A5060701006- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Fungal and yeast genetics research
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Hepatitis B Virus Studies
- Cytokine Signaling Pathways and Interactions
- Gene expression and cancer classification
- Hepatitis C virus research
- Nematode management and characterization studies
- Hepatitis Viruses Studies and Epidemiology
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Genomics and Rare Diseases
- Evolution and Genetic Dynamics
- Biomedical and Engineering Education
- Psoriasis: Treatment and Pathogenesis
- Liver Disease and Transplantation
- Cell Image Analysis Techniques
- Marine Biology and Ecology Research
- IL-33, ST2, and ILC Pathways
- Research Data Management Practices
- Genetic Associations and Epidemiology
Pfizer (United Kingdom)
2024-2025
European Bioinformatics Institute
2014-2022
Open Targets
2021
Wellcome Trust
2020
University of Cambridge
2009-2012
Natural History Museum
2006
National Oceanography Centre
2006
University of Southampton
2006
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by either curated from the literature or direct depositions. has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool now utilized multiple additional teams, all whom annotate directly into database. Members team supply appropriate levels training, perform quality control on entries take...
Abstract The current wealth of genomic variation data identified at nucleotide level presents the challenge understanding by which mechanisms amino acid affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in development disease. Physical interactions molecules are linking steps underlying most, if not all, Understanding that sequence has on a molecule’s is key step towards connecting mechanistic characterization...
The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of interactions, derived from the scientific literature and direct data depositions. As August 2021, provides more than one million binary by twelve global partners International Molecular Exchange consortium, for which shared curation dissemination platform. IMEx policy has always emphasised fine-grained model, aiming to capture relevant experimental detail essential interpretation provided data....
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database that collates and summarizes information on stable, macromolecular complexes of known function. It captures complex composition, topology function links out to large range domain-specific resources hold more detailed data, such as PDB or Reactome. We have made several significant improvements since our last update, including improving compliance the FAIR data principles by providing...
The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/ complex), through which protein complexes from major model organisms are being collated and made available for search, viewing download.It been built in close collaboration with other bioinformatics services populated data ChEMBL, MatrixDB, PDBe, Reactome UniPro-tKB.Each entry contains information about participating molecules (including small...
Abstract There are thousands of distinct disease entities and concepts, each which known by different sometimes contradictory names. The lack a unified system for managing these poses major challenge both machines humans that need to harmonize information better predict causes treatments disease. Mondo Disease Ontology is an open, community-driven ontology integrates key medical biomedical terminologies, supporting data integration improve diagnosis, treatment, translational research....
Tunisia is a medium-level epidemic country for hepatitis B virus (HBV). This study characterizes, the first time, full genome HBV strains from Tunisia. Viral load quantification and phylogenetic analyses of or pre-S/S sequences were performed on 196 surface antigen (HBsAg)-positive plasma samples Tunisian blood donors. The median viral was 64.65 IU ml(-1) (range<5-7.7x10(8) ml(-1)) 89% had loads below 10,000 ml(-1). Fifty-nine formed novel subgenotype D7, 41 clustered in D1, seven A2 one...
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from range model organisms. It summarizes complex composition, topology and along links to large domain-specific resources (i.e. wwPDB, EMDB Reactome). Since the last update in 2019, we have produced first draft complexome for Escherichia coli, maintained updated that Saccharomyces cerevisiae, added over 40 coronavirus increased human 1100 include...
Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order effectively achieve this goal, it is critical that researchers have high quality datasets available them, in standard format, also suite tools with which analyse such form experimentally testable hypotheses from them. The PSI-MI XML interchange format was initially published 2004, expanded 2007 enable download data. PSI-XML2.5 designed describe...
Abstract The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome (SARS-CoV)-2, has spurred a wave research nearly unprecedented scale. Among different strategies that are being used to understand and develop effective treatments, study physical molecular interactions can provide fine-grained resolution mechanisms behind virus biology human organism response. We present curated dataset focused on proteins from SARS-CoV-2, SARS-CoV-1 other...
Background and Objectives Hepatitis E virus (HEV) infection is emerging as a potential new threat to blood safety after several cases of transfusion–transmission were reported from non‐epidemic countries. On the basis seroprevalence data, HEV endemic in Ghana where poor sanitary conditions regular flooding are prevalent. However, no data available for prevalence donors. Materials Methods Plasma samples 239 Ghanaian donors tested anti‐HEV IgG IgM by ELISA (two three assays, respectively)...
Abstract The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending number complexes, we have massively extended coverage human complexome through incorporation high confidence assemblies predicted by machine-learning algorithms trained large-scale experimental...
Summary. Malaysia is a medium endemic country for hepatitis B virus (HBV) infection but little known about HBV strains circulating in Malaysian blood donors. Viral load, HBsAg concentrations and nested PCR products from 84 surface antigen (HBsAg) positive samples were analysed detail. Median viral load was 3050 IU/mL median 1150 IU/mL. Fifty-six full genome, 20 pre-S/S, 1 S gene six basic core promoter/precore-only sequences obtained. Genotypes C present at ratio of 2:1, two genotype D...
The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well processing pipelines tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. aim this project, funded by the Alzheimer’s Research United Kingdom (ARUK) foundation led University College London (UCL) biocuration team, was enhance GO developing new neurological terms, use terms annotate products associated with dementia....
Proteins frequently function as parts of complexes, assemblages multiple proteins and other biomolecules, yet network visualizations usually only show binary interactions. ComplexViewer visualizes interactions with more than two participants thereby avoids the need to first expand these into Furthermore, if binding regions between molecules are known then can be displayed in context larger complex.freely available under Apache version 2 license; EMBL-EBI Complex Portal:...
The domain of transcription regulation has been notoriously difficult to annotate in the Gene Ontology, partly because intricacies gene which involve molecular interactions with DNA as well amongst protein complexes. function 'transcription coregulator activity' is a part biological process 'regulation transcription, DNA-templated' that occurs cellular component 'chromatin'. It can mechanistically link sequence-specific DNA-binding factor (dbTF) regulatory target sites coactivator and...
Proteins seldom function individually. Instead, they interact with other proteins or nucleic acids to form stable macromolecular complexes that play key roles in important cellular processes and pathways. One of the goals Saccharomyces Genome Database (SGD; www.yeastgenome.org) is provide a complete picture budding yeast biological processes. To this end, we have collaborated Molecular Interactions team provides Complex Portal database at EMBL-EBI manually curate complexome. These data, from...
Abstract The EMBL-EBI Complex Portal is a knowledgebase of macromolecular complexes providing persistent stable identifiers. Entries are linked to literature evidence and provide details complex membership, function, structure complex-specific Gene Ontology annotations. Data freely available downloadable in HUPO-PSI community standards missing entries can be requested for curation. In collaboration with Saccharomyces Genome Database UniProt, the yeast complexome, compendium all known...
A number of different molecular interactions data download formats now exist, designed to allow access these valuable by diverse user groups. These include the PSI-XML and MITAB standard interchange developed Molecular Interaction workgroup HUPO-PSI in addition other, use-specific downloads produced other resources. The onus is currently on ensure that a piece software capable read/writing all necessary versions each format. This problem may increase, as providers strive meet ever more...