dorsal/arxiv
View SchemaMicroarray Data Management. An Enterprise Information Approach: Implementations and Challenges
| Authors | Willy Valdivia-Granda, Christopher Dwan |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0605005 |
| URL | https://arxiv.org/abs/q-bio/0605005 |
Abstract
The extraction of information form high-throughput experiments is a key aspect of modern biology. Early in the development of microarray technology, researchers recognized that the size of the datasets and the limitations of both computational and visualization techniques restricted their ability to find the biological meaning hidden in the data. In addition, most researchers wanted to make their datasets accessible to others. This resulted in the development of new and advanced data storage, analysis, and visualization tools enabling the cross-platform validation of the experiments and the identification of previously undetected patterns. In order to reap the benefits of this microarray data, researchers have needed to implement database management systems providing integration of different experiments and data types. Moreover, it was necessary to standardize the basic data structure and experimental techniques for the standardization of microarray platforms. In this chapter, we introduce the reader to the major concepts related to the use of controlled vocabularies (ontologies), the definition of Minimum Information About a Microarray Experiment (MIAME) and provide an overview of different microarray data management strategies in use today. We summarize the main characteristics of microarray data storage and sharing strategies including warehouses, datamarts, and federations. The fundamental challenges involved in the distribution, and retrieval of microarray data are presented, along with an overview of some emerging technologies.
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"abstract": "The extraction of information form high-throughput experiments is a key\naspect of modern biology. Early in the development of microarray technology,\nresearchers recognized that the size of the datasets and the limitations of\nboth computational and visualization techniques restricted their ability to\nfind the biological meaning hidden in the data. In addition, most researchers\nwanted to make their datasets accessible to others. This resulted in the\ndevelopment of new and advanced data storage, analysis, and visualization tools\nenabling the cross-platform validation of the experiments and the\nidentification of previously undetected patterns. In order to reap the benefits\nof this microarray data, researchers have needed to implement database\nmanagement systems providing integration of different experiments and data\ntypes. Moreover, it was necessary to standardize the basic data structure and\nexperimental techniques for the standardization of microarray platforms. In\nthis chapter, we introduce the reader to the major concepts related to the use\nof controlled vocabularies (ontologies), the definition of Minimum Information\nAbout a Microarray Experiment (MIAME) and provide an overview of different\nmicroarray data management strategies in use today. We summarize the main\ncharacteristics of microarray data storage and sharing strategies including\nwarehouses, datamarts, and federations. The fundamental challenges involved in\nthe distribution, and retrieval of microarray data are presented, along with an\noverview of some emerging technologies.",
"arxiv_id": "q-bio/0605005",
"authors": [
"Willy Valdivia-Granda",
"Christopher Dwan"
],
"categories": [
"q-bio.GN"
],
"title": "Microarray Data Management. An Enterprise Information Approach: Implementations and Challenges",
"url": "https://arxiv.org/abs/q-bio/0605005"
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