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TRUNCATULIX--a data warehouse for the legume community.

Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A - BMC Plant Biol. (2009)

Bottom Line: For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations.The results can be exported as Excel, HTML, or as csv files for further usage.The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany. khenckel@cebitec.uni-bielefeld.de

ABSTRACT

Background: Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database - hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data.

Results: The TRUNCATULIX data warehouse integrates five public databases for gene sequences, and gene annotations, as well as a database for microarray expression data covering raw data, normalized datasets, and complete expression profiling experiments. It can be accessed via an AJAX-based web interface using a standard web browser. For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage.

Conclusion: The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available. TRUNCATULIX is freely available at http://www.cebitec.uni-bielefeld.de/truncatulix/.

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The first filterstep – gene annotation. The screenshot shows the filter page for the gene annotation data. The annotation descriptions can be queried, as well as the gene names, sequences and EC numbers.
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Figure 2: The first filterstep – gene annotation. The screenshot shows the filter page for the gene annotation data. The annotation descriptions can be queried, as well as the gene names, sequences and EC numbers.

Mentions: To calculate this query, a user first specifies the standard search dialog on the left (see Figure 2). The user is guided through the different filter steps with an indicator bar on the top of the web pages. Help texts give examples and describe the options given by the different filters. Because some filters are more commonly used than others, the most commonly selected filters are highlighted in red.


TRUNCATULIX--a data warehouse for the legume community.

Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A - BMC Plant Biol. (2009)

The first filterstep – gene annotation. The screenshot shows the filter page for the gene annotation data. The annotation descriptions can be queried, as well as the gene names, sequences and EC numbers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654896&req=5

Figure 2: The first filterstep – gene annotation. The screenshot shows the filter page for the gene annotation data. The annotation descriptions can be queried, as well as the gene names, sequences and EC numbers.
Mentions: To calculate this query, a user first specifies the standard search dialog on the left (see Figure 2). The user is guided through the different filter steps with an indicator bar on the top of the web pages. Help texts give examples and describe the options given by the different filters. Because some filters are more commonly used than others, the most commonly selected filters are highlighted in red.

Bottom Line: For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations.The results can be exported as Excel, HTML, or as csv files for further usage.The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany. khenckel@cebitec.uni-bielefeld.de

ABSTRACT

Background: Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database - hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data.

Results: The TRUNCATULIX data warehouse integrates five public databases for gene sequences, and gene annotations, as well as a database for microarray expression data covering raw data, normalized datasets, and complete expression profiling experiments. It can be accessed via an AJAX-based web interface using a standard web browser. For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage.

Conclusion: The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available. TRUNCATULIX is freely available at http://www.cebitec.uni-bielefeld.de/truncatulix/.

Show MeSH