUALITY CONTROL; REFERENCE DATABASE; REPRODUCIBILITY; SYSTEM ANALYSIS; VALIDATION STUDY; WORKFLOW INSTANCE GENERATION AND SPECIALIZATION; BIOLOGY; GENETICS; HUMAN; NEOPLASM; PROCEDURES; WORKFLOW;

COMPUTATIONAL BIOLOGY; HUMANS; NEOPLASMS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; WORKFLOW;

EID: 84939458021     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0202-y     Document Type: Article

References (68)

1. Saracchi E, Fermi S, Brighina L. Emerging candidate biomarkers for Parkinson's disease: a review. Aging Dis. 2013;5:27-34.
2. Thomas L, Di Stefano AL, Ducray F. Predictive biomarkers in adult gliomas: the present and the future. Curr Opin Oncol. 2013;25:689-94.
3. Kim Y, Kislinger T. Novel approaches for the identification of biomarkers of aggressive prostate cancer. Genome Med. 2013;5:56.
4. Ellis MJ, Perou CM. The genomic landscape of breast cancer as a therapeutic roadmap. Cancer Discov. 2013;3:27-34.
5. Church D, Kerr R, Domingo E, Rosmarin D, Palles C, Maskell K, et al. Toxgnostics': an unmet need in cancer medicine. Nat Rev Cancer. 2014;14:440-5.
6. James LP. Metabolomics: integration of a new "omics" with clinical pharmacology. Clin Pharmacol Ther. 2013;94:547-51.
7. Li H, Jia W. Cometabolism of microbes and host: implications for drug metabolism and drug-induced toxicity. Clin Pharmacol Ther. 2013;94:574-81.
8. Lopez-Lopez E, Gutierrez-Camino A, Bilbao-Aldaiturriaga N, Pombar-Gomez M, Martin-Guerrero I, Garcia-Orad A. Pharmacogenetics of childhood acute lymphoblastic leukemia. Pharmacogenomics. 2014;15:1383-98.
9. Pouget JG, Muller DJ. Pharmacogenetics of antipsychotic treatment in schizophrenia. Methods Mol Biol. 2014;1175:557-87.
10. Lymperopoulos A, French F. Pharmacogenomics of heart failure. Methods Mol Biol. 2014;1175:245-57.
11. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012;148:1293-307.
12. Ransohoff DF. Promises and limitations of biomarkers. Recent Results Cancer Res. 2009;181:55-9.
13. Ransohoff DF. The process to discover and develop biomarkers for cancer: a work in progress. J Natl Cancer Inst. 2008;100:1419-20.
14. Micheel CM, Nass S, Omenn GS, Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Board on Health Care Services; Board on Health Sciences Policy; Institute of Medicine. Evolution of translational omics: Lessons learned and the path forward. Washington, DC: The National Academies Press; 2012. http://iom.nationalacademies.org/Reports/2012/Evolution-of-Translational-Omics.aspx .
15. Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014;32:246-51.
16. Collins FS, Hamburg MA. First FDA authorization for next-generation sequencer. N Engl J Med. 2013;369:2369-71.
17. FDA Public Workshop: Next Generation Sequencing Standards. http://www.fda.gov/ScienceResearch/SpecialTopics/RegulatoryScience/ucm389561.htm .
18. Baggerly KA, Coombes KR. What information should be required to support clinical "omics" publications? Clin Chem. 2011;57:688-90.
19. Baggerly KA, Coombes KR. Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology. Annals Appl Stat. 2009;3:1309-34.
20. Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, et al. On the reproducibility of science: unique identification of research resources in the biomedical literature. Peer J. 2013;1:e148.
21. Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012;483:531-3.
22. Anderson WP. Reproducibility: stamp out shabby research conduct. Nature. 2015;519:158.
23. Garijo D, Kinnings S, Xie L, Xie L, Zhang Y, Bourne PE, et al. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS One. 2013;8:e80278.
24. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451-5.
25. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, et al. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004;20:3045-54.
26. Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, et al. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. 2014;13:5898-908.
27. Gil Y, McWeeney S, Mason CE. Using semantic workflows to disseminate best practices and accelerate discoveries in multi-omic data analysis. http://www.isi.edu/~gil/papers/gil-etal-hiai13.pdf .
28. Gil Y, Ratnakar V, Kim J, Gonzalez-Calero PA, Groth P, Moody J, et al. Wings: intelligent workflow-based design of computational experiments. IEEE Intelligent Syst. 2011;26:1.
29. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011;39:D945-50.
30. Bhagwat M. Searching NCBI's dbSNP database. Curr Protoc Bioinformatics. 2010;1:1.19.
31. Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M. VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. Bioinformatics. 2014;30:2076-8.
32. Gil Y, Gonzalez-Calero PA, Kim J, Moody J, Ratnakar V. A semantic framework for automatic generation of computational workflows using distributed data and component catalogs. J Exper Theor Artificial Intell. 2011;23:389-467.
33. Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, et al. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 2013;29:1325-32.
34. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6:R44.
35. Mungall CJ, Batchelor C, Eilbeck K. Evolution of the Sequence Ontology terms and relationships. J Biomed Inform. 2011;44:87-93.
36. Gil Y. Intelligent workflow systems and provenance-aware software. http://www.isi.edu/~gil/papers/gil-iemss14.pdf .
37. Gil Y, Ratnakar V, Deelman E, Mehta G, Ki J. Wings for Pegasus: creating large-scale scientific applications using semantic representations of computational workflows. https://pegasus.isi.edu/publications/gil-etal-iaai07.pdf .
38. Gil Y. Mapping semantic workflows to alternative workflow execution engines. In: Proceedings of the 7th IEEE International Conference on Semantic Computing (ICSC). Irvine, CA, 2013, p. 377-82.
39. Mattmann C, Crichton D, Medvidovic N, Hughes S. A software architecture-based framework for highly distributed and data intensive scientific applications. In: Proceedings of the 28th International Conference on Software Engineering (ICSE06); Shanghai, China. 2006, ACM, New York, NY, USA, p. 721-30.
40. Deelman E, Singh G, Su MH, Blythe J, Gil Y, Kesselman C, et al. Pegasus: a framework for mapping complex scientific workflows onto distributed systems. Sci Prog J. 2005;13:219-37.
41. Gil Y, Ratnakar V, Verma R, Hart A, Ramirez P, Mattmann C, et al. Time-bound analytic tasks on large datasets through dynamic configuration of workflows. http://www.isi.edu/~gil/papers/gil-etal-works13.pdf .
42. PROV-O: The PROV Ontology. http://www.w3.org/TR/prov-o/ .
43. The OPMW-PROV Ontology. http://www.opmw.org/model/OPMW/
44. Moreau L, Clifford B, Freire J, Futrelle J, Gil Y, Groth P, et al. The open provenance model core specification (v1.1). Future Gen Comp Sys. 2011;27:6.
45. Garijo D, Gil Y. A new approach for publishing workflows: abstractions, standards, and linked data. http://www.isi.edu/~gil/papers/garijo-gil-works11.pdf .
46. Garijo D, Gil Y, Corcho O. Towards workflow ecosystems through semantic and standard representations. http://conferences.computer.org/works/2014/papers/7067a094.pdf .
47. Dinov I, Van Horn JD, Lozev KM, Magsipoc R, Petrosyan P, Liu Z, et al. Efficient, distributed and interactive neuroimaging data analysis using the LONI pipeline. Front Neuroinform. 2009;3:1-10.
48. Garijo D, Corcho O, Gil Y, Gutman BA, Dinov ID, Thompson P, et al. FragFlow: automated fragment detection in scientific workflows. In: Proceedings of the IEEE Conference on e-Science; Guarujua, Brazil. 2014, IEEE Computer Society, Los Alamitos, CA, USA, p. 281-9.
49. Garijo D, Gil Y. Augmenting PROV with Plans in P-PLAN: scientific processes as linked data http://linkedscience.org/wp-content/uploads/2012/05/lisc2012_submission_12.pdf
50. Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, et al. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010;26:2354-6.
51. De Roure D, Goble C, Stevens R. The design and realisation of the myExperiment virtual research environment for social sharing of workflows. Future Generation Comp Sys. 2009;25:561-7.
52. Mates P, Santos S, Freire J, Silva CT. CrowdLabs: social analysis and visualization for the sciences. In: Cushing JB, French J, Bowers, editors. SSDBM'11 Proceedings of the 23rd international conference on Scientific and statistical database management. Berlin, Heidelberg: Springer, Velag; 2011. p. 555-64.
53. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet. 2006;38:500-1.
54. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
55. Wilkinson MD, Vandervalk B, McCarthy L. The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and reference implementation. J Biomed Semantics. 2011;2:8. -1480-2-8.
56. Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, et al. The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics. 2008;24:2767-72.
57. NCBI. Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2014;42:D7-17.
58. Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res. 2014;42:D18-25.
59. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42:D764-70.
60. Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012;40:D130-5.
61. Fernandez-Suarez XM, Schuster MK. Using the ensembl genome server to browse genomic sequence data. Curr Protoc Bioinformatics. 2010;1:1.15.
62. Wu PY, Phan JH, Wang MD. Assessing the impact of human genome annotation choice on RNA-seq expression estimates. BMC Bioinformatics. 2013;14:S8-2105-14-S11-S8. Epub 2013 Nov 4.
63. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980-5.
64. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008;Chapter 10:10.11.
65. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
66. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.
67. Qu H, Fang X. A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project. Genomics Proteomics Bioinformatics. 2013;11:135-41.
68. Tomczak K, Czerwinska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19:A68-77.