About This Database

SRA

Data description

Data name

SRA

DOI

10.18908/lsdba.nbdc01181-006.V002

Description of data contents

Metadata and taxonomic/functional compositions of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples. Metadata were annotated by several ontologies (i.e., MEO, MSV, and NCBI Taxonomy). Data file (compressed in tar.gzip) consists of some directories (see the following table).

Data file

File name :

sra.tar.gz

File URL :

https://dbarchive.biosciencedbc.jp/data/microbedb/LATEST/sra.tar.gz

File size :

8.4 GB

Simple search URL

Data acquisition method

Metadata and DNA sequence data of each 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing sample were obtained from INSDC DRA/ERA/SRA.

Data analysis method

After quality filtering of reads, DNA sequence data of all 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples were phylogenetically analyzed by VITCOMIC2. Functional composition of metagenomic shotgun sequencing samples were analyzed by the combination of MetaGeneMark, GHOSTX, and Refsequences database.

Number of data entries

1,926,303,942 triples

Data detail

Data item	Description
sra/metadata/meo_mapping/	The MEO annotation results of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/metadata/msv_mapping/	The MSV annotation results of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/metadata/host_taxonomy_mapping/	The NCBI Taxonomy annotation results of host organisms of microbes for 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/metadata/sra_description/	The metadata descriptions of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/mbgd/	The MBGD ortholog cluster composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/mgfo/	The MBGD ortholog functional composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/ko/	The KEGG ortholog composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/function/pathway/	The KEGG pathway composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/sra/taxonomy/	The taxonomic composition of 16S rRNA gene-based amplicon sequencing and metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA.
sra/analysis/env/function/mbgd/	The MBGD ortholog cluster composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/function/mgfo/	The MBGD ortholog function composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/function/ko/	The KEGG ortholog composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/function/pathway/	The KEGG pathway composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/taxonomy/meta16s/	The taxonomic composition of 16S rRNA gene-based amplicon sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.
sra/analysis/env/taxonomy/metagenome/	The taxonomic composition of metagenomic shotgun sequencing samples in INSDC DRA/ERA/SRA that were annotated to each MEO category.