A5051806625- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Microbial infections and disease research
- Genetic Associations and Epidemiology
- Natural Language Processing Techniques
- Bacteriophages and microbial interactions
- Biomedical and Engineering Education
- Plant Virus Research Studies
- Virology and Viral Diseases
- Advanced Proteomics Techniques and Applications
- Research Data Management Practices
- Genetic Syndromes and Imprinting
- Insect symbiosis and bacterial influences
- Malaria Research and Control
- Epigenetics and DNA Methylation
- Cell Image Analysis Techniques
- Electronic Health Records Systems
- Advanced Text Analysis Techniques
- Viral Infectious Diseases and Gene Expression in Insects
University of Colorado Anschutz Medical Campus
2023
European Bioinformatics Institute
2018-2022
University of California, San Diego
2015-2016
University of Pennsylvania
2002-2014
Stanford University
2009-2014
University of Oxford
2012
Translational Research Informatics Center (Japan)
2010
University of Victoria
2009
The Nature Conservancy
2009
University of Delaware
1996-2003
The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. scope the has also expanded targeted exome arrays with 1000 new associations added these technologies. As September 2018, contains 5687 comprising 71673 variant-trait from 3567 publications. New content includes 284 full P-value summary statistics datasets...
Abstract The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare industry. contains variant-trait associations supporting metadata for >45 published across >5000 human traits, >40 full P-value summary statistics datasets. Content curated publications or acquired via author submission...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical that provides access via Web services browsers developed in OWL, RDF, OBO format Protégé frames. functionality includes the ability browse, search visualize ontologies. The interface also facilitates community-based participation evaluation...
The National Center for Biomedical Ontology (NCBO) is one of the Centers Computing funded under NIH Roadmap Initiative. Contributing to national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access library biomedical ontologies and terminologies ( http://bioportal.bioontology.org ) via Web services. BioPortal enables community participation in evaluation evolution ontology content by providing features add mappings between terms, comments linked specific...
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,...
The National Center for Biomedical Ontology is now in its seventh year. goals of this Computing are to: create and maintain a repository biomedical ontologies terminologies; build tools web services to enable the use terminologies clinical translational research; educate their trainees scientific community broadly about ontology ontology-based technology best practices; collaborate with variety groups who develop biomedicine. centerpiece web-based resource known as BioPortal. BioPortal makes...
Efficient tools for data management and integration are essential many aspects of high-throughput biology. In particular, annotations genes human genetic variants commonly used but highly fragmented across resources. Here, we describe MyGene.info MyVariant.info, high-performance web services querying gene variant annotation information. These currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model organizing biological MyVariant.info...
Abstract Motivation: The generation of large amounts microarray data and the need to share these bring challenges for both management annotation highlights standards. MIAME specifies minimum information needed describe a experiment Microarray Gene Expression Object Model (MAGE-OM) resulting MAGE-ML provide mechanism standardize representation exchange, however common terminology is support Results: Here we MGED Ontology (MO) developed by Working Group Data (MGED) Society. MO provides terms...
Abstract There are thousands of distinct disease entities and concepts, each which known by different sometimes contradictory names. The lack a unified system for managing these poses major challenge both machines humans that need to harmonize information better predict causes treatments disease. Mondo Disease Ontology is an open, community-driven ontology integrates key medical biomedical terminologies, supporting data integration improve diagnosis, treatment, translational research....
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing ontologies, semantic models, knowledge graphs translational research. App an integrated platform combining about genes, phenotypes, diseases across species. Monarch's APIs enable access to carefully...
Abstract Background Translational medicine requires the integration of knowledge using heterogeneous data from health care to life sciences. Here, we describe a collaborative effort produce prototype Medicine Knowledge Base (TMKB) capable answering questions relating clinical practice and pharmaceutical drug discovery. Results We developed Ontology (TMO) as unifying ontology integrate chemical, genomic proteomic with disease, treatment, electronic records. demonstrate use Semantic Web...
The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other resources. has recently undergone major changes, both in terms of data content supporting infrastructure. more than doubled from around 2 million samples 2014 just over 5 2018. Fast, reciprocal exchange was fully established between sister Biosample databases INSDC partners, enabling worldwide common representation centralization metadata. platform been upgraded accommodate anticipated...
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
Abstract Motivation: Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary practices, supporting geographically distributed players. Results: OntoMaton an open source solution brings ontology lookup tagging capabilities into a cloud-based editing environment, harnessing Google Spreadsheets the NCBO Web services. It general purpose, format-agnostic tool may serve as component of...
As new biomedical technologies are developed, the amount of publically available data continues to increase. To help manage these vast and disparate sources, researchers have turned Semantic Web. Specifically, ontologies used in annotation, natural language processing, information retrieval, clinical decision support, integration tasks. The development software applications perform tasks requires Web services incorporate wide variety health care life sciences. National Center for Biomedical...
Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing GWAS summary statistics (SumStats) is essential facilitating the larger meta-analyses needed for increased power resolving genetic basis disease. However, most SumStats are not readily accessible because limited and a lack defined standards. With aim increasing availability, quality, utility SumStats, National Human Genome Research Institute-European Bioinformatics Institute...
A 150-kDa cytadhesin-like protein from Mycoplasma gallisepticum has been identified. previously described 583-bp fragment (J.E. Dohms, L.L. Hnatow, P. Whetzel, R. Morgan and C.L. Keeler, Jr., Avian Dis. 37:380-388, 1993) was used to probe a genomic library of M. DNA. An 8.0-kb SacI identified, cloned, partially sequenced. Analysis the resulting 3,750-bp sequence revealed presence 3,366-nucleotide open reading frame, mgc1. The 1,122-amino-acid encoded by this MGC1, characteristics class I...