brenda a european elixir core data resource in de.nbi fkz ... · the data life cycle”was...

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