MicrobeDB.jp

2017/06/29

Web Site: http://microbedb.jp/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/microbedb/

The database is integrating various microbiological knowledge centered on genome information.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Refsequence
  3. Ortholog
  4. SRA
  5. BRC
  6. GOLD
  7. NCBI
  8. Disease
  9. Ontology
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "MicrobeDB.jp" data.
File README_e.html (English)
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2.2 Refsequence

Data name Refsequence
Description of data contents

Microbial complete genome and high quality draft genome annotation RDF data. We used corresponding amino acid sequence data for MBGD ortholog clustering and functional assignments of metagenome data. Information on each replicon in the genomes are described in a RDF file using FALDO, SO, and other ontologies.
Data file (compressed in tar.gzip) consists of directories divided by genome. Each directory has a genome RDF file to indicate replicon.
File refsequence.tar.gz (49 GB)
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2.3 Ortholog

Data name Ortholog
Description of data contents

Microbial ortholog RDF data obtained from MBGD. Genome sequences of Refsequence data were used for ortholog clustering in MBGD. In those RDF files, the IDs and host phylogenetic information of genes belong to each ortholog cluster are described. Functional categories of the ortholog clusters are also described.
File ortholog.tar.gz (5.5 GB)
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2.4 SRA

Data name SRA
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).
File sra.tar.gz (8.4 MB)

Data items are the following:
Data itemDescription
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.
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2.5 BRC

Data name BRC
Description of data contents

Metadata of strains in NBRC and JCM with the annotation results of ontologies (i.e., MCCV and MEO).
Data file (compressed in tar.gzip) consists of 2 directories (see the following table).
File brc.tar.gz (6.7 MB)

Data items are the following:
Data itemDescription
brc/nbrc/ Metadata of strains in NBRC.
brc/jcm/ Metadata of strains in JCM.
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2.6 GOLD

Data name GOLD
Description of data contents

Annotation results of phenotypes of genome-sequenced microbes in JGI GOLD by using MPO.
File gold.tar.gz (882 KB)
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2.7 NCBI

Data name NCBI
Description of data contents

The RDF data of several NCBI related data (i.e., BioProject, BioSample, PubMed, and Assembly) which are important to integrate data in MicrobeDB.jp version 2.
Data file (compressed in tar.gzip) consists of 4 directories (see the following table).
File ncbi.tar.gz (79 MB)

Data items are the following:
Data itemDescription
ncbi/bioproject/ The RDF files of metadata of NCBI BioProject.
ncbi/biosample/ The RDF files of metadata of NCBI BioSample with the annotations of MEO, MSV, and NCBI Taxonomy.
ncbi/pubmed/ The RDF files of metadata of PubMed.
ncbi/assembly/ The RDF files of metadata of Assembly Reports in NCBI Assembly.
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2.8 Disease

Data name Disease
Description of data contents

The PDO annotation results of microbes including pathogenic disease name, symptom, causal genes, and related taxa.
File disease.tar.gz (1.2 MB)
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2.9 Ontology

Data name Ontology
Description of data contents

The ontology files that are used in MicrobeDB.jp version 2.
Data file (compressed in tar.gzip) consists of some directories (see the following table).
File ontology.tar.gz (91 MB)

Data items are the following:
Data itemDescription
ontology/meo/meo.ttl An ontology for describing organismal habitats (especially focused on microbes).
ontology/meo/meo_fma_mapping.ttl An ontology mapping files that was mapped between MEO and FMA.
ontology/msv/msv.ttl An ontology for describing several states of sampling environment for metagenome analyses.
ontology/mdbv/mdbv.rdf A vocabulary for describing data schema in MicrobeDB.jp version 2.
ontology/mgfo/mgfo.ttl An ontology for describing the gene function category that is used in MBGD.
ontology/pdo/pdo.owl An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection.
ontology/csso/csso.owl An ontology for describing clinical signs and symptoms.
ontology/mpo/mpo.ttl An ontology for describing microbial phenotypes.
ontology/mccv/mccv.ttl Structured controlled vocabulary for describing meta information of microbial culture collection maintained in biological resource centers.
ontology/taxonomy/taxonomy.ttl Modified NCBI Taxonomy ontology for describing taxonomic relationships of organisms.
ontology/insdc/nucleotide.ttl A vocabulary for describing metadata of INSDC entries.
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3. License

Last updated : 2017/06/29

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "MicrobeDB.jp c Ken Kurokawa (Center for Information Biology, National Institute of Genetics) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

1111 Yata, Mishima, Shizuoka 41-8540, Japan
National Institute of Genetics
Center for Information Biology
Ken Kurokawa
E-mail: kk[at]nig[dot]ac[dot]jp

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4. Update History

DateUpdate contents
2017/06/29 Archive V2 is released and MicrobeDB.jp English archive site is opened.
The following data are added. The following data are updated.
2014/03/31 MicrobeDB.jp archive site is opened.
(Archive V1)
2011/12/12 MicrobeDB (http://microbedb.jp/) is opened.
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5. Literature

-
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6. Contact address

When you have any question about "MicrobeDB.jp", contact the following:

1111 Yata, Mishima, Shizuoka 41-8540, Japan
National Institute of Genetics
Center for Information Biology
Ken Kurokawa
E-mail: kk[at]nig[dot]ac[dot]jp

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