A5042870272- Research Data Management Practices
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Data Quality and Management
- Bioinformatics and Genomic Networks
- Neurobiology and Insect Physiology Research
- Artificial Intelligence in Healthcare and Education
- COVID-19 diagnosis using AI
- Cell Image Analysis Techniques
- Social Media in Health Education
- Data Mining Algorithms and Applications
- Big Data and Business Intelligence
- AI in cancer detection
- Nerve injury and regeneration
- Silk-based biomaterials and applications
- Insect symbiosis and bacterial influences
- Cerebrovascular and Carotid Artery Diseases
- Gene expression and cancer classification
- Topic Modeling
- Viral Infectious Diseases and Gene Expression in Insects
- Insect Resistance and Genetics
- COVID-19 and healthcare impacts
University of Oxford
2016-2023
University of Leeds
2019
University of Cambridge
2008-2019
California Institute of Technology
2014
University of Missouri
2014
Carnegie Department of Plant Biology
2014
National Center for Biotechnology Information
2014
Technical University of Munich
2014
Harvard University
2008-2013
University of Birmingham
2006-2008
FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes wild-type gene products: their molecular function, the biological processes in which they play role, subcellular location. This article describes recent changes GO annotation strategy that improving quality data. Many these stem from our participation Reference Genome Annotation Project--a multi-database collaboration producing comprehensive...
FlyBase (http://flybase.org) is the leading database and web portal for genetic genomic information on fruit fly Drosophila melanogaster related species. Whether you use as an experimental system or want to apply biological knowledge another field of study, can help successfully navigate wealth available data. Here, we review site with novice less-experienced users in mind point out recent developments stemming from availability genome-wide data modENCODE project. The first section this...
FlyBase (http://flybase.org) is the leading website and database of Drosophila genes genomes. Whether you are using fruit fly melanogaster as an experimental system or wish to understand biological knowledge in relation human disease other model systems, can help successfully find information looking for. Here, we demonstrate some our more advanced searching systems highlight new tools for wealth data on FlyBase. The first section explores gene function FlyBase, TermLink tool search with...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
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...
BioSharing (http://www.biosharing.org) is a manually curated, searchable portal of three linked registries. These resources cover standards (terminologies, formats and models, reporting guidelines), databases, data policies in the life sciences, broadly encompassing biological, environmental biomedical sciences. Launched 2011 built by same core team as successful MIBBI portal, harnesses community curation to collate cross-reference across sciences from around world. makes these findable...
Abstract Transparent evaluations of FAIRness are increasingly required by a wide range stakeholders, from scientists to publishers, funding agencies and policy makers. We propose scalable, automatable framework evaluate digital resources that encompasses measurable indicators, open source tools, participation guidelines, which come together accommodate domain relevant community-defined FAIR assessments. The components the are: (1) Maturity Indicators – community-authored specifications...
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These meant replace biocurators, instead assist them in one or more curation steps. To do so, the user interface is an important aspect that needs be considered for tool adoption. The BioCreative Interactive task (IAT) a track designed exploring user-system interactions, promoting development of useful TM tools, providing...
Neurotrophic interactions occur in Drosophila, but to date, no neurotrophic factor had been found. Neurotrophins are the main vertebrate secreted signalling molecules that link nervous system structure and function: they regulate neuronal survival, targeting, synaptic plasticity, memory cognition. We have identified a flies, Drosophila Neurotrophin (DNT1), structurally related all known neurotrophins highly conserved insects. By investigating with genetics consequences of removing DNT1 or...
The breadth and depth of biomedical literature are increasing year upon year. To keep abreast these increases, FlyBase, a database for Drosophila genomic genetic information, is constantly exploring new ways to mine the published increase efficiency accuracy manual curation automate some aspects, such as triaging entity extraction. Toward this end, we present 'tagtog' system, web-based annotation framework that can be used mark up biological entities (such genes) concepts Gene Ontology...
Gene ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It time-consuming and labor-intensive task, thus often considered as one of the bottlenecks in literature curation. There growing need semiautomated or fully automated GO curation techniques that will help database curators to rapidly accurately identify information full-length Despite multiple attempts past, few studies have proven be useful with...
Gene function curation via Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification GO terms and supporting information from full text. However, few systems delivered an accuracy that comparable with humans. One recognized challenge developing such lack marked sentence-level evidence text provides basis for making...
Abstract Background Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach improve way which FlyBase curators navigate an article. In paper, we discuss how observing at work informed design and evaluation of PaperBrowser. Then, present appraise PaperBrowser's...
Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in form that is human-readable, programatically accessible and can be used to group annotations biologically meaningful ways. Accurate manual annotation requires clear textual definitions terms. grouping fruitful programatic usage require high-quality formal automate classification. The Drosophila phenotype ontology (DPO) has been annotate over 159,000 FlyBase date,...
Abstract Transparent evaluations of FAIRness are increasingly required by a wide range stakeholders, from scientists to publishers, funding agencies and policy makers. We propose scalable, automatable framework evaluate digital resources that encompasses measurable indicators, open source tools, participation guidelines, which come together accommodate domain relevant community-defined FAIR assessments. The components the are: (1) Maturity Indicators - community-authored specifications...
ABSTRACT The use of community-driven metadata standards, such as minimal information guidelines, terminologies, formats/models, is essential to ensure that data and other digital research outputs are Findable, Accessible, Interoperable, Reusable, according the FAIR principles. As with types assets, standards also need be FAIR. Their discoverability accessibility ensured by BioSharing, most comprehensive resource interlinked repositories policies, available in life, environmental biomedical...
<ns3:p><ns3:bold>Background: </ns3:bold>Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, be unaware biocuration career path or because is only part their role. The lack clear, up-to-date profile creates challenges for organisations like ELIXIR, ISB GOBLET to systematically support biocurators themselves develop own careers. Therefore, ELIXIR Training Platform launched an Implementation Study in order i) identify...
The FAIR principles articulate the behaviors expected from digital artifacts that are Findable, Accessible, Interoperable and Reusable by machines people. Although now widely accepted, Principles design do not explicitly consider actual implementation choices enabling behaviors. As different communities have their own, often well-established preferences priorities for data reuse, coordinating a broadly used approach remains global challenge. In an effort to accelerate broad community...
Thousands of community-developed (meta)data guidelines, models, ontologies, schemas and formats have been created implemented by several thousand data repositories knowledge-bases, across all disciplines. These resources are necessary to meet government, funder publisher expectations greater transparency access preservation related research publications. This obligates researchers ensure their is FAIR, share using the appropriate standards, store in sustainable community-adopted...
Abstract In this modern, data-driven age, governments, funders and publishers expect greater transparency reuse of research data, as well access to preservation the data that supports findings. Community-developed standards, such those for identification 1 reporting 2 underpin reproducible reusable research, aid scholarly publishing, drive both discovery evolution scientific practice. The number these standardization efforts, driven by large organizations or at grass root level, has been on...