Leyla García
A5108009730- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Semantic Web and Ontologies
- Research Data Management Practices
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- scientometrics and bibliometrics research
- COVID-19 diagnosis using AI
- Enzyme Structure and Function
- Biomedical and Engineering Education
- thermodynamics and calorimetric analyses
- Digital Imaging for Blood Diseases
- Advanced Proteomics Techniques and Applications
- Algorithms and Data Compression
- Advanced Biosensing Techniques and Applications
- Environmental Science and Technology
- Data Quality and Management
- Phytoplasmas and Hemiptera pathogens
- vaccines and immunoinformatics approaches
- Open Source Software Innovations
- Evolution and Genetic Dynamics
- Smart Agriculture and AI
- Genomics and Rare Diseases
ZB MED - Information Centre for Life Sciences
2019-2023
European Bioinformatics Institute
2011-2020
Elixir Medical (United States)
2019
Universitat Jaume I
2017-2018
Hague Institute of Private International and Foreign Law
2017
Wellcome Trust
2011-2014
SIB Swiss Institute of Bioinformatics
2014
Florida State University
2013
University of Cape Town
2011-2013
Centre National de la Recherche Scientifique
2013
The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility, interoperability and reusability of digital research objects for both humans machines.Until now principles have been mostly applied data.The ideas behind these are, however, also directly relevant software.Hence there is a distinct need explore how can be software.In this work, we summarize current status debate around software, as basis development community-agreed software future.We discuss what...
Abstract Motivation: Resource description framework (RDF) is an emerging technology for describing, publishing and linking life science data. As a major provider of bioinformatics data services, the European Bioinformatics Institute (EBI) committed to making readily accessible community in ways that meet existing demand. The EBI RDF platform has been developed increasing demand coordinate activities across institute provides new entry point querying exploring integrated resources available...
Abstract The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good stewardship prerequisite reproducibility. Nowadays, guides policy actions professional practices in public private sectors. Despite such endorsements, however, Principles are aspirational, remaining elusive at best, intimidating worst. To address lack of practical guidance, help with capability gaps, we developed Cookbook, an open,...
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does aim to propose new development best practices, but rather provide simple recommendations encourage the adoption of existing practices. Software promote better improves reproducibility reusability research. These are designed around Open Source values, practical suggestions contribute making source code more discoverable,...
Abstract Summary: BioJS is an open-source project whose main objective the visualization of biological data in JavaScript. provides easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes collection components purposely designed to require very simple configuration and installation. In addition programming framework, centralized repository available reutilization by community. Availability implementation:...
ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity relationships this wealth data pose challenge interpretation. Integrative approaches such as provided by are thus essential researchers to understand and, instance, discover patterns affecting function disease associations.ProtVista JavaScript component released an open source project...
Glycoinformatics plays a major role in glycobiology research, and the development of comprehensive glycoinformatics knowledgebase is critical. This application note describes GlyGen data model, processing workflow access interfaces featuring programmatic use case example queries based on specific biological questions. The project integration, harmonization dissemination for carbohydrate glycoconjugate-related retrieved from multiple international sources including UniProtKB, GlyTouCan,...
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors influenced growth user and developer community, outline our strategy building this growth. The lessons have learned may also be relevant to other projects.
BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development has been prompted by growing need for bioinformatics visualisation tools be easily shared, reused discovered. Its modular architecture makes it easy users find specific functionality without needing know how built, while can extended or created implementing new functionality. community developers currently provides range that open access freely...
<ns4:p>The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such needs open research practices sharing outputs, such as data code, thereby facilitating reproducibility beyond borders. The Research Data Alliance Working Group recently published set recommendations guidelines on related best for research. These include clinicians, researchers, policy- decision-makers, funders, publishers, public health experts, disaster...
UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute this with a FAIRness assessment our UniProtKB dataset followed by critical reflection on challenges and future directions adoption validation FAIR principles metrics.
Dasty3 is a highly interactive and extensible Web-based framework. It provides rich Application Programming Interface upon which it possible to develop specialized clients capable of retrieving information from DAS sources as well data providers not using the protocol. significant improvements on previous frameworks implemented 1.6 specification.Dasty3 an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under terms GNU General public license. Source documentation can be found...
FeatureViewer is a BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This highly flexible customizable, allowing the presentation of by rows, all centered, or distributed in non-overlapping tracks. It uses either lines shapes sites rectangles regions. The result powerful visualization tool can be easily integrated into web applications as well documents it provides an export-to-image...
The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such needs open research practices sharing outputs, such as data code, thereby facilitating reproducibility beyond borders. Research Data Alliance Working Group recently published set recommendations guidelines on related best for research. These include researchers, policymakers, funders, publishers infrastructure providers from perspective different domains (Clinical...
A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through computational query. One approach facilitate reuse the scientific structure this information as linked data using standardized web technologies. In paper we present second version Biotea, semantic, open-access subset PubMed Central has been enhanced with specialized annotation pipelines uses existing infrastructure from National Center...
<ns4:p><ns4:bold>Summary: </ns4:bold>FeatureViewer is a BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This highly flexible customizable, allowing the presentation of by rows, all centered, or distributed in non-overlapping tracks. It uses either lines shapes sites rectangles regions. The result powerful visualization tool can be easily integrated into web applications as well documents it provides an export-to-image...
<ns4:p>Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies increasingly becoming primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous remains be developed. The aim this white paper provide a guiding framework future contributions ELIXIR’s recently established <ns4:italic>h</ns4:italic><ns4:italic>uman CNV Community,...