Microbiome analysis data of MicrobeDB.jp ver. 3Hiroshi Mori、Takatomo Fujisawa、Zenichi Nakagawa、Takuji Yamada、Ken Kurokawa
1) Department of Informatics, National Institute of Genetics、2) School of Life Sciences, Tokyo Institute of Technology
Abstract Microbes inhabit almost everywhere on earth and conduct a variety of metabolic process. Microbiome sequencing analyses (e.g., metagenomic analysis and 16S rRNA gene
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RDF is a standard data model of Semantic Web technology
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RDF (Resource Description Framework) Data model which uses Triples (Subject – Predicate – Object)
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Organism1 has Genome Genome1Organism1 has Genome Genome1Organism1 has Genome Genome1
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OntologyTriple store
SPARQL
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gtps:Gene1 rdfs:label “16S rRNA gene”
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URI node can be linked to other nodes
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To prepare data in RDF, the database management system automatically recognize same resources.
Overview of MicrobeDB.jp What is RDF? Sequence based integration in MicrobeDB.jp
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amplicon sequencing analysis) are powerful analysis methods to identify microbial community compositions (i.e., phylogenetic composition and gene function composition), and therefore widelyapplied to various microbial communities. We are developing MicrobeDB.jp (http://microbedb.jp/), which is an integrated database of publicly available microbial genome and metagenome data. We are conducting an automatic and manual annotations of microbial habitats of each genome and metagenome sample in MicrobeDB.jp using an onyology MEO. In addition, we are analyzing microbial community compositions of each microbiome sequencing data. These combination of data will support microbiome studies . MicrobeDB.jp web site ( http://microbedb.jp ).
Data sources of MicrobeDB.jp ver. 3
16S rRNA gene amplicon / Metagenome analysis
pipeline in MicrobeDB.jp ver. 3 (MeGAP3)
Different types of data can be integrate based on the
DNA/Protein sequence similarities
16S rRNA gene amplicon / Metagenome analysispipeline in MicrobeDB.jp ver. 3 (MeGAP3)
Metagenome sequence data
analysis strategies
Number of microbiome samples in INSDC Example of Metagenome databases
Number of microbiome samples per env. Number of human microbiome samples
How tosearchsamples?
Search samplesby keyword andontology
Comparetaxonomic orfunctionalcompositionamongsamples
MicrobeDB.jpver. 3 datawill be opensoon !
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