The metagenomics focus of BIOBITS project is on studying the tripartite system: (i) endobacteria living in AM fungi, (ii) AM fungi living in plant roots, and (iii) plant roots, by the employment of a massive large-scale analysis and genomic comparison study of genomes belonging to phylogenetically related free-living bacteria. In this chapter we report specifically on a step of BIOBITS whose goal, roughly, is to develop a modular database which allows to import and store massive genomic data. Later in BIOBITS we will extensively develop computational genomic comparison (syntheny) focused on the above bacterium and fungi genomes. BIOBITS deploys a data warehouse that stores in a multi-dimensional model the interesting metagenomic components of the project. Such a metagenomic component should have the following characteristics: i) being able to store genomic data from multiple organisms, possibly taken from different public database sources; ii) annotating the genomic data making use of the alignment between the given sequences and the genomic sequences of other similar organisms; iii) annotating the genomic sequences and the protein transcript products by the full use of ontologies developed by the biology and bioinformatics communities; iv) comparing and visually presenting the results of the genomic alignment; iv) being able to cluster genomic or proteomic data coming from different organisms in order to easily find increasing levels of similarity and induce on one side the steps of the phylogenetic evolution and on the other side investigate on the metabolic pathways.

BIOBITS: A Study on Candidatus Glomeribacter Gigasporarum with a Data Warehouse

CORDERO, Francesca;LANFRANCO, Luisa;MEO, Rosa;ROVERSI, Luca
2010

Abstract

The metagenomics focus of BIOBITS project is on studying the tripartite system: (i) endobacteria living in AM fungi, (ii) AM fungi living in plant roots, and (iii) plant roots, by the employment of a massive large-scale analysis and genomic comparison study of genomes belonging to phylogenetically related free-living bacteria. In this chapter we report specifically on a step of BIOBITS whose goal, roughly, is to develop a modular database which allows to import and store massive genomic data. Later in BIOBITS we will extensively develop computational genomic comparison (syntheny) focused on the above bacterium and fungi genomes. BIOBITS deploys a data warehouse that stores in a multi-dimensional model the interesting metagenomic components of the project. Such a metagenomic component should have the following characteristics: i) being able to store genomic data from multiple organisms, possibly taken from different public database sources; ii) annotating the genomic data making use of the alignment between the given sequences and the genomic sequences of other similar organisms; iii) annotating the genomic sequences and the protein transcript products by the full use of ontologies developed by the biology and bioinformatics communities; iv) comparing and visually presenting the results of the genomic alignment; iv) being able to cluster genomic or proteomic data coming from different organisms in order to easily find increasing levels of similarity and induce on one side the steps of the phylogenetic evolution and on the other side investigate on the metabolic pathways.
Database Technology for Life Sciences and Medicine
World Scientific Publishing Company
Science, Engineering, and Biology Informatics -- World Scientific
6
139
155
9789814307703
981430770X
http://www.biobits.di.unipmn.it/
http://www.worldscibooks.com/compsci/7772.html
Bioinformatics; data warehouse
Francesca Cordero; Stefano Ghignone; Luisa Lanfranco; Giorgio Leonardi; Rosa Meo; Stefania Montani; Luca Roversi
File in questo prodotto:
File Dimensione Formato  
CorGhiLanLeoMeoMonRovBIOBITS-chapter-book.pdf

Accesso riservato

Tipo di file: POSTPRINT (VERSIONE FINALE DELL’AUTORE)
Dimensione 571.38 kB
Formato Adobe PDF
571.38 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2318/81397
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact