27 papers · ranked by Valyu relevance
Mikołaj Danielewski, Marlena Szalata, Jan Krzysztof Nowak, Jarosław Walkowiak + 3 more
With the development of genome sequencing technologies, the amount of data produced has greatly increased in the last two decades. The abundance of digital sequence information (DSI) has provided research opportunities, improved our understanding of the genome, and led to the discovery of new solutions in industry and…
Gerda Cristal Villalba, Ursula Matte
Public databases are essential to the development of multi-omics resources. The amount of data created by biological technologies needs a systematic and organized form of storage, that can quickly be accessed, and managed. This is the objective of a biological database. Here, we present an overview of human databases…
Shahid Ullah, Wajeeha Rahman, Farhan Ullah, Gulzar Ahmad + 2 more
'Muhmmad Ijaz' 'Tianshun Gao'] Background: The achievement of the human genome project provides a basis for the systematic study of the human genome from evolutionary history to disease-specific medicine. With the explosive growth of biological data, a growing number of biological databases are being established to…
Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori + 3 more
'Rafael Berlanga-Llavori' 'Paolo Perlasca' 'Giorgio Valentini' 'David Manset'] Background The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for…
Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery + 7 more
The volume of biological database records is growing rapidly, populated by complex records drawn from heterogeneous sources. A specific challenge is duplication, that is, the presence of redundancy (records with high similarity) or inconsistency (dissimilar records that correspond to the same entity). The…
A. C. Gorakshakar, K. Ghosh
Bioinformatics is a relatively new discipline. It is a field of science in which Computer science, Mathematics, Molecular biology and Information technology merges to form a single discipline. Database development, sequence alignment, protein structure prediction, RNA folding, evolutionary tree construction are some of…
Rosalia Moreddu
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for research. Traditional static databases have been invaluable in providing standardized…
Heidi J. Imker
Online resources enable unfettered access to and analysis of scientific data and are considered crucial for the advancement of modern science. Despite the clear power of online data resources, including web-available databases, proliferation can be problematic due to challenges in sustainability and long-term…
Raja A. Moftah, Abdelsalam M. Maatuk, Richard White
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased…
Nicos Angelopoulos, Jan Wielemaker
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer in this area. Here, we detail advances that highlight two of the strengths of…
Edvard Pedersen, Lars Ailo Bongo
Up-to-date meta-databases are vital for the analysis of biological data. However, the current exponential increase in biological data leads to exponentially increasing meta-database sizes. Large-scale meta-database management is therefore an important challenge for production platforms providing services for biological…
Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook + 4 more
'Uğis Sarkans' 'Ardan Patwardhan' 'Alvis Brāzma' 'Ewan Birney'] Public data archives are the backbone of modern biological and biomedical research. While archives for biological molecules and structures are well-established, resources for imaging data do not yet cover the full range of spatial and temporal scales or…
Michael J. Bell, Phillip Lord
As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that data percolates between different databases, which causes particular concerns…
SA Kirov, X Peng, E Baker, D Schmoyer + 2 more
Background The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a…
Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M. Good + 20 more
Wikidata is a community-maintained knowledge base that epitomizes the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. Here, we describe the breadth and depth of biomedical knowledge contained within Wikidata, assembled from primary knowledge repositories on genomics, proteomics…
Tamer Gur
Due to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manual or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the…
Charles Tapley Hoyt, Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llaó + 12 more
The integration of heterogeneous, multiscale, and multimodal knowledge and data has become a common prerequisite for joint analysis to unravel the mechanisms and aetiologies of complex diseases. Because of its unique ability to capture this variety, Biological Expression Language (BEL) is well suited to be further used…
Michael J. Bell, Matthew Collison, Phillip Lord
A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge. Many databases reuse existing knowledge, during the curation process…
Christopher Southan
This article assesses a key aspect of data sharing that has the potential to accelerate the progress and impact of medicinal chemistry. To achieve this the community needs to increase the outward flow of experimental results locked-up in millions of published PDFs into structured open databases that explicitly capture…
José J. Naveja-Romero, Fernanda I. Saldívar-González, Diana L. Prado-Romero, Angel J. Ruiz-Moreno + 3 more
The manuscript discusses recent advances on computer-aided drug discovery (CADD) with focus on data-dependent drug discovery. Herein, we do not intend to review the many CADD methodologies comprehensively. Instead, the review discusses progress on selected concepts, methodologies, resources, and applications that are…
Tiqing Liu, Linda Hwang, Stephen K Burley, Carmen I Nitsche + 3 more
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models, and computational chemistry…
Alejandro Gómez-García, Daniel A. Acuña Jiménez, William J. Zamora, Haruna L. Barazorda-Ccahuana + 12 more
Natural product (NP) databases are crucial tools in computer-aided drug design (CADD). Over the last decade, there has been a worldwide effort to assemble information regarding natural products (NPs) isolated and characterized in certain geographical regions. In 2023, it was published LANaPDB, to our knowledge, it is…
Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan + 10 more
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl “Core” database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome…
Christopher Southan
This report covers academic small-molecule drug development with a view to distilling guidelines. The first section covers research productivity feeding into commercial development before reviewing the literature on statistics of academic development It then considers differences between probes and drugs before…
Christopher Southan
This report covers academic small-molecule drug development with a view to distilling guidelines. The first section covers research productivity feeding into commercial development before reviewing the literature on statistics of academic development It then considers differences between probes and drugs before…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Dionisio A. Olmedo, Armando A. Durant-Archibold, José Luis López-Pérez, Jose L. Medina-Franco
Chemical libraries and compound data sets are among the main inputs to start the drug discovery process at universities, research institutes, and the pharmaceutical industry. The approach used in the design of compound libraries, the chemical information they possess, and the representation of structures, play a…