A5076014872- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Research Data Management Practices
- Semantic Web and Ontologies
- Cell Image Analysis Techniques
- Functional Brain Connectivity Studies
- Genetics, Bioinformatics, and Biomedical Research
- Health, Environment, Cognitive Aging
- Cognitive Computing and Networks
- Distributed and Parallel Computing Systems
- Monoclonal and Polyclonal Antibodies Research
- Bioinformatics and Genomic Networks
- Brain Tumor Detection and Classification
- Fuzzy Logic and Control Systems
- Meta-analysis and systematic reviews
- Advanced Proteomics Techniques and Applications
- Ethics in Clinical Research
- Gene expression and cancer classification
- Vestibular and auditory disorders
- Biomedical and Engineering Education
- Hearing, Cochlea, Tinnitus, Genetics
- Traumatic Brain Injury and Neurovascular Disturbances
- EEG and Brain-Computer Interfaces
- Advanced MRI Techniques and Applications
- Genomics and Rare Diseases
University of California, San Diego
2015-2024
University of Kentucky
2024
Neurological Surgery
2023
University of California, San Francisco
2023
UC San Diego Health System
2019
University of California System
2008-2018
La Jolla Alcohol Research
2018
Center for Systems Biology
2017
Harvard University
2012
California Institute of Technology
2012
There is an urgent need to improve the infrastructure supporting reuse of scholarly data. A diverse set stakeholders-representing academia, industry, funding agencies, and publishers-have come together design jointly endorse a concise measureable principles that we refer as FAIR Data Principles. The intent these may act guideline for those wishing enhance reusability their data holdings. Distinct from peer initiatives focus on human scholar, Principles put specific emphasis enhancing ability...
The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/ ) is a database associated computational infrastructure that provides single system depositing, locating, analyzing, visualizing sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects links metadata relevant to environmental metagenome sets with annotation in semantically-aware environment allowing users write expressive...
With support from the Institutes and Centers forming NIH Blueprint for Neuroscience Research, we have designed implemented a new initiative integrating access to use of Web-based neuroscience resources: Information Framework. The Framework arises expressed need community neuroinformatic tools resources aid scientific inquiry, builds upon prior development neuroinformatics by Human Brain Project others, directly derives Society Neuroscience's Database Gateway. Partnered with Society, its...
Reaching movements performed without vision of the moving limb are continuously monitored, during their execution, by feedback loops (designated nonvisual). In this study, we investigated functional anatomy these nonvisual using positron emission tomography (PET). Seven subjects had to "look at" (eye) or and point to" (eye-arm) visual targets whose location either remained stationary changed undetectably ocular saccade (when is suppressed). Slightly changing target gaze shift causes an...
A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although original NIF specification called loosely structured controlled vocabulary neuroscience resources, as system evolved, requirement formally ontology with sufficient granularity to describe access diverse collection information became obvious. This led standardized (NIFSTD) ontology, comprehensive common...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
There has been a recent major upsurge in the concerns about reproducibility many areas of science. Within neuroimaging domain, one approach is to promote target re-executability publication. The information supporting such can enable detailed examination how an initial finding generalizes across changes processing approach, and sampled population, controlled scientific fashion. ReproNim: A Center for Reproducible Neuroimaging Computation recently funded initiative that seeks facilitate 'last...
Abstract This article presents a practical roadmap for scholarly data repositories to implement citation in accordance with the Joint Declaration of Data Citation Principles, synopsis and harmonization recommendations major science policy bodies. The was developed by Repositories Expert Group, as part Implementation Pilot (DCIP) project, an initiative FORCE11.org NIH-funded BioCADDIE ( https://biocaddie.org ) project. makes 11 specific recommendations, grouped into three phases...
Antibodies are ubiquitous key biological research resources yet tricky to use as they prone performance issues and represent a major source of variability across studies. Understanding what antibody was used in published study is therefore necessary repeat and/or interpret given study. However, reagents still frequently not cited with sufficient detail determine which experiments. The Antibody Registry public, open database that enables citation antibodies by providing persistent record for...
The functional correlates of movement extent, speed, and covariates were investigated using PET mapping regional cerebral blood flow (rCBF) in 13 healthy right-handed adults. A whole-arm smooth pursuit tracking task was used to strictly control potential confounds such as duration, error, feedback control. During each four scans, images relative rCBF obtained while subjects matched the constant velocity movements a target joystick-controlled cursor. Between completely adapted one...
The aggregation of imaging, clinical, and behavioral data from multiple independent institutions researchers presents both a great opportunity for biomedical research as well formidable challenge. Many groups have well-established collection analysis procedures, metadata format requirements that are particular to group. Moreover, the types collected quite diverse, including image, physiological, data, descriptions experimental design, preprocessing methods. Each these utilizes variety...
Abstract Today’s science increasingly requires effective ways to find and access existing datasets that are distributed across a range of repositories. For researchers in the life sciences, discoverability may soon become as essential identifying latest publications via PubMed. Through an international collaborative effort funded by National Institutes Health (NIH)’s Big Data Knowledge (BD2K) initiative, we have designed implemented DAta Tag Suite (DATS) model support DataMed data discovery...
<ns4:p>A central tenet in support of research reproducibility is the ability to uniquely identify resources, i.e., reagents, tools, and materials that are used perform experiments. However, current reporting practices for resources insufficient allow humans algorithms exact reported or answer basic questions such as “What other studies resource X?” To address this issue, Resource Identification Initiative was launched a pilot project improve standards methods sections papers thereby...
Abstract Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement citation in accordance with widely accepted principles. Local may however be prefixed a namespace identifier, providing global uniqueness. Such “compact identifiers” have been used informatics support resource identification local identifier assignment. We report...
Abstract Objective Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it challenging given volume and complexity of data. Here we describe development an open source discovery system called DataMed, with goal building additional indexes domain. Materials Methods which can efficiently index search diverse types across repositories, developed through National Institutes Health–funded healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium. It...
The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, simulation tools for mammalian autonomic nervous system. experimental data mathematical models supplied to DRC by consortium are curated, annotated semantically linked via a single knowledgebase. A portal has been developed that allows discovery both semantic search an interface includes Google Map-like 2D flatmaps displaying connectivity, 3D anatomical organ scaffolds provide...
Abstract In this perspective article, we consider the critical issue of data and other research object standardisation and, specifically, how international collaboration, organizations such as International Neuroinformatics Coordinating Facility (INCF) can encourage that emerging neuroscience be Findable, Accessible, Interoperable, Reusable (FAIR) . As neuroscientists engaged in sharing integration multi-modal multiscale data, see current insufficiency standards a major impediment...
An initiative of the NIH Blueprint for neuroscience research, Neuroscience Information Framework (NIF) project advances by enabling discovery and access to public research data tools worldwide through an open source, semantically enhanced search portal. One critical components overall NIF system, Standardized Ontologies (NIFSTD), provides extensive collection standard concepts along with their synonyms relationships. The knowledge models defined in NIFSTD ontologies enable effective...
The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is a U.S. National Institutes of Health (NIH) funded effort enhance our understanding the neural circuitry responsible for visceral control. SPARC's mission identify, extract, and compile overall existing knowledge autonomic nervous system (ANS) connectivity between central end organs. A major goal SPARC use this promote development next generation neuromodulation devices bioelectronic medicine diseases. As part...