James A. Overton
A5009238690- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- vaccines and immunoinformatics approaches
- Bioinformatics and Genomic Networks
- SARS-CoV-2 and COVID-19 Research
- Research Data Management Practices
- Natural Language Processing Techniques
- Scientific Computing and Data Management
- COVID-19 Clinical Research Studies
- Bacterial Infections and Vaccines
- Monoclonal and Polyclonal Antibodies Research
- Long-Term Effects of COVID-19
- Influenza Virus Research Studies
- Philosophy and History of Science
- Radiomics and Machine Learning in Medical Imaging
- Cell Image Analysis Techniques
- Genomics and Rare Diseases
- Machine Learning in Bioinformatics
- AI in cancer detection
- Artificial Intelligence in Healthcare and Education
- Wikis in Education and Collaboration
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Database Systems and Queries
- Service-Oriented Architecture and Web Services
- Science and Climate Studies
La Jolla Institute for Immunology
2013-2025
Arconic (United States)
2024-2025
Western University
2008-2012
Northwest Mississippi Community College
2004
The Immune Epitope Database (IEDB, iedb.org) captures experimental data confined in figures, text and tables of the scientific literature, making it freely available easily searchable to public. scope IEDB extends across immune epitope related all species studied includes antibody, T cell, MHC binding contexts associated with infectious, allergic, autoimmune, transplant diseases. Having been publicly accessible for >10 years, recent focus has improved query reporting functionality meet needs...
The IEDB, www.iedb.org, contains information on immune epitopes--the molecular targets of adaptive responses--curated from the published literature and submitted by National Institutes Health funded epitope discovery efforts. From 2004 to 2012 IEDB curation journal articles since 1960 has caught up present day, with >95% relevant manually curated amounting more than 15,000 704,000 experiments date. revised target been make recent research findings quickly available in thereby ensure that it...
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners quality control checks, extracting dependencies application-specific subsets, generating standard reports, release files multiple formats. Similar to more general software development, automation is key executing managing these effectively releasing robust products forms. For using Web Ontology Language (OWL), OWL...
Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple can be problematic, as they developed independently, which lead incompatibilities. The Open Biomedical Ontologies (OBO) Foundry was created address by facilitating development, harmonization, application sharing ontologies, guided set overarching principles. One challenge in reaching these...
Abstract Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated female sex distinctive comorbidities. During...
Abstract Despite progress in the development of standards for describing and exchanging scientific information, lack easy-to-use mapping between different representations same or similar objects databases poses a major impediment to data integration interoperability. Mappings often metadata needed be correctly interpreted applied. For example, are two terms equivalent merely related? Are they narrow broad matches? Or associated some other way? Such relationships mapped not documented, which...
Abstract Similar to managing software packages, the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities powerful ontology-engineering environmentsr. Particularly in biomedical domain, which has developed highly yet inter-dependent ontologies, standardizing release practices metadata establishing shared...
The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1–3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling >15,000 longitudinal blood nasal samples 540 participants the using 14 distinct assays. These unbiased analyses identify cellular molecular signatures present within 72 h hospital admission that...
Abstract The glycosylation of IgG plays a critical role during human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, activating immune cells and inducing cytokine production. However, the IgM N-glycosylation has not been studied viral infection. analysis from healthy controls hospitalized disease 2019 (COVID-19) patients reveals increased high-mannose sialylation that correlates with COVID-19 severity. These trends are confirmed within SARS-CoV-2-specific...
MHC molecules are a highly diverse family of proteins that play key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) molecule involved recognition context. No consistent nomenclature exists across vertebrate species.To correctly represent related data The Immune Epitope Database (IEDB), we built upon previously established ontology created an as they relate immunological experiments.This models protein...
Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, frequently a crucial part modern information systems. Most these structures change over time, incorporating new or that was previously missing. Managing changes is challenge, both in terms communicating to users providing mechanisms make it easier for multiple stakeholders contribute. To fill need, we have created KGCL, the Knowledge Graph Change Language...
Abstract Background While unstructured data, such as free text, constitutes a large amount of publicly available biomedical it is underutilized in automated analyses due to the difficulty extracting meaning from it. Normalizing free-text i.e. , removing inessential variance, enables use structured vocabularies like ontologies represent data and allow for harmonized queries over This paper presents an adaptable tool normalization evaluation application this two different fields curated...
Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing differences in outcome. Comparing such is challenging due variability study designs. To address this, we established a community resource compare predicting B. pertussis booster generate experimental data for explicit purpose of model evaluation. We here describe our second prediction challenge using this resource, where benchmarked 49...
The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating recognition of immune epitopes easily available scientific public. By presenting curated in a searchable database, we have liberated it from tables and figures journal articles, making more accessible usable by immunologists. Recently, principles Findability, Accessibility, Interoperability Reusability been formulated as goals that repositories should meet enhance usefulness...
Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology a controlled structured vocabulary consisting general terms (such as "cell" or "image" "tissue" "microscope") that form the basis such These are designed to represent types entities in domain reality has been devised capture; provided with logical definitions thereby also supporting reasoning over tagged data.This paper provides survey biomedical imaging ontologies have...
Abstract Over the past 20 years, Immune Epitope Database (IEDB, iedb.org) has established itself as foremost resource for immune epitope data. The IEDB catalogs published epitopes and their contextual experimental data in a freely searchable public resource. team manually curates from literature into structured format spans infectious, allergic, autoimmune, transplant diseases. Here, we describe enhancements made since our 2018 paper, capturing user-directed updates to search interface,...
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome 2 (SARS-CoV-2) has seen multiple anti-SARS-CoV-2 antibodies being generated globally. It is difficult, however, to assemble a useful compendium of these biological properties if they are derived from experimental measurements performed at different sites under conditions. Coronavirus Immunotherapeutic Consortium (COVIC) circumvents issues experimentally testing blinded side for several functional...
Abstract Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple can be problematic, as they developed independently, which lead incompatibilities. The Open Biomedical Ontologies (OBO) Foundry was created address by facilitating development, harmonization, application, sharing ontologies, guided set overarching principles. One challenge in...
Abstract Computational models that predict an individual's response to a vaccine offer the potential for mechanistic insights and personalized vaccination strategies. These often stem from small cohort studies focusing on single vaccines limiting their generalizability. The ability assess performance of resulting would be improved by comparing independent datasets. We established prototype platform evaluates Models Immunity Pertussis Booster vaccinations (CMI-PB). It aims generate...
In radiology, a vast amount of diverse data is generated, and unstructured reporting standard. Hence, much useful information trapped in free-text form, often lost translation transmission. One relevant source consists reports covering the assessment changes tumor burden, which are needed for evaluation cancer treatment success. Any change lesion size critical factor follow-up examinations. It difficult to retrieve specific from compare them over time. Therefore, prototype was implemented...