Motivation and Results: A relational schema is described for capturing
highly parallel gene expression experiments using different technologies.
This schema grew out of efforts to build a database for collaborators
working on different biological systems and using different types
of platforms in their gene expression experiments as well as different
types of image quantification software. The tables are conceptually
organized into three categories of information: Platform, Experiment
(which includes image scanning and quantification), and Data. The
strengths of the schema are: (i) integrating information on array
elements using a gene index; (ii) describing samples using ontologies;
(iii) reducing an experiment to a single RNA source for precise descriptions
yet not losing the relationships between experiments done at the
same time or for the same project; and (iv) maintaining both raw
and processed (e.g. cleansed and normalized) data and recording how
the data is processed. The result is a novel schema, which can hold
both array and non-array data, is extensible for detailed experimental
descriptions that are precise and consistent, and allows for meaningful
comparisons of genes between experiments.
%0 Journal Article
%1 Stoeckert:2001
%A Stoeckert, C.
%A Pizarro, A.
%A Manduchi, E.
%A Gibson, M.
%A Brunk, B.
%A Crabtree, J.
%A Schug, J.
%A Shen-Orr, S.
%A and G. C. Overton,
%D 2001
%J Bioinformatics
%K imported
%N 4
%P 300--308
%T A relational schema for both array--based and SAGE gene expression
experiments
%U http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/4/300
%V 17
%X Motivation and Results: A relational schema is described for capturing
highly parallel gene expression experiments using different technologies.
This schema grew out of efforts to build a database for collaborators
working on different biological systems and using different types
of platforms in their gene expression experiments as well as different
types of image quantification software. The tables are conceptually
organized into three categories of information: Platform, Experiment
(which includes image scanning and quantification), and Data. The
strengths of the schema are: (i) integrating information on array
elements using a gene index; (ii) describing samples using ontologies;
(iii) reducing an experiment to a single RNA source for precise descriptions
yet not losing the relationships between experiments done at the
same time or for the same project; and (iv) maintaining both raw
and processed (e.g. cleansed and normalized) data and recording how
the data is processed. The result is a novel schema, which can hold
both array and non-array data, is extensible for detailed experimental
descriptions that are precise and consistent, and allows for meaningful
comparisons of genes between experiments.
@article{Stoeckert:2001,
abstract = {Motivation and Results: A relational schema is described for capturing
highly parallel gene expression experiments using different technologies.
This schema grew out of efforts to build a database for collaborators
working on different biological systems and using different types
of platforms in their gene expression experiments as well as different
types of image quantification software. The tables are conceptually
organized into three categories of information: Platform, Experiment
(which includes image scanning and quantification), and Data. The
strengths of the schema are: (i) integrating information on array
elements using a gene index; (ii) describing samples using ontologies;
(iii) reducing an experiment to a single RNA source for precise descriptions
yet not losing the relationships between experiments done at the
same time or for the same project; and (iv) maintaining both raw
and processed (e.g. cleansed and normalized) data and recording how
the data is processed. The result is a novel schema, which can hold
both array and non-array data, is extensible for detailed experimental
descriptions that are precise and consistent, and allows for meaningful
comparisons of genes between experiments.},
added-at = {2007-10-23T13:35:30.000+0200},
author = {Stoeckert, C. and Pizarro, A. and Manduchi, E. and Gibson, M. and Brunk, B. and Crabtree, J. and Schug, J. and Shen-Orr, S. and and G. C. Overton},
biburl = {https://www.bibsonomy.org/bibtex/2acc05c6d38f402f9c4d770e3b7cbeb23/tkirsten},
interhash = {522e42882d1b54e0cf07cee380c66531},
intrahash = {acc05c6d38f402f9c4d770e3b7cbeb23},
journal = {Bioinformatics},
keywords = {imported},
number = 4,
owner = {tkirsten},
pages = {300--308},
timestamp = {2007-10-23T13:35:41.000+0200},
title = {{A relational schema for both array--based and SAGE gene expression
experiments}},
url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/4/300},
volume = 17,
year = 2001
}