A5080598287- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Data Quality and Management
- Service-Oriented Architecture and Web Services
- Advanced Text Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Topic Modeling
- Natural Language Processing Techniques
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Healthcare Systems and Public Health
- Species Distribution and Climate Change
- Data-Driven Disease Surveillance
- Advanced Database Systems and Queries
- Machine Learning in Bioinformatics
- Electronic Health Records Systems
- Genomics and Rare Diseases
- HIV Research and Treatment
- Wastewater Treatment and Nitrogen Removal
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- HIV/AIDS drug development and treatment
Rothamsted Research
2024
University of New Brunswick
2014-2023
University of Calgary
2021
RELX Group (Netherlands)
2017
McGill University
2015
Yale University
2014
Concordia University
2005-2011
SIB Swiss Institute of Bioinformatics
2011
Institute for Infocomm Research
2007-2008
Iogen Corporation
2001
The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description arbitrary (real, hypothesized, virtual, fictional) objects, processes their attributes. specifies design patterns describe associate qualities, capabilities, functions, quantities, informational entities including textual, geometrical, mathematical entities, provides specific extensions...
Organizational structure for the proposed IsoBank. A central executive group would oversee four subcommittees (SC): Information technology, integrative disciplinary, education and training, analytical expertise. GNIP, Global Network of Isotopes in Precipitation; IAEA, International Atomic Energy Association; QA/QC, quality assurance/quality control.
Competitions in text mining have been used to measure the performance of automatic processing solutions against a manually annotated gold standard corpus (GSC). The preparation GSC is time-consuming and costly final consists at most few thousand documents with limited set semantic groups. To overcome these shortcomings, CALBC project partners (PPs) produced large-scale biomedical four different groups through harmonisation annotations from solutions, first version Silver Standard Corpus...
Abstract Motivation: Semantic tagging of organism mentions in full-text articles is an important part literature mining and semantic enrichment solutions. Tagged also play a pivotal role disambiguating other entities text, such as proteins. A high-precision system must be able to detect the numerous forms mentions, including common names well traditional taxonomic groups: genus, species strains. In addition, resolve abbreviations acronyms, assign scientific name if possible link detected...
The indexing of scientific literature and content is a relevant contemporary requirement within life science information systems. Navigating available in legacy formats continues to be challenge both enterprise academic domains. emergence semantic web technologies their fusion with artificial intelligence techniques has provided new toolkit which address these data integration challenges. In the emerging field lipidomics such navigation challenges are barriers translation results into...
The trait approach has already indicated significant potential as a tool in understanding natural variation among species sensitivity to contaminants the process of ecological risk assessment. However, realize its full potential, defined nomenclature for traits is urgently required, and effort required populate databases species-trait relationships. Recently, there have been advances area information management discovery semantic web. Combined with continuing progress biological knowledge,...
Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation systems. Protein mutations and their impacts on protein properties are hidden scientific literature, making them poorly accessible for engineers inaccessible phenotype-prediction systems that currently depend manually curated genomic variation databases.We present first rule-based approach properties, categorizing directionality as positive, negative or neutral. Furthermore mentions grounded to...
Threatened freshwater ecosystems urgently require improved tools for effective management. Food web analysis is currently under-utilised, yet can be used to generate metrics support biomonitoring assessments by measuring the stability and robustness of ecosystems. Using a previously developed pipeline, we combined taxonomic outputs from DNA metabarcoding with text-mining routine extract trait information directly literature. This pipeline allowed us heuristic food webs sites within lower...
Malaria is a leading cause of death in Africa. Many organizations, NGO's, and government agencies are collaborating to prevent, control, eliminate malaria. In order succeed these shared goals, an integrated, consistent knowledge source empower informed decision-making required. surveillance currently performed using dynamic, interconnected, systems which require rapid data exchange between different platforms. An important challenge must overcome the occurrence dynamic changes one or more...
<ns3:p>Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used the life sciences, though their composition has remained a cumbersome manual process due to lack standards for annotation, assembly, and implementation. Recent technological advances returned long-standing vision workflow into focus.</ns3:p><ns3:p> This article summarizes recent Lorentz Center workshop dedicated sciences. We survey...
Abstract Background The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, deposited numerous online databases. Unfortunately, efforts annotate, classify, analyze these chemical entities have largely remained the hands human curators using manual or semi-automated protocols, leaving many novel unclassified. Since function is often closely linked structure, accurate structure-based...
Clinical Intelligence, as a research and engineering discipline, is dedicated to the development of tools for data analysis purposes clinical research, surveillance, effective health care management. Self-service ad hoc querying one desirable type functionality. Since most are currently stored in relational or similar form, problematic it requires specialised technical skills knowledge particular schemas.A possible solution semantic where user formulates queries terms domain ontologies that...
Abstract Objectives Automatic job coding tools were developed to reduce the laborious task of manually assigning codes based on free-text descriptions in census and survey data sources, including large occupational health studies. The objective this study is provide a case comparative performance JEM (Job-Exposure Matrix)-assigned exposures agreement using existing tools. Methods We compared three automatic [AUTONOC, CASCOT (Computer-Assisted Structured Coding Tool), LabourR], which selected...
Summary Recently it has been demonstrated that the single‐copy malate synthase (MS) and isocitrate lyase (ICL) genes from cucumber are regulated by nutritional status in cell cultures. In this paper a new mesophyll protoplast transient expression system is described which electroporated MS promoter—GUS reporter gene constructs exhibit same pattern of as endogenous gene. Both MS—GUS expressed when protoplasts cultured for 48 h on non‐metabolizable carbon source such mannitol or...
The development of text analysis systems targeting the extraction information about mutations from research publications is an emergent topic in biomedical research. Current differ both scope and approach, thus preventing a meaningful comparison their performance therefore possible synergies. To overcome this evaluation bottleneck, we developed comprehensive framework for systematic mutation systems, precisely defining tasks corresponding metrics, that will allow existing future applications.
Mutation impact extraction is an important task designed to harvest relevant annotations from scientific documents for reuse in multiple contexts. Our previous work on text mining mutation impacts resulted (i) the development of a GATE-based pipeline that mines texts information about mutations proteins, (ii) population this into our OWL DL ontology, and (iii) establishing experimental semantic database storing results mining.This article explores possibility using SADI framework as medium...