A5008629865- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Research Data Management Practices
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Banana Cultivation and Research
- Gene expression and cancer classification
- Genomics and Rare Diseases
- Data Quality and Management
- Topic Modeling
- Cell Image Analysis Techniques
- Academic Publishing and Open Access
- Computational Drug Discovery Methods
- Cancer Genomics and Diagnostics
- Cleft Lip and Palate Research
- Data Mining Algorithms and Applications
- Cancer Research and Treatments
- Protein Tyrosine Phosphatases
- Biofuel production and bioconversion
- Mycorrhizal Fungi and Plant Interactions
- Plant Pathogens and Fungal Diseases
- Biomedical and Engineering Education
- Advanced Text Analysis Techniques
European Bioinformatics Institute
2016-2025
Wellcome Trust
2017-2025
Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier
2016-2018
Université de Montpellier
2018
Centre National de la Recherche Scientifique
2018
RedBite (United Kingdom)
2016-2017
Institut de Recherche pour le Développement
2017
Institut de Recherche pour le Développement
2017
Norwegian University of Science and Technology
2010-2014
Tamil Nadu Government Dental College and Hospital
2012
Supplementary data are available at Bioinformatics online.
Abstract Europe PMC (https://europepmc.org) is a database of research articles, including peer reviewed full text articles and abstracts, preprints - all freely available for use via website, APIs bulk download. This article outlines new developments since 2017 where work has focussed on three key areas: (i) added to its core content include life science preprint abstracts special collection COVID-19-related preprints. unique as an aggregator biomedical alongside peer-reviewed with over 180...
Europe PMC (https://europepmc.org) is a comprehensive resource of biomedical research publications that offers advanced tools for search, retrieval, and interaction with the scientific literature. This article outlines new developments since 2014. In addition to delivering core database services, focuses on three areas development: individual user data integration, infrastructure support text mining. now provides accounts save search queries claim ORCIDs, as well open access profiles authors...
Abstract Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts 9 full text accessible via the website, APIs bulk download. This publication outlines new developments to platform since last update in 2020 (1) focuses on five main areas. (i) Improving discoverability, reproducibility trust preprints by indexing preprint content, enriching metadata identifying withdrawn removed preprints. (ii)...
Abstract Summary The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionise drug discovery by extracting evidence from scientific literature for target identification validation. This novel framework combines Named Entity Recognition (NER) identifying gene/protein (target), disease, organism, chemical/drug within texts, entity normalisation map these entities databases like Ensembl, Experimental Factor Ontology...
Abstract Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use logics ontologies ranges from sound modelling to practical querying that knowledge, thus adding a considerable value. We conceive reasoning on bio-ontologies as semi-automated process three steps: (i) defining logic-based representation language; (ii) building consistent ontology using and (iii) exploiting through querying. Results: Here, we report how implemented...
The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionise drug discovery by extracting evidence from scientific literature for target identification validation. This novel framework combines Named Entity Recognition (NER) identifying genes/proteins, diseases, organisms, chemicals/drugs within texts, entity normalisation map these entities databases like Ensembl, Experimental Factor Ontology (EFO), ChEMBL....
More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying browsing terms, visualization of parts ontology graphs is rather limited inflexible. We created OLSVis web application, a visualiser all in database. shows customisable subgraphs ontologies. Subgraphs animated via real-time force-based layout algorithm which fully interactive: each time user makes...
<ns4:p>The tremendous growth in biological data has resulted an increase the number of research papers being published. This presents a great challenge for scientists searching and assimilating facts described those papers. Particularly, databases depend on curators to add highly precise useful information that are usually extracted by reading articles. Therefore, there is urgent need find ways improve linking literature underlying data, thereby minimising effort browsing content identifying...
In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop interoperability guidelines. Interoperability is ability two or more systems devices cooperate exchange data, interpret that shared information. growing concern scientific agriculture in general, as need deluge obtained through high-throughput technologies grows. Agreeing on common formats, metadata, vocabulary standards an important step obtain required level order...
<ns4:p>Biological databases are fundamental to biological research and discovery. Database curation adds highly precise useful information, usually extracted from the literature through experts reading articles. The significant amount of time effort put in by curators, against backdrop tremendous data growth, makes manual a high value task. Therefore, there is an urgent need find ways scale efforts improving integration, linking underlying data.</ns4:p><ns4:p> As part development Europe PMC,...
Recent advances in high-throughput technologies have resulted a tremendous increase the amount of omics data produced plant science. This increase, conjunction with heterogeneity and variability data, presents major challenge to adopt an integrative research approach. We are facing urgent need effectively integrate assimilate complementary datasets understand biological system as whole. The Semantic Web offers for integration heterogeneous their transformation into explicit knowledge thanks...
Named entity recognition (NER) is a widely used text-mining and natural language processing (NLP) subtask. In recent years, deep learning methods have superseded traditional dictionary- rule-based NER approaches. A high-quality dataset essential to fully leverage advancements. While several gold-standard corpora for biomedical entities in abstracts exist, only few are based on full-text research articles. The Europe PMC literature database routinely annotates Gene/Proteins, Diseases,...
<ns3:p>In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop interoperability guidelines. Interoperability is ability two or more systems devices cooperate exchange data, interpret that shared information. growing concern scientific agriculture in general, as need deluge obtained through high-throughput technologies grows. Agreeing on common formats, metadata, vocabulary standards an important step obtain required level...
The biosciences increasingly face the challenge of integrating a wide variety available data, information and knowledge in order to gain an understanding biological systems. Data integration is supported by diverse series tools, but lack consistent terminology label these data still presents significant hurdles. As consequence, much remains disconnected or worse: becomes misconnected. need address this problem has spawned building large number bio-ontologies. OBOF, RDF OWL are among most...
The European Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources public biomolecular data. Based at Wellcome Genome Campus in Hinxton, UK, EMBL-EBI six sites Laboratory, Europe's only intergovernmental life sciences organization. This overview summarizes latest developments services that data resources provide to scientific communities globally (https://www.ebi.ac.uk/services).
Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which patterns and dynamics 'omics' can be interpreted. The background information required construction such is often dispersed across multitude bases in variety formats. seamless integration this one main challenges bioinformatics. Semantic Web offers powerful technologies assembly integrated that are computationally comprehensible,...
In the recent years, data deluge in many areas of scientific research brings challenges treatment and improvement agricultural data. Research bioinformatics field does not outside this trend. This paper presents some approaches aiming to solve Big Data problem by combining increase semantic search capacity on existing plant laboratories. helps us strengthen user experiments obtained infering new knowledge. To achieve this, there exist several having different characteristics using platforms....
<ns4:p><ns4:bold>Background:</ns4:bold> Manual curation is a cornerstone of public biological data resources. However, it time-consuming process that urgently needs supportive technical solutions in the face rapid growth. Supporting scalable part mission Elixir Data Platform. Thus far, we have established infrastructure capable ingesting and aggregating text-mined outputs from multiple providers making these available via an API. This API used by Europe PMC to display specific entities...
Abstract Motivation Life science research in academia, industry, agriculture, and the health sector depends critically on free open data resources. ELIXIR ( www.elixir-europe.org ), European Research Infrastructure for life sciences data, has identified a set of Core Data Resources within Europe that are most fundamental importance long-term preservation biological data. We explore characteristics their usage, impact assured funding horizon to assess value as an infrastructure, understand...
Abstract Recent advances in high-throughput technologies have resulted a tremendous increase the amount of omics data produced plant science. This increase, conjunction with heterogeneity and variability data, presents major challenge to adopt an integrative research approach. We are facing urgent need effectively integrate assimilate complementary datasets understand biological system as whole. The Semantic Web offers for integration heterogeneous their transformation into explicit...
The vast amounts of knowledge in the biomedical domain have paved way for a new paradigm biological research called Systems Biology, essentially an approach that relies on integration all available system single model. This promotes comprehensive understanding systems, driven by data and mathematical modelling. However, sheer volume, variation complexity current pose number hurdles management need to be overcome. Semantic Web offers various solutions these challenges. With our initiative,...