brenda a european elixir core data resource in de.nbi fkz ... · the data life cycle”was...
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Further details of the cooperation and the mutual data integration were discussed with BacDive.
Short description of the project
Progress report
www.denbi.de
Publications
de.NBI Training and education
de.NBI services
Lisa Jeske, Sandra Placzek, Antje Chang, Ida Schomburg, Dietmar SchomburgDepartment of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Germany
BRENDA – A European Elixir Core Data Resource
in de.NBIFKZ 031A539D
General information on the project
Three scentists are paid from the de.NBI grant. The PI, two furtherscientists and several external contributors are paid by the university(PI) and the sale of in-house licenses to the industry.
BRENDA, in the beginning of 2018 appointed Elixir Core DataResource, is the world‘s largest widely used information center forenzymes and enzyme ligands. Its 4.3 million data in 50 informationfields extracted manually from primary publications make it absolutelyunique world-wide. The manual information core is complemented bydata obtained by text mining and calculations, e.g. genome annotationand enzyme localization. In order to provide a „one stop shopping“ forenzyme information this is combined with data from public-domaindatabases like sequences and 3D-structures. In addition to the in-detailenzyme information a quick-overview characterisation, pathwayinformation, and statistical data are provided.
BRENDA in 2019: a European ELIXIR core data resourceJeske L., Placzek S., Schomburg I., Chang A., Schomburg D., NucleicAcids Res., in print (2019)
In September 2018, a five day de.NBI & GFBio summer school “Riding
the Data Life Cycle” was organized together with members of BioData,
GCBN, and de.NBI-SysBio at the TU Braunschweig. The BRENDA
(video) tutorials and training materials on the website were updated
and supplemented.
• change in the license model (now CC BY-ND)• new full download option of the manually annotated data for all users• establishment of a Scientific Advisory Board
A first version of organism word maps is provided, focusing on archaea, bacteria, fungi, and plants. New organism summary pages were created linked to 16S/18S and 23S/28S rRNA of SILVA.
Organism summary page
A new class EC 7, Translocases, will be available in release 2019.1!
: new reaction specific pathway view
The BRENDA team is working together with de.NBI cloud site Gießen to implement a faster
and more sophisticated version of BRENDA's new text mining approach,
EXOMEDA, and the creation of organism word maps on the de.NBI cloud.
new search types:- similarity search- isomer search
Revised structure search
+
new layoutto improvethe usability
structurediagramwith zoom function
Since the beginning of de.NBI 2.1 million sessions by 1.1 milliondifferent users and 10 million page views were counted by GoogleAnalytics. Excluding webcrawlers and internal traffic a text filecomprehending the BRENDA database was downloaded approx. 9,500times since the appointment as a Elixir Core Data Resource.
Graphic-based
Queries and
VisualizationsPathway Maps
interactive visualizations of
BRENDA pathways providing
information on metabolites
and enzymes by links
Sequence Searcha search for amino acid
sequences in combination
with a distribution of hits in the
EC System
SBML outputthe download of data in XML-
based format for the
construction of metabolic
models from kinetic data
SOAP servicea simple and direct way to
access data via almost 150
different methods without the
requirement of parsingAdvanced Searchsophisticated queries in about
50 data categories by
combining different search
criteria
Genome Explorera genome visualization tool to
compare enzyme locations
and to show enzymes in their
genomic context
Word Mapsgraphical representations of
enzyme or organism specific
terms classified into different
categories
Structure Searcha search for BRENDA ligands
using a chemical structure
(substructure) drawn with a
molecule editor
Functional Parameters~456,000 manually annotated
kinetic data and ~12,400
kinetic values from text mining
methods
Text-based
Queries
Ontology Explorer/BTOa variety of about 40
biologically and biochemically
relevant ontologies