| Data name ⇅ | Database name ⇅ | DOI ⇅ | Description of data contents ⇅ | Data file ⇅ | Simple search URL ⇅ | Data acquisition method ⇅ | Data analysis method ⇅ | Number of data entries ⇅ | Data detail |
|---|---|---|---|---|---|---|---|---|---|
| GOLD | MicrobeDB.jp | 10.18908/lsdba.nbdc01181-008.V002 |
Annotation results of phenotypes of genome-sequenced microbes in JGI GOLD by using MPO. |
gold.tar.gz
(882 KB) |
- |
Metadata of genome-sequenced microbes were obtained from JGI GOLD. |
138,948 triples |
Data detail
open_in_full
|
|
| NCBI | MicrobeDB.jp | 10.18908/lsdba.nbdc01181-009.V002 |
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.
|
ncbi.tar.gz
(79 MB) |
- |
The data that are important to integrate data in MicrobeDB.jp version 2 were obtained by parsing XML and TSV format files in NCBI. |
14,905,682 triples |
Data detail
open_in_full
|
|
| Ontology | MicrobeDB.jp | 10.18908/lsdba.nbdc01181-004.V002 |
The ontology files that are used in MicrobeDB.jp version 2.
|
ontology.tar.gz
(91 MB) |
- |
The MPO and MCCV files were obtained from a collaborator. The NCBI Taxonomy and INSDC ontology files were obtained from the DDBJ web site. Other ontologies were developed in this project. |
21,722,610 triples |
Data detail
open_in_full
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|
| Ortholog | MicrobeDB.jp | 10.18908/lsdba.nbdc01181-010.V002 |
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. |
ortholog.tar.gz
(5.5 GB) |
- |
We obtained these ortholog RDF data from MBGD in January 2015. |
1,610,893,814 triples |
Data detail
open_in_full
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|
| Refsequence | MicrobeDB.jp | 10.18908/lsdba.nbdc01181-005.V002 |
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.
|
refsequence.tar.gz
(49 GB) |
- |
Microbial high quality draft (identified by using the MBGD criteria) and complete genome annotation data were obtained from NCBI RefSeq and GenBank. |
4,165,436,499<span style="font-size: 12px;"> triples</span> |
Data detail
open_in_full
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|
| Data name | Database name | DOI | Description of data contents | Data file | Simple search URL | Data acquisition method | Data analysis method | Number of data entries | Data detail |
List of Data Metadata