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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Gene1 has Function

GO:0003700

RDF is a standard data model of Semantic Web technology

Genome1 organism Escherichia coli

Search

RDF (Resource Description Framework) Data model which uses Triples (Subject – Predicate – Object)

Gene1 has Function

GO:0003700Gene1 has

FunctionGO:

0003700

Genome1 organism Escherichia coliGenome1 organism Escherichia

coli

Organism1 has Genome Genome1Organism1 has Genome Genome1Organism1 has Genome Genome1

Organism1 inhabit LakeOrganism1 inhabit LakeOrganism1 inhabit Lake

RDF

OntologyTriple store

SPARQL

S P O

gtps:Gene1 rdfs:label “16S rRNA gene”

KO:03043

<URI> <URI> <URI>/Literal

URI node can be linked to other nodes

S P O/S P O

S P O

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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