scholarly journals BRENDA in 2019: a European ELIXIR core data resource

2018 ◽  
Vol 47 (D1) ◽  
pp. D542-D549 ◽  
Author(s):  
Lisa Jeske ◽  
Sandra Placzek ◽  
Ida Schomburg ◽  
Antje Chang ◽  
Dietmar Schomburg
Keyword(s):  
Data Resource ◽  
Core Data

scholarly journals BRENDA, the ELIXIR core data resource in 2021: new developments and updates

2020 ◽  
Vol 49 (D1) ◽  
pp. D498-D508
Author(s):  
Antje Chang ◽  
Lisa Jeske ◽  
Sandra Ulbrich ◽  
Julia Hofmann ◽  
Julia Koblitz ◽  
...  
Keyword(s):  
Intracellular Localization ◽  
Easy Access ◽  
New Developments ◽  
Data Resource ◽  
Core Data ◽  
Related Data ◽  
Primary Literature ◽  
Ligand Interactions ◽  
Genome Annotations ◽  
Individual Enzyme

Abstract The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for ∼90 000 enzymes from ∼13 000 organisms, manually extracted from ∼157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, ligand information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.

scholarly journals The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

2019 ◽  
Author(s):  
Rachel Drysdale ◽  
Charles E. Cook ◽  
Robert Petryszak ◽  
Vivienne Baillie-Gerritsen ◽  
Mary Barlow ◽  
...  
Keyword(s):  
Life Science ◽  
Life Sciences ◽  
Health Sector ◽  
Biological Data ◽  
Supplementary Information ◽  
Science Data ◽  
Data Infrastructure ◽  
Data Resource ◽  
Core Data ◽  
The Core

AbstractMotivationLife science research in academia, industry, agriculture, and the health sector depends critically on free and open data resources. ELIXIR (www.elixir-europe.org), the European Research Infrastructure for life sciences data, has identified a set of Core Data Resources within Europe that are of most fundamental importance for the long-term preservation of biological data. We explore characteristics of their usage, impact and assured funding horizon to assess their value and importance as an infrastructure, to understand sustainability of the infrastructure, and to demonstrate a model for assessing Core Data Resources worldwide.ResultsThe nineteen resources currently designated ELIXIR Core Data Resources form a data infrastructure in Europe which is a subset of the worldwide open life science data infrastructure. We show that, from 2014 to 2018, data managed by the Core Data Resources more than tripled while staff numbers increased by less than a tenth. Additionally, support for the Core Data Resources is precarious: together they have assured funding for less than a third of current staff after four years.Our findings demonstrate the importance of the ELIXIR Core Data Resources as repositories for research data and knowledge, while also demonstrating the uncertain nature of the funding environment for this infrastructure. ELIXIR is working towards longer-term support for the Core Data Resources and, through the Global Biodata Coalition, aims to ensure support for the worldwide life science data resource infrastructure of which the ELIXIR Core Data Resources are a [email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals The EU Child Cohort Network’s core data: establishing a set of findable, accessible, interoperable and re-usable (FAIR) variables

2021 ◽  
Author(s):  
Angela Pinot de Moira ◽  
◽  
Sido Haakma ◽  
Katrine Strandberg-Larsen ◽  
Esther van Enckevort ◽  
...  
Keyword(s):  
Statistical Power ◽  
Major Product ◽  
Multiple Birth ◽  
Birth Cohorts ◽  
Data Resource ◽  
Core Data ◽  
Number Of Children ◽  
Analysis Platform ◽  
Early Life Exposures ◽  
The Eu

AbstractThe Horizon2020 LifeCycle Project is a cross-cohort collaboration which brings together data from multiple birth cohorts from across Europe and Australia to facilitate studies on the influence of early-life exposures on later health outcomes. A major product of this collaboration has been the establishment of a FAIR (findable, accessible, interoperable and reusable) data resource known as the EU Child Cohort Network. Here we focus on the EU Child Cohort Network’s core variables. These are a set of basic variables, derivable by the majority of participating cohorts and frequently used as covariates or exposures in lifecourse research. First, we describe the process by which the list of core variables was established. Second, we explain the protocol according to which these variables were harmonised in order to make them interoperable. Third, we describe the catalogue developed to ensure that the network’s data are findable and reusable. Finally, we describe the core data, including the proportion of variables harmonised by each cohort and the number of children for whom harmonised core data are available. EU Child Cohort Network data will be analysed using a federated analysis platform, removing the need to physically transfer data and thus making the data more accessible to researchers. The network will add value to participating cohorts by increasing statistical power and exposure heterogeneity, as well as facilitating cross-cohort comparisons, cross-validation and replication. Our aim is to motivate other cohorts to join the network and encourage the use of the EU Child Cohort Network by the wider research community.

scholarly journals Identifying ELIXIR Core Data Resources

F1000Research ◽  
2017 ◽  
Vol 5 ◽  
pp. 2422 ◽  
Author(s):  
Christine Durinx ◽  
Jo McEntyre ◽  
Ron Appel ◽  
Rolf Apweiler ◽  
Mary Barlow ◽  
...  
Keyword(s):  
Life Science ◽  
Life Sciences ◽  
Life Cycles ◽  
Biological Data ◽  
Biological Information ◽  
Biological Research ◽  
Scientific Quality ◽  
Data Resource ◽  
Core Data

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

scholarly journals The SILVA Database Project: An ELIXIR core data resource for high-quality ribosomal RNA sequences

2019 ◽  
Vol 3 ◽  
Author(s):  
Frank Oliver Glöckner
Keyword(s):  
High Throughput ◽  
Ribosomal Rna ◽  
High Throughput Sequencing ◽  
Large Subunit ◽  
Small Subunit ◽  
Environmental Sciences ◽  
Rna Sequences ◽  
Data Resource ◽  
Core Data ◽  
Rdna Sequences

Ribosomal DNA (rDNA) has become the primary target molecule for phylogenetic reconstruction and the cultivation-independent detection and quantification of microorganisms (barcoding). With the advent of high-throughput sequencing technologies (Next Generation Sequencing (NGS), PCR-based amplicon sequencing of rDNA fragments for diversity screening is now a routine technology, at least in environmental sciences. The resulting exponential increase of publicly available rDNA sequences demands specialized reference databases (Fig. 1). SILVA (from Latin silva, meaning forest) is designed to provide a comprehensive web resource for up-to-date, quality-controlled databases of aligned rDNA sequences from the Bacteria, Archaea and Eukaryota domains and the corresponding online services (Glöckner et al. 2017, Quast et al. 2012). The current SILVA database (release 132) contains 6,073,181 small subunit and 907,382 large subunit rRNA gene sequences. All sequences are checked for anomalies, carry a rich set of sequence-associated contextual information, multiple taxonomic classifications (EMBL-EBI/ENA, RDP and GTDB) and the latest validly-described nomenclature. SILVA maintains manually curated reference alignments of 75,000 ribosomal RNA genes, both 16S/18S (small subunit, SSU) and 23S/28S (large subunit, LSU). With every full release, a manually curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences where no validly-described cultivated representative is available (Yilmaz et al. 2014). SILVA incorporates other unique features, including a comprehensive 23S/28S database of aligned rDNA sequences and alignments that contain Eukaryota sequences. SILVA is an active partner of RNACentral. RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. The SILVA team is a member of the Bergey’s Board of Trustees which provides the authoritative taxonomy for Bacteria and Archaea as well as the Protist Reference Taxonomy Project UniEuk funded by the Gordon and Betty Moore Foundation to create a unified taxonomic framework In 2018 SILVA became an ELIXIR Core Data Resource. ELIXIR Core Data Resources are a set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data. To facilitate classification tasks for high-throughput rDNA data the SILVAngs has been implemented and released in 2013. SILVAngs is a data analysis service for rDNA reads from high-throughput sequencing (NGS) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download. SILVAngs serves several thousands of registered users, which processes thousands of projects per year. The application spectrum of the SILVA databases ranges from environmental sciences, microbiology, agriculture, biochemistry, biotechnology to medicine in academia and industry.

scholarly journals Identifying ELIXIR Core Data Resources

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2422 ◽  
Author(s):  
Christine Durinx ◽  
Jo McEntyre ◽  
Ron Appel ◽  
Rolf Apweiler ◽  
Mary Barlow ◽  
...  
Keyword(s):  
Life Science ◽  
Life Sciences ◽  
Life Cycles ◽  
Biological Data ◽  
Biological Information ◽  
Biological Research ◽  
Scientific Quality ◽  
Data Resource ◽  
Core Data

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

Historical text archives and prosopography: the COEL database system

1998 ◽  
Vol 10 (1-3) ◽  
pp. 57-72 ◽  
Author(s):  
K. S. B. Keats-Rohan
Keyword(s):  
Research Tool ◽  
Direct Access ◽  
Specific Situation ◽  
Core Data ◽  
Secondary Sources ◽  
The Core ◽  
Level 3 ◽  
Full Discussion ◽  
Available Information ◽  
Level 2

The COEL database and database software, a combined reference and research tool created by historians for historians, is presented here through Screenshots illustrating the underlying theoretical model and the specific situation to which that has been applied. The key emphases are upon data integrity, and the historian's role in interpreting and manipulating what is often contentious data. From a corpus of sources (Level 1) certain core data are extracted for separate treatment at an interpretive level (Level 3), based upon a master list of the core data (Level 2). The core data are interdependent: each record in Level 2 is of interest in itself; and it either could or should be associated with an(other) record(s) as a specific entity. Sometimes the sources are ambiguous and the association is contentious, necessitating a probabilty-coding approach. The entities created by the association process can then be treated at a commentary level, introducing material external to the database, whether primary or secondary sources. A full discussion of the difficulties is provided within a synthesis of available information on the core data. Direct access to the source texts is only ever a mouse click away. Fully query able, COEL is formidable look-up and research tool for users of all levels, who remain free to exercise an alternative judgement on the associations of the core data. In principle, there is no limit on the type of text or core data that could be handled in such a system.

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