Claire O’Donovan
A5066278201- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Scientific Computing and Data Management
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Enzyme Structure and Function
- Computational Drug Discovery Methods
- Traditional Chinese Medicine Studies
- Natural Language Processing Techniques
- Semantic Web and Ontologies
- Molecular Biology Techniques and Applications
- Nutritional Studies and Diet
- Mass Spectrometry Techniques and Applications
- Research Data Management Practices
- Microbial Natural Products and Biosynthesis
- Enzyme Catalysis and Immobilization
- Consumer Attitudes and Food Labeling
- Protein Structure and Dynamics
Dalhousie University
2025
European Bioinformatics Institute
2015-2024
Wellcome Trust
2008-2021
Fiona Stanley Hospital
2019
Open Targets
2016
SIB Swiss Institute of Bioinformatics
2012-2014
Georgetown University
2012-2014
Georgetown University Medical Center
2014
Heidelberg Institute for Theoretical Studies
2013
Wellcome Sanger Institute
2008-2012
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, Swiss-Prot, TrEMBL PIR database activities have united to form Universal Protein Knowledgebase (UniProt) consortium. Our mission is comprehensive, fully classified, richly accurately annotated sequence knowledgebase, extensive cross-references query interfaces. The central will two sections, corresponding familiar Swiss-Prot (fully manually curated entries)...
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in Life Sciences. Each entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features sometimes even contradictory conclusions. Detailed expertise that goes beyond scope is made available via direct links to specialised databases. annotated entries for all species,...
Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic manual GO annotations provided by Consortium annotation groups has been popular browser for many years, but after recent redevelopment it now able to offer greater range facilities including bulk downloads data which can be extensively filtered different parameters slim set generation.
The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references querying interfaces freely accessible the scientific community. UniProt produced Consortium which consists groups from European Bioinformatics Institute (EBI), Swiss (SIB) Information (PIR). comprised four major components, each optimized for...
MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The cross-species cross-technique it covers metabolite structures reference spectra as well biological roles locations. the recommended repository number of leading journals ELIXIR, European infrastructure life science information. In this article, we describe significant updates that have made over last two years to resource respond increasing amount diversity being submitted by...
The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual provided by curators are supplemented manual and automatic from model organism databases specialist annotation groups. GOA currently supplies 368 million GO almost 54 more than 480,000 taxonomic now five times number of it did 4 years ago. As a member Consortium, we adhere most up-to-date Consortium-agreed guidelines via...
The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of (GO) terms to UniProt Knowledgebase (UniProtKB) entries. Annotations created by are collated with annotations from external databases provide an extensive, publicly available GO annotation resource. Currently covering over 160 000 taxa, greater than 32 million annotations, GOA remains largest most comprehensive open-source contributor...
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over past year, GOC has implemented several processes to increase quantity, quality and specificity GO annotations. First, number manual, literature-based annotations grown at an increasing rate. Second, as result new 'phylogenetic annotation' process, manually reviewed, homology-based...
We have designed and developed a data integration visualization platform that provides evidence about the association of known potential drug targets with diseases. The is to support identification prioritization biological for follow-up. Each target linked disease using integrated genome-wide from broad range sources. either target-centric workflow identify diseases may be associated specific target, or disease-centric disease. Users can easily transition between these target- workflows....
The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 proteins in more than 360,000 taxa, this has increased 2-fold last 2 years benefited wealth checks improve correctness consistency as well now greater information content enabled format developments. Detailed, manual obtained...
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of International Genome Sequencing (IRGSP), manually curated annotation sequence, and other genomics information that could be useful for comprehensive understanding rice biology. Since last publication RAP-DB, IRGSP has been revised reassembled. In addition, a large number rice-expressed tags have released, functional resources produced worldwide. Thus, we thoroughly updated our by manual...
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) UniProt. two teams have developed semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, all protein chains PDB entries present database. This carried out every weekly release stored SIFTS includes cross-references other biological resources such as Pfam, SCOP, CATH, GO,...
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts/) was established in 2002 continues to operate as a collaboration between the Protein Data Bank Europe (PDBe; http://pdbe.org) UniProt Knowledgebase (UniProtKB; http://uniprot.org). is instrumental transfer of annotations protein structure sequence resources through provision up-to-date residue-level mappings entries from PDB UniProtKB. SIFTS also incorporates other biological resources,...
Abstract MetaboLights is a global database for metabolomics studies including the raw experimental data and associated metadata. The cross-species cross-technique covers metabolite structures their reference spectra as well biological roles locations where available. recommended repository number of leading journals ELIXIR, European infrastructure life science information. In this article, we describe continued growth diversity submissions significant developments in recent years....
Abstract Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over past decade, majority acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect library, consisting 87,916 annotated derived from hundreds millions originating published experiments. Entries this or “suspects,” were that could be linked molecular network to an spectrum....
The human genome sequence defines our inherent biological potential; the realization of biology encoded therein requires knowledge function each gene. Currently, in this area is still limited. Several lines investigation have been used to elucidate structure and genes genome. Even so, gene prediction remains a difficult task, as varieties transcripts may vary great extent. We thus performed an exhaustive integrative characterization 41,118 full-length cDNAs that capture complete functional...
SWISS-PROT is a curated protein sequence database which strives to provide high level of annotation (such as the description function protein, its domain structure, post-translational modifications, variants, etc.), minimal redundancy and integration with other databases. Together automatically annotated supplement TrEMBL, it provides comprehensive high-quality view current state knowledge about proteins. Ongoing developments include further improvement functional automatic in databases...
We present here the annotation of complete genome rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions identified or inferred in 19,969 (70%) proteins, 131 possible npRNAs (including 58 antisense transcripts) found. Almost 5000 annotated protein-coding genes found to be disrupted insertional mutant lines, which will accelerate future experimental validation annotations....
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. number GO annotations products has increased due to curation efforts among Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. ontologies continue expand improve as result targeted ontology development, introduction computable logical definitions...
Abstract The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). UniProt Web site receives ∼400,000 unique visitors per month the primary means to access UniProt. Along with various datasets that you can search, provides three main tools. These are ‘BLAST’ tool similarity searching, ‘Align’ multiple alignment, ‘Retrieve/ID Mapping’ using list of identifiers retrieve UniProtKB proteins convert database from...
Experimental data exists for only a vanishingly small fraction of sequenced microbial genes. This community page discusses the progress made by COMBREX project to address this important issue using both computational and experimental resources.
Metabolomics is the comprehensive study of a multitude small molecules to gain insight into an organism's metabolism. The research field dynamic and expanding with applications across biomedical, biotechnological, many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, repositories, analysis tools. However, rapid progress resulted in mosaic independent, sometimes incompatible, methods that are difficult connect useful...