Search for Database Metadata
| Database name ⇅ | DOI ⇅ | Database classification ⇅ | Organism ⇅ | Database description ⇅ | Features and manner of utilization of database ⇅ | Database maintenance site ⇅ | License ⇅ |
|---|---|---|---|---|---|---|---|
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SSBD
(Systems Science of Biological Dynamics database) |
10.18908/lsdba.nbdc01349-000 |
Other Molecular Biology Databases
動態データベース
|
Homo sapiens
(9606)
Mus musculus
(10090)
Canis lupus familiaris
(9615)
Rattus norvegicus
(10116)
Xenopus laevis
(8355)
Danio rerio
(7955)
Drosophila melanogaster
(7227)
Dictyostelium discoideum
(44689)
Caenorhabditis elegans
(6239)
Escherichia coli
(562)
|
Systems Science of Biological Dynamics database (SSBD) is an open database for collecting and sharing microscopy image data and quantitative data of biological dynamics, which are generated from image analysis or computer simulation. SSBD provides a wide variety of data from single-molecules to cell to organism in different species. A web browser based multidimensional visualization tool is available for viewing data interactively online. |
The image data and its meta-information are provided in the raw image file format. Downloaded files can be imorted into ImageJ using Bio-Formats. The quantitative data and its meta-information are provided in the Biological Dynamics Markup Language (BDML) format, which is a unified format for representing quantitative data of biological dynamics. The image data and quantitative data are provided through API, which allows third parties to develop their applications. In addition, SSBD also provides software tools for data visualization and analysis. |
RIKEN
|
CC BY-SA |
| ChIP-Atlas | 10.18908/lsdba.nbdc01558-000.V020 |
Nucleotide Sequence Databases - Transcriptional regulator sites and transcription factors
Genomics Databases (non-vertebrate) - Genome annotation terms, ontologies and nomenclature
Human and other Vertebrate Genomes - Human genome databases, maps and viewers
|
Homo sapiens
(9606)
Mus musculus
(10090)
Drosophila melanogaster
(7227)
Caenorhabditis elegans
(6239)
Saccharomyces cerevisiae
(4932)
Rattus norvegicus
(10116)
|
ChIP-Atlas is the database and its web interface to provide the result of analysis processed from the entire ChIP-Seq data archived in Sequence Read Archive. We have curated metadata described by original data submitter to enable further data analysis. See details here: https://github.com/inutano/chip-atlas/wiki |
Users can browse all peaks from published ChIP-Seq data, and the result of target gene analysis and Colocalization analysis. Users also can perform enrichment analysis by querying user data. |
Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine |
CC BY-SA |
| Metabolonote | 10.18908/lsdba.nbdc01324-000 |
Experimental Metadata (Materials and Methods)
|
A database specified for managing information on experimental methods (metadata) which is accompanied with the experimental data obtained from metabolomics studies. This system aims to promote the publication and utilization of metabolomics data by simplifying the metadata record process.
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Separation of the management of metadata from that of experimental data has the following two advantages: (1) Multiple databases that stores experimental data can share the same metadata, and (2) the submitter can manage the metadata at one site. The Wiki-based recording system helps submitters to prepare metadata with ease. The system allowes submitters to attach additional information such as image files of the sample, movie files of tricky experiments, and hyperlinks to the related web resources. Such a user-centric design of the system contributes to accelarate publication of metabolomics data. |
Kazusa DNA Research Institute 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan |
CC BY-SA | |
|
eSOL
(Solubility database of all E.coli proteins) |
10.18908/lsdba.nbdc00440-000 |
Protein sequence databases - Protein properties
|
Escherichia coli
(562)
|
The database of solubilities and synthetic yields of all E.coli proteins translated by using an in vitro reconstituted translation system. For 788 aggregation-prone proteins, the data of chaperone effects on the prevention of aggregate formation were added on May 2012.
|
Since PURE system is a reconstituted chaperone-free translation system, it is possible to evaluate the solubilities of translated proteins and the chaperone effects accurately. The acquired data will form the basis of protein folding studies and be useful for planning researches and industries using protein expression and improving their efficiencies. |
The Targeted Proteins Research Program promoted by the MEXT |
CC BY-SA |
|
SAHG
(Structure Atlas of Human Genome) |
10.18908/lsdba.nbdc01193-000 |
Protein sequence databases - Protein properties
Structure Databases - Protein structure
Human and other Vertebrate Genomes - Human ORFs
|
Homo sapiens
(9606)
|
All of the Open Reading Frames in the human genome are subjected to a fully automated, exhaustive protein-structure-prediction pipeline to generate protein structure models. SAHG contains 42,577 domain-structure models in ~24900 unique human protein sequences from the RefSeq database. |
SAHG is distinct in that the prediction pipeline is focus on proteins of higher organisms, and in that conformational changes of proteins were predicted and displayed as animated image. |
* The original website was terminated.
|
CC BY-SA |
| Database name | DOI | Database classification | Organism | Database description | Features and manner of utilization of database | Database maintenance site | License |