Dataset Information

ViPR: an open bioinformatics database and analysis resource for virology research.

ABSTRACT: The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal 'Workbenches' for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

SUBMITTER: Pickett BE

PROVIDER: S-EPMC3245011 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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ViPR: an open bioinformatics database and analysis resource for virology research.

Pickett Brett E BE Sadat Eva L EL Zhang Yun Y Noronha Jyothi M JM Squires R Burke RB Hunt Victoria V Liu Mengya M Kumar Sanjeev S Zaremba Sam S Gu Zhiping Z Zhou Liwei L Larson Christopher N CN Dietrich Jonathan J Klem Edward B EB Scheuermann Richard H RH

Nucleic acids research 20111017 Database issue

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae ...[more]

PMID: 22006842

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Project description:While art is omnipresent in human history, the neural mechanisms of how we perceive, value and differentiate art has only begun to be explored. Functional magnetic resonance imaging (fMRI) studies suggested that art acts as secondary reward, involving brain activity in the ventral striatum and prefrontal cortices similar to primary rewards such as food. However, potential similarities or unique characteristics of art-related neuroscience (or neuroesthetics) remain elusive, also because of a lack of adequate experimental tools: the available collections of art stimuli often lack standard image definitions and normative ratings. Therefore, we here provide a large set of well-characterized, novel art images for use as visual stimuli in psychological and neuroimaging research. The stimuli were created using a deep learning algorithm that applied different styles of popular paintings (based on artists such as Klimt or Hundertwasser) on ordinary animal, plant and object images which were drawn from established visual stimuli databases. The novel stimuli represent mundane items with artistic properties with proposed reduced dimensionality and complexity compared to paintings. In total, 2,332 novel stimuli are available open access as "art.pics" database at https://osf.io/BTWNQ/ with standard image characteristics that are comparable to other common visual stimuli material in terms of size, variable color distribution, complexity, intensity and valence, measured by image software analysis and by ratings derived from a human experimental validation study [n = 1,296 (684f), age 30.2 ± 8.8 y.o.]. The experimental validation study further showed that the art.pics elicit a broad and significantly different variation in subjective value ratings (i.e., liking and wanting) as well as in recognizability, arousal and valence across different art styles and categories. Researchers are encouraged to study the perception, processing and valuation of art images based on the art.pics database which also enables real reward remuneration of the rated stimuli (as art prints) and a direct comparison to other rewards from e.g., food or money. Key Messages: We provide an open access, validated and large set of novel stimuli (n = 2,332) of standardized art images including normative rating data to be used for experimental research. Reward remuneration in experimental settings can be easily implemented for the art.pics by e.g., handing out the stimuli to the participants (as print on premium paper or in a digital format), as done in the presented validation task. Experimental validation showed that the art.pics' images elicit a broad and significantly different variation in subjective value ratings (i.e., liking, wanting) across different art styles and categories, while size, color and complexity characteristics remained comparable to other visual stimuli databases.

Project description:BackgroundThe use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.ResultsThe process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes.ConclusionsThis database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.

Dataset Information

ViPR: an open bioinformatics database and analysis resource for virology research.

Publications

ViPR: an open bioinformatics database and analysis resource for virology research.

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