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 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.

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 Bioinformatics: scope and challenges in aquaculture research of Bangladesh- a review

2021 ◽  
Vol 10 (2) ◽  
pp. 137-145
Author(s):  
KMS Rana ◽  
K Ahammad ◽  
MA Salam
Keyword(s):  
Health Management ◽  
National Level ◽  
Work Force ◽  
Disease Diagnosis ◽  
Software Tools ◽  
Biological Data ◽  
Biological Information ◽  
Biological Research ◽  
Future Research ◽  
Data Set

Bioinformatics is one of the ongoing trends of biological research integrating gene based information and computational technology to produce new knowledge. It works to synthesize complex biological information from multiomics data (results of high throughput technologies) by employing a number of bioinformatics tools (software). User convenience and availability are the determining factors of these tools being widely used in bioinformatics research. BLAST, FASTA (FAST-All), EMBOSS, ClustalW, RasMol and Protein Explorer, Cn3D, Swiss PDB viewer, Hex, Vega, Bioeditor etc. are commonly operated bioinformatics software tools in fisheries and aquaculture research. By default, these software tools mine and analyze a vast biological data set using the available databases. However, aquaculture scientists can use bioinformatics for genomic data manipulation, genome annotation and expression profiling, molecular folding, modeling, and design as well as generating biological network and system biology. Therefore, they can contribute in specified fields of aquaculture such as disease diagnosis and aquatic health management, fish nutritional aspects and culture-able strain development. Although having huge prospects, Bangladesh is still in infancy of applying bioinformatics in aquaculture research with limited resources. Research council at national level should be formed to bring all the enthusiastic scientists and skilled manpower under a single umbrella and facilitate to contribute in a collaborative platform. Besides, fully-fledged bioinformatics degree should be launched at University levels to produce knowledgeable and trained work force for future research. This review was attempted to shed light on bioinformatics, as young integrated field of bio-computational research, and its significance in aquaculture research of Bangladesh. Int. J. Agril. Res. Innov. Tech. 10(2): 137-145, December 2020

scholarly journals Towards Coordinated International Support of Core Data Resources for the Life Sciences

2017 ◽  
Author(s):  
W. Anderson ◽  
R. Apweiler ◽  
A. Bateman ◽  
G.A. Bauer ◽  
H. Berman ◽  
...  
Keyword(s):  
Life Sciences ◽  
Science Program ◽  
Senior Managers ◽  
Scientific Impact ◽  
International Support ◽  
Core Data ◽  
Funding Model ◽  
International Funding ◽  
Strong Consensus

On November 18-19, 2016, the Human Frontier Science Program Organization (HFSPO) hosted a meeting of senior managers of key data resources and leaders of several major funding organizations to discuss the challenges associated with sustaining biological and biomedical (i.e., life sciences) data resources and associated infrastructure. A strong consensus emerged from the group that core data resources for the life sciences should be supported through a coordinated international effort(s) that better ensure long-term sustainability and that appropriately align funding with scientific impact. Ideally, funding for such data resources should allow for access at no charge, as is presently the usual (and preferred) mechanism. Below, the rationale for this vision is described, and some important considerations for developing a new international funding model to support core data resources for the life sciences are presented.

scholarly journals The roles of code in biology

2021 ◽  
Vol 104 (2) ◽  
pp. 003685042110105
Author(s):  
Brendan Lawlor ◽  
Roy D Sleator
Keyword(s):  
Research Team ◽  
Life Science ◽  
Life Sciences ◽  
Three Dimensional ◽  
Science Research ◽  
Computer Code ◽  
Biological Research ◽  
Sweet Spot ◽  
Optimal Outcomes ◽  
Software Engineers

The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the confusion is due in part to a misunderstanding of the function of code when applied to the life sciences. Code has many roles, and in this paper we present a three-dimensional taxonomy to classify those roles and map them specifically to the life sciences. We identify a “sweet spot” in the taxonomy—a convergence where bioinformaticians should concentrate their efforts in order to derive the most value from the time they spend using code. We suggest the use of the “inverse Conway maneuver” to shape a research team so as to allow dedicated software engineers to interface with researchers working in this “sweet spot.” We conclude that in order to address current issues in the use of software in life science research such as reproducibility and scalability, the field must reevaluate its relationship with software engineering, and adapt its research structures to overcome current issues in bioinformatics such as reproducibility, scalability and productivity.

scholarly journals Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 160 ◽  
Author(s):  
David Bousfield ◽  
Johanna McEntyre ◽  
Sameer Velankar ◽  
George Papadatos ◽  
Alex Bateman ◽  
...  
Keyword(s):  
Open Access ◽  
Method Development ◽  
Science Research ◽  
Data Bank ◽  
Biological Data ◽  
Biomedical Literature ◽  
Data Resource ◽  
Grant Applications ◽  
European Nucleotide Archive

Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry.  We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications.

Impact of long-term trials on crop production research and education

2010 ◽  
Vol 58 (Supplement 1) ◽  
pp. 1-5 ◽  
Author(s):  
M. Jolánkai ◽  
F. Nyárai ◽  
K. Kassai
Keyword(s):  
Crop Production ◽  
Life Sciences ◽  
Ecological Models ◽  
Dynamic Databases ◽  
Production Research ◽  
Research And Education

Long-term trials have a twofold role in life sciences, acting as both live laboratories and public collections. Long-term trials are not simply scientific curios or the honoured relics of a museum, but highly valuable live ecological models that can never be replaced or restarted if once terminated or suspended. These trials provide valuable and dynamic databases for solving scientific problems. The present paper is intended to give a brief summary of the crop production aspects of long-term trials.

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

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