Modeling and managing experimental data using FuGE. Export

@article{citeulike:4540763, abstract = {The Functional Genomics Experiment data model (FuGE) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. FuGE can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which method-specific models can be developed. FuGE is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying FuGE in a given context. This paper captures emerging best practice in the use of FuGE in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the FuGE data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit (STK) that supports application development using FuGE. We anticipate that these guidelines will encourage consistent usage of FuGE, and as such, will contribute to the development of convergent data standards in omics research.}, author = {Jones, Andrew R. and Lister, Allyson L. and Hermida, Leandro and Wilkinson, Peter and Eisenacher, Martin and Belhajjame, Khalid and Gibson, Frank and Lord, Phil and Pocock, Matthew and Rosenfelder, Heiko and Santoyo-Lopez, Javier and Wipat, Anil and Paton, Norman W.}, citeulike-article-id = {4540763}, citeulike-linkout-0 = {http://dx.doi.org/10.1089/omi.2008.0080}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19441879}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19441879}, day = {14}, doi = {10.1089/omi.2008.0080}, issn = {1557-8100}, journal = {Omics : a journal of integrative biology}, keywords = {data\_representation, database}, month = {June}, number = {3}, pages = {239--251}, posted-at = {2009-06-15 18:06:25}, priority = {2}, title = {Modeling and managing experimental data using FuGE.}, url = {http://dx.doi.org/10.1089/omi.2008.0080}, volume = {13}, year = {2009} }

TY - JOUR ID - citeulike:4540763 L3 - citeulike-article-id:4540763 N2 - The Functional Genomics Experiment data model (FuGE) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. FuGE can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which method-specific models can be developed. FuGE is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying FuGE in a given context. This paper captures emerging best practice in the use of FuGE in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the FuGE data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit (STK) that supports application development using FuGE. We anticipate that these guidelines will encourage consistent usage of FuGE, and as such, will contribute to the development of convergent data standards in omics research. IS - 3 JF - Omics : a journal of integrative biology SN - 1557-8100 EP - 251 TI - Modeling and managing experimental data using FuGE. VL - 13 SP - 239 KW - data_representation KW - database AU - Jones, Andrew AU - Lister, Allyson AU - Hermida, Leandro AU - Wilkinson, Peter AU - Eisenacher, Martin AU - Belhajjame, Khalid AU - Gibson, Frank AU - Lord, Phil AU - Pocock, Matthew AU - Rosenfelder, Heiko AU - Santoyo-Lopez, Javier AU - Wipat, Anil AU - Paton, Norman PY - 2009/06/14/ UR - http://dx.doi.org/10.1089/omi.2008.0080 ER -