Combining computational models, semantic annotations and simulation experiments in a graph database

Database

Volumn 2015, Issue , 2015, Pages

  Henkel, Ron ^a   Wolkenhauer, Olaf ^a,b   Waltemath, Dagmar ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; BIOLOGICAL ONTOLOGY; FACTUAL DATABASE; INFORMATION PROCESSING; PROCEDURES; SYSTEMS BIOLOGY;

BIOLOGICAL ONTOLOGIES; DATA CURATION; DATABASES, FACTUAL; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY;

EID: 84938773260     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau130     Document Type: Article

References (63)

1. Li, C., Donizelli, M., Rodriguez, N. et al. (2010) Biomodels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 4, 92.
2. Yu, T., Lloyd, C.M., Nickerson, D.P. et al. (2011) The physiome model repository 2. Bioinformatics, 27, 743-744.
3. Olivier, B.G. and Snoep, J.L. (2004) Web-based kinetic modelling using JWS online. Bioinformatics, 20, 2143-2144.
4. Hucka, M., Bergmann, F.T., Keating, S.M. et al. (2010) The systems biology markup language (SBML): Language specification for level 3 version 1 core. Specification at sbml.org: http://sbml. org/Documents/Specifications#SBML-Level-3-Version-1- Core.
5. Lloyd, C.M., Halstead, M.D., and Nielsen, P.F. (2004) CellML: its future, present and past. Prog. Biophys.Mol. Biol., 85, 433-450.
6. Hucka, M., Bergmann, F.T., Keating, S.M. et al. (2011) A profile of today's SBML-compatible software. In: Proceedings of the 2011 IEEE Seventh International Conference on e-Science (eScienceW), IEEE, Stockholm. pp. 143-150.
7. Knüpfer, C., Beckstein, C., Dittrich, P. et al. (2013) Structure, function, and behaviour of computational models in systems biology. BMC Syst. Biol., 7, 43.
8. Botstein, D., Cherry, J., Ashburner, M. et al. (2000) Gene Ontology: tool for the unification of biology. Nat.Genet., 25, 25-29.
9. Dumontier, M., Chepelev, L., and Hoehndorf, R. (2013) Semantic systems biology: formal knowledge representation in systems biology for model construction, retrieval, validation and discovery. In: Prokop A., Csuká s B. (eds). Systems Biology. Springer, Netherlands. pp. 355-373.
10. Henkel, R., Endler, L., Peters, A. et al. (2010) Ranked retrieval of computational biology models. BMC Bioinformatics, 11, 423.
11. Schulz, M., Krause, F., Le Novere, N. et al. (2011). Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol. Syst. Biol., 7, 512
12. Thavappiragasam, M., Lushbough, C.M., and Gnimpieba, E.Z. (2014) Automatic biosystems comparison using semantic and name similarity. In: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM, New York, NY, pp. 790-796.
13. Le Novère, N., Finney, A., Hucka, M. et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 23, 1509-1515.
14. Waltemath, D., Adams, R., Beard, D.A. et al. (2011) Minimum information about a simulation experiment (MIASE). PLoS Comput. Biol., 7, e1001122.
15. Le Novère, N., Hucka, M., Anwar, N. et al. (2011) Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand. Genomic Sci., 5, 230.
16. Henkel, R., Le Novère, N., Wolkenhauer, O. et al. (2012) Considerations of graph-based concepts to manage of computational biology models and associated simulations. In: Proceedings of the 2012 GI-Jahrestagung, pp. 1545-1551.
17. Waltemath, D., Henkel, R., Hälke, R. et al. (2013). Improving the reuse of computational models through version control. Bioinformatics, 29, 742-748.
18. Waltemath, D., Wolkenhauer, O., Le Novère, N. et al. (2013) Possibilities for integrating model-related data in computational biology. In: Proceedings of the 9th International Conference on Data Integration in the Life Sciences, Montreal, Canada, CEUR Workshops.
19. Waltemath, D., Adams, R., Bergmann, F.T. et al. (2011) Reproducible computational biology experiments with SEDML- the simulation experiment description markup language. BMC Syst. Biol., 5, 198.
20. Buneman, P. (1997) Semistructured data. In: Proceedings of the Sixteenth ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, ACM, Tucson, Arizona, pp. 117-121.
21. Robinson, I., Webber, J., and Eifrem, E. (2013) Graph Databases. O'Reilly Media, CA, USA.
22. Splendiani, A., Rawlings, C.J., Kuo, S.-C. et al. (2012) Lost in translation: data integration tools meet the semantic web (experiences from the Ondex project). In: Recent Progress in Data Engineering and Internet Technology. Springer, pp 87-97.
23. Ghemawat, S., Gobioff, H., and Leung, S.-T. (2003) The google file system. SIGOPS Oper. Syst. Rev., 37, 29-43.
24. Angles, R. and Gutierrez, C. (2008) Survey of graph database models. ACM Comput. Surv. (CSUR), 40, 1.
25. Vicknair, C., Macias, M., Zhao, Z. et al. (2010) A comparison of a graph database and a relational database: a data provenance perspective. In: Proceedings of the 48th Annual Southeast Regional Conference. ACM, Oxford, Mississippi, p. 42.
26. Chelliah, V., Endler, L., Juty, N. et al. (2009) Data integration and semantic enrichment of systems biology models and simulations. In: Proceedings of the 6th International Conference on Data Integration in the Life Sciences, Vol. 5647, Springer, pp. 5-15.
27. Hucka, M., Finney, A., Sauro, H.M. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
28. Cuellar, A., Lloyd, C., Nielsen, P. et al. (2003) An overview of cellML 1.1, a biological model description language. Simulation, 79, 740-747.
29. Le Novère, N., Hucka, M., Mi, H. et al. (2009) The systems biology graphical notation. Nat. Biotechnol., 27, 735-741.
30. Waltemath, D., Bergmann, F.T., Adams, R. et al. (2011) Simulation Experiment Description Markup Language (SEDML): Level 1 Version 1 (Specification).
31. Dada, J.O., Spasić, I., Paton, N.W. et al. (2010) SBRML: a markup language for associating systems biology data with models. Bioinformatics, 26, 932-938.
32. Demir, E., Cary, M.P., Paley, S. et al. (2010) The biopax community standard for pathway data sharing. Nat. Biotechnol., 28, 935-942.
33. Gennari, J.H., Neal, M.L., Galdzicki, M. et al. (2011) Multiple ontologies in action: composite annotations for biosimulation models. J. Biomed. Inform., 44, 146-154.
34. Waltemath, D., Swainston, N., Lister, A. et al. (2011) SBML Level 3 Package: Annot (Proposal), http://sbml.org/Documents/ Specifications/SBML-Level-3/Packages/Annotations-%28annot %29.
35. Hettne, K.M., Dharuri, H., Zhao, J. et al. (2014) Structuring research methods and data with the research object model: genomics workflows as a case study. J. Biomed. Semantics, 5, 41.
36. Bergmann, F.T., Rodriguez, N., Le Novère, N. et al. (2014) COMBINE Archive Specification: Version 1 Release Candidate 2. http://co.mbine.org/specifications/omex.version-1.
37. Seligman, L. and Roenthal, A. (2001) Xml's impact an databases and data sharing. Computer, 34, 59-67.
38. Gleeson, P., Crook, S., Cannon, R.C. et al. (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput. Biol., 6, e1000815.
39. Büchel, F., Rodriguez, N., Swainston, N. et al. (2013) Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol., 7, 116.
40. Cooper, J., Vik, J.O., and Waltemath, D. (2014) A call for virtual experiments: accelerating the scientific process. Prog. Biophys. Mol. Biol., 104, 2-21.
41. Swat, M., Moodie, S., Kristensen, N.R. et al. (2013) PharmML-An Exchange Standard for Models in Pharmacometrics: Version 0.2.1 (Specification). https://sites.goo gle.com/site/pharmmltemp/documentation2.
42. Bergmann, F.T., Cooper, J., Nickerson, D. et al. (2013) Simulation Experiment Description Markup Language (SEDML): Level 1 Version 2 (Specification).
43. Cooper, J., Mirams, G.R., and Niederer, S.A. (2011) Highthroughput functional curation of cellular electrophysiology models. Prog. Biophys. Mol. Biol., 107, 11-20.
44. Gruber, T.R. (1993) A translation approach to portable ontology specifications. Knowledge Acquisition, 5, 199-220.
45. Noy, N.F., Shah, N.H., Whetzel, P.L. et al. (2009) Bioportal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res., 37(Suppl. 2), W170-W173.
46. Lassila, O., Swick, R.R., and Consortium WWW. (1998) Resource description framework (RDF) model and syntax specification. http://www.w3.org/TR/REC-rdf-syntax/.
47. Alm, R., Waltemath, D., Wolkenauer, O. et al. (2014) Annotation-based feature extraction from sets of SBML models. In Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Vol. 8574. Springer, Lissabon, pp. 81-95.
48. Degtyarenko, K., de Matos, P., Ennis, M. et al. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res., 36(Suppl. 1), D344-D350.
49. Juty, N., Le Novère, N., and Laibe, C. (2012) Identifiers. org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res., 40, D580-D586.
50. Tyson, J.J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl Acad. Sci. U. S. A., 88, 7328-7332.
51. Köhn, D. and Strömbäck, L. (2008) A method for semiautomatic standard integration in systems biology. In: Proceedings of the 19th International Conference on Database and Expert Systems Applications, Vol. 5181. Springer, pp. 745-752.
52. Wimalaratne, S.M., Halstead, M.D., Lloyd, C.M. et al. (2009) Biophysical annotation and representation of cellML models. Bioinformatics, 25, 2263-2270.
53. de Bono, B., Hoehndorf, R., Wimalaratne, S. et al. (2011) The ricordo approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res. Notes, 4, 313.
54. Courtot, M., Juty, N., Knüpfer, C. et al. (2011) Controlled vocabularies and semantics in systems biology. Mol. Syst. Biol., 7, 543.
55. Novak, B. and Tyson, J.J. (1997) Modeling the control of DNA replication in fission yeast. Proc. Natl Acad. Sci. U. S. A., 94, 9147-9152.
56. Wimalaratne, S.M., Grenon, P., Hermjakob, H. et al. (2014) Biomodels linked dataset. BMC Syst. Biol., 8, 91.
57. Hoehndorf, R., Dumontier, M., Gennari, J.H. et al. (2011) Integrating systems biology models and biomedical ontologies. BMC Syst. Biol., 5, 124.
58. Lister, A.L., Lord, P., Pocock, M. et al. (2010) Annotation of SBML models through rule-based semantic integration. J. Biomed. Semantics, 1(Suppl. 1), S3.
59. Belleau, F., Nolin, M.-A., Tourigny, N. et al. (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform., 41, 706-716.
60. Jupp, S., Malone, J., Bolleman, J. et al. (2014) The EBI RDF platform: linked open data for the life sciences. Bioinformatics, 30, 1338-1339.
61. Przyjaciel-Zablocki, M., Schätzle, A., Hornung, T. et al. (2012) Rdfpath: path query processing on large RDF graphs with mapreduce. In: Proceedings of the 2011 ESWC Workshops, Vol. 7117. Springer, pp. 50-64.
62. Scharm, M., Wendland, F., Peters, M. et al. (2014) The CombineArchiveWeb application-a web based tool to handle files associated with modelling results. In: Proceedings of the 7th International SWAT4LS Workshop, PeerJ PrePrints 2:e639v1. http://dx.doi.org/10.7287/peerj.preprints.639v1.
63. Dräger, A., Rodriguez, N., Dumousseau, M. et al. (2011) JSBML: a flexible java library for working with SBML. Bioinformatics 27, 2167-2168.