A5100599538- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- vaccines and immunoinformatics approaches
- Natural Language Processing Techniques
- Genomics and Rare Diseases
- Cell Image Analysis Techniques
- linguistics and terminology studies
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Machine Learning in Bioinformatics
- Syntax, Semantics, Linguistic Variation
- Identification and Quantification in Food
- Climate Change and Health Impacts
- Food Security and Health in Diverse Populations
- Health, Environment, Cognitive Aging
- Public Health Policies and Education
- Hearing, Cochlea, Tinnitus, Genetics
- SARS-CoV-2 and COVID-19 Research
- Genetic diversity and population structure
- Microbial Natural Products and Biosynthesis
- Language, Metaphor, and Cognition
- Ethics in Clinical Research
University of Michigan
2011-2024
National Institutes of Health
2021-2024
American Axle & Manufacturing (United States)
2024
National Human Genome Research Institute
2021-2022
Henan University
2022
Sichuan University
2022
Center for Devices and Radiological Health
2020
University of Miami
2015-2018
Chinese Academy of Fishery Sciences
2017
Michigan United
2016
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,...
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information Description Frameworks (RDFs) HTTP. Ontologies, which logically represent relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology server that stores RDF triple store technology supports query, visualization linkage terms. also default for publishing browsing biomedical ontologies Open Biological...
A medical intervention is a procedure or application intended to relieve prevent illness injury. Examples of interventions include vaccination and drug administration. After intervention, adverse events (AEs) may occur which lie outside the consequences intervention. The representation analysis AEs are critical improvement public health. Ontology Adverse Events (OAE), previously named Event (AEO), community-driven ontology developed standardize integrate data relating arising subsequent...
Cell lines have been widely used in biomedical research. The community-based Line Ontology (CLO) is a member of the OBO Foundry library that covers domain cell lines. Since its publication two years ago, significant updates made, including new groups joining CLO consortium, line cells, upper level alignment with (CL) and for Biomedical Investigation, logical extensions. Collaboration among CLO, CL, OBI has established consensus definitions line-specific terms such as ‘cell line’, cell’,...
One of the most successful approaches to develop new small molecule therapeutics has been start from a validated druggable protein target. However, only subset potentially targets attracted significant research and development resources. The Illuminating Druggable Genome (IDG) project develops resources catalyze likely targetable, yet currently understudied prospective drug targets. A central component IDG program is comprehensive knowledge resource genome. As part that effort, we have...
It is time-consuming to build an ontology with many terms and axioms. Thus it desired automate the process of development. Ontology Design Patterns (ODPs) provide a reusable solution solve recurrent modeling problem in context engineering. Because often follow specific ODPs, for Biomedical Investigations (OBI) developers proposed Quick Term Templates (QTTs) targeted at generating new classes following same pattern, using term templates spreadsheet format.Inspired by ODPs QTTs, Ontorat web...
Cancer vaccines have been increasingly studied and developed to prevent or treat various types of cancers. To systematically survey analyze different reported cancer vaccines, we CanVaxKB (https://violinet.org/canvaxkb), the first web-based vaccine knowledgebase that compiles over 670 therapeutic preventive experimentally verified be effective at stages. Vaccine construction host response data are also included. These against such as melanoma, hematological cancer, prostate cancer. has...
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....
Abstract Background Caused by intracellular Gram-negative bacteria Brucella spp., brucellosis is the most common bacterial zoonotic disease. Extensive studies in have yielded a large number of publications and data covering various topics ranging from basic genetic study to vaccine clinical trials. To support interoperability reasoning, community-based brucellosis-specific biomedical ontology needed. Results The Brucellosis Ontology (IDOBRU: http://sourceforge.net/projects/idobru ), domain,...
BioHackathon 2010 was the third in a series of meetings hosted by Database Center for Life Sciences (DBCLS) Tokyo, Japan. The overall goal is to improve quality and accessibility life science research data on Web bringing together representatives from public databases, analytical tool providers, cyber-infrastructure researchers jointly tackle important challenges area silico biological research. theme 'Semantic Web', all attendees gathered with shared producing Semantic their respective...
Neuropathy often occurs following drug treatment such as chemotherapy. Severe instances of neuropathy can result in cessation life-saving chemotherapy treatment. To support data representation and analysis drug-associated adverse events (AEs), we developed the Ontology Drug Adverse Events (ODNAE). ODNAE extends (OAE). Our combinatorial approach identified 215 US FDA-licensed small molecule drugs that induce signs symptoms various types neuropathy. imports related from (DrON) with their...
Statistics play a critical role in biological and clinical research. However, most reports of scientific results the published literature make it difficult for reader to reproduce statistical analyses performed achieving those because they provide inadequate documentation tests algorithms applied. The Ontology Biological Clinical (OBCS) is put forward here as step towards solving this problem. terms OBCS including 'data collection', transformation statistics', visualization', 'statistical...
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...
Although signing a vaccination (or immunization) informed consent form is not federal requirement in the US and Canada, such practice required by many states pharmacies. The content structures of these forms vary, which makes it hard to compare analyze without standardization. To facilitate data standardization integration, important examine various forms, patient answers, results. In this study, we report Vaccination Informed Consent Ontology (VICO) that extends integrates related OBO...
The characteristics of a person's health status are often guided by how they live, grow, learn, their genetics, as well access to care. Yet, all too often, studies examining the relationship between social determinants (behavioral, sociocultural, and physical environmental factors), role demographics, outcomes poorly represent these relationships, leading misinterpretations, limited study reproducibility, datasets with representativeness secondary research use capacity. This is profound...
Due to human variations in genetic susceptibility, vaccination often triggers adverse events a small population of vaccinees. Based on our previous work ontological modeling susceptibility disease, we developed an Ontology Genetic Susceptibility Factors (OGSF), biomedical ontology the domain and factors. The OGSF framework was then applied area vaccine (VAEs).OGSF aligns with Basic Formal (BFO). defines 'genetic susceptibility' as subclass BFO:disposition has material basis factor'....
Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs' functions are realized by regulating their respective target genes (targets). It is thus critical to identify analyze miRNA-target interactions for better understanding delineation functions. However, conventional knowledge discovery acquisition methods have many limitations. Fortunately, semantic technologies...
The exploration of cancer vaccines has yielded a multitude studies, resulting in diverse collection information. heterogeneity vaccine data significantly impedes effective integration and analysis. While CanVaxKB serves as pioneering database for over 670 manually annotated vaccines, it is important to distinguish that database, on its own, does not offer the structured relationships standardized definitions found an ontology. Recognizing this, we expanded Vaccine Ontology (VO) include those...
Aiming to understand cellular responses different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as default ontology for LINCS line representation integration. CLO has consistently represented all 1097 lines included information extracted from Data Portal ChEMBL. Using MCF 10A cells an example, we...
The development of SARS-CoV-2 vaccines during the COVID-19 pandemic has prompted emergence vaccine data. Timely access to information is crucial researchers and public. To support more comprehensive annotation, integration, analysis information, we have developed Cov19VaxKB, a knowledge-focused database (http://www.violinet.org/cov19vaxkb/). Cov19VaxKB features lists vaccines, formulations, clinical trials, publications, news articles, adverse event case reports. A web-based query interface...