A5005828535- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Research Data Management Practices
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Genomics and Rare Diseases
- Head and Neck Cancer Studies
- Advances in Oncology and Radiotherapy
- Dental Health and Care Utilization
- Oral microbiology and periodontitis research
- Topic Modeling
- Distributed and Parallel Computing Systems
- Genomics and Phylogenetic Studies
- Natural Language Processing Techniques
- Advanced Radiotherapy Techniques
- Oral health in cancer treatment
- Ovarian cancer diagnosis and treatment
- Dental Radiography and Imaging
- Dental Research and COVID-19
- Multi-Agent Systems and Negotiation
- Animal testing and alternatives
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- Dental materials and restorations
- Health, Environment, Cognitive Aging
University of Florida
2022-2024
Roswell Park Comprehensive Cancer Center
2016-2024
Florida College
2022-2024
Lawrence Berkeley National Laboratory
2020-2022
University at Buffalo, State University of New York
2013-2020
Regenstrief Institute
2018-2020
Buffalo State University
2013
Royal Society of Edinburgh
1986-1989
University of Dundee
1987
University of Glasgow
1987
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...
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific taxon-neutral protein-related entities in three major areas: proteins related by evolution; produced from a given gene; protein-containing complexes. PRO thus serves as tool for referencing protein at any level of specificity. To enhance this ability, to facilitate the comparison such described different resources, we developed standardized representation proteoforms using UniProtKB...
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...
Microbiome samples are inherently defined by the environment in which they found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, critical.
Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge an accurate computable form. However, their construction maintenance demand substantial resources necessitate collaboration between domain experts, curators, ontology experts. We present Dynamic Retrieval Augmented Generation using AI (DRAGON-AI), generation method employing Large Language Models (LLMs) (RAG). DRAGON-AI can...
Abstract Background Evaluating the impact of environmental exposures on organism health is a key goal modern biomedicine and critically important in an age greater pollution chemicals our environment. Environmental utilizes many different research methods generates variety data types. However, to date, no comprehensive database represents full spectrum data. Due lack interoperability between databases, tools for integrating these resources are needed. In this manuscript we present...
The National Microbiome Data Collaborative (NMDC) Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed framework aligned with the FAIR (Findable, Accessible, Interoperable Reusable) principles (1). NMDC currently hosts 10.2 terabytes of data, spanning five types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, natural organic matter characterizations), generated at two Department Energy User...
Abstract Background We are developing the Neurological Disease Ontology (ND) to provide a framework enable representation of aspects neurological diseases that relevant their treatment and study. ND is representational tool addresses need for unambiguous annotation, storage, retrieval data associated with study diseases. being developed in compliance Open Biomedical Foundry principles builds upon paradigm established by General Medical Science (OGMS) entities domain disease medical practice....
Abstract Objectives The aim of this study is to determine the feasibility conducting clinical research using electronic dental record (EDR) data from U.S. solo and small-group general practices in National Dental Practice-Based Research Network (network) evaluate completeness correctness before performing survival analyses root canal treatment (RCT) posterior composite restorations (PCR). Methods Ninety-nine network dentistry that used Dentrix or EagleSoft EDR shared de-identified patients...
Abstract Background The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 2012 have resulted in a series major global public health crises. We argue that interest developing effective safe vaccines drugs to better understand coronaviruses associated disease mechenisms it is necessary integrate large exponentially growing body heterogeneous coronavirus data. Ontologies play an important role standard-based knowledge data representation, integration, sharing, analysis....
Streptococcus gordonii (S. gordonii, Sg) is one of the early colonizing, supragingival commensal bacterium normally associated with oral health in human dental plaque. MicroRNAs (miRNAs) play an important role inflammation-mediated pathways and are involved periodontal disease (PD) pathogenesis. PD a polymicrobial dysbiotic immune-inflammatory initiated by microbes gingival sulcus/pockets. The objective this study to determine global miRNA expression kinetics S. DL1-infected C57BL/6J mice....
The translational research community, in general, and the Clinical Translational Science Awards (CTSA) particular, share vision of repurposing EHRs for that will improve quality clinical practice. Many members these communities are also aware electronic health records (EHRs) suffer limitations data becoming poorly structured, biased, unusable out original context. This creates obstacles to continuity care, utility, improvement, research. Analogous sharing objective other areas natural...
Abstract Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge integration. The Kidney Precision Medicine Project (KPMP) team contributed the representation addition of 329 phenotype terms Human Phenotype Ontology (HPO), identified many subcategories acute injury (AKI) chronic disease (CKD). Tissue Atlas (KTAO) imports integrates kidney-related from existing (e.g.,...
The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, knowledge generation. However, the biodiversity omics communities, converging on have historically developed adopted their own distinct standards, hindering effective (meta)data integration collaboration. In response to this challenge, Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from...
Limited treatment options are available for oral mucositis, a common, debilitating complication of cancer therapy. We examined the association between daily delivery time radiotherapy and severity mucositis in patients with head neck cancer.We used electronic medical records 190 squamous cell carcinoma who completed radiotherapy, or without concurrent chemotherapy, at Roswell Park Comprehensive Cancer Center (Buffalo, NY) 2015 2017. Throughout 7-week course, patient mouth throat soreness...
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...
Few studies have examined the longevity of endodontically treated teeth in nonacademic clinical settings where most population receives its care. This study aimed to quantify general dentistry practices and test hypothesis that significantly differed by patient's age, gender, dental insurance, geographic region, placement a crown and/or other restoration soon after root canal treatment (RCT). retrospective used deidentified data patients who underwent RCT permanent through October 2015 99...
T. forsythia is a subgingival periodontal bacterium constituting the pathogenic polymicrobial milieu during periodontitis (PD). miRNAs play pivotal role in maintaining tissue homeostasis at transcriptional, post-transcriptional, and epigenetic levels. The aim of this study was to characterize global microRNAs (miRNA, miR) expression kinetics 8- 16-week-old forsythia-infected C57BL/6J mouse mandibles identify miRNA bacterial biomarkers disease process specific time points. We examined...
Within the cancer domain, ontologies play an important role in integration and annotation of data order to support numerous biomedical tools applications. This work seeks leverage existing standards immunophenotyping cell types found hematologic malignancies provide ontological representation them aid analysis for patient data.We have developed Cancer Cell Ontology according OBO Foundry principles as extension Ontology. We define classes by using a genus-differentia approach logical axioms...
There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and are difficult ontologically for a variety reasons. Blindness has escaped ontological capture at least in part because: employment term 'blindness' seems vary from context context, can present myriad types degrees, there no precedent representing complex such blindness.We explore current blindness, show how these fail subtypes (viz., color flash...