Center for Biological Data (BioData)

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About

The Center for Biological Data consists of the four databases SILVA, PANGAEA, BacDive and BRENDA. Together they provide access to and services for ribosomal RNA genes from all three domains of life (SILVA), georeferenced data from earth system research (PANGAEA), detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity (BacDive) and the comprehensive enzyme information system BRENDA. All databases provide a set of highly curated reference datasets and three of these databases have been maintained for more than 25 years, indicating the importance of quality controlled reference datasets for the advancement in science.

Services

A core mission of the database providers is to offer high-quality datasets and related services for users in academia and industry. Each database reflects the core expertise of their home institutes.

SILVA

SILVA offers quality-controlled, curated rRNA alignments, taxonomies, and reference databases for Bacteria, Archaea and Eukarya. Services offered by the SILVA website are the rRNA gene aligner, tools for probe and primer evaluation, advanced browsing, searching, and download of pre-configured, as well as user generated datasets. SILVAngs provides fast and accurate classification for next generation amplicon data.

PANGAEA

Essential services supplied by PANGAEA are data curation, long-term data archiving and data publication. Data curation includes quality control of metadata and the development of ontologies and vocabularies according to international protocols and standards. Each dataset can be cited using a universally unique Digital Object Identifier (DOI). Metadata and data can be accessed via the website and web services.

BacDive

The BacDive portal offers manually annotated information on bacterial and archaeal strains. Each strain entry gives a comprehensive overview on the strain's properties. The combination of several strain entries serves as a versatile basis for further biodiversity informatics analyses performed by the individual user. Data can be retrieved via the webportal and individual sets of strain information can be exported as CSV.

BRENDA

BRENDA is the internationally leading information system on all aspects of enzymes, including function, structure, involvement in diseases, application, engineering, and molecular properties. The database includes hundreds of milllions of enzyme data and is compiled from manual literature annotation, data integration from other databases and predicted enzyme functions and locations. Textual and structural queries are possible as well as browsing in ontologies, display of chemical and 3D-structures and different visualisation of enzymic features and statistics.

Developments

All databases will make best use of the de.NBI resources to improve their curational capacities to mobilise and structure data for the provisioning of high quality datasets to the scientific community. They will further enhance data exchange and interoperability within the databases/data resource unit as well as to external databases to improve the quality of services provided within de.NBI and the community.

Project Management

SILVA: The ribosomal RNA database Website
Prof. Dr. Frank Oliver Glöckner (Coordinator)
Department of Life Sciences and Chemistry
Jacobs University Bremen gGmbH and Max Planck Institute for Marine Microbiology
Campus Ring 1
28759 Bremen
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PANGAEA: Environmental Data Integration and Data Publication
Dr. Michael Diepenbroek (Partner)
MARUM-Center for Marine Environmental Sciences
University Bremen
Leobener Strasse
POP 330 440
28359 Bremen
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BacDive: The Bacterial Diversity Metadatabase
Prof. Dr. Jörg Overmann (Partner)
Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Inhoffenstraße 7B
38124 Braunschweig
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BRENDA: The Comprehensive Enzyme Information System
Prof. Dr. Dietmar Schomburg (Partner)
Department of Bioinformatics and Biochemistry
Institute for Biochemistry and Biotechnology
Technische Universität Braunschweig
Langer Kamp 19B
38106 Braunschweig
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Supplementary Information

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SAB-Poster
SILVA
SAB-Poster
PANGAEA
SAB-Poster
BacDive
SAB-Poster
BRENDA
SAB-Poster
Enzyme Struct.