Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Visualization for constructing and sharing geo-scientific concepts.

ABSTRACT: Representations of scientific knowledge must reflect the dynamic nature of knowledge construction and the evolving networks of relations between scientific concepts. In this article, we describe initial work toward dynamic, visual methods and tools that support the construction, communication, revision, and application of scientific knowledge. Specifically, we focus on tools to capture and explore the concepts that underlie collaborative science activities, with examples drawn from the domain of human-environment interaction. These tools help individual researchers describe the process of knowledge construction while enabling teams of collaborators to synthesize common concepts. Our visualization approach links geographic visualization techniques with concept-mapping tools and allows the knowledge structures that result to be shared through a Web portal that helps scientists work collectively to advance their understanding. Our integration of geovisualization and knowledge representation methods emphasizes the process through which abstract concepts can be contextualized by the data, methods, people, and perspectives that produced them. This contextualization is a critical component of a knowledge structure, without which much of the meaning that guides the sharing of concepts is lost. By using the tools we describe here, human-environment scientists are given a visual means to build concepts from data (individually and collectively) and to connect these concepts to each other at appropriate levels of abstraction.

SUBMITTER: MacEachren AM

PROVIDER: S-EPMC387308 | biostudies-other | 2004 Apr

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Loose programming of GIS workflows with geo-analytical concepts.

Project description:Loose programming enables analysts to program with concepts instead of procedural code. Data transformations are left underspecified, leaving out procedural details and exploiting knowledge about the applicability of functions to data types. To synthesize workflows of high quality for a geo-analytical task, the semantic type system needs to reflect knowledge of geographic information systems (GIS) at a level that is deep enough to capture geo-analytical concepts and intentions, yet shallow enough to generalize over GIS implementations. Recently, core concepts of spatial information and related geo-analytical concepts were proposed as a way to add the required abstraction level to current geodata models. The core concept data types (CCD) ontology is a semantic type system that can be used to constrain GIS functions for workflow synthesis. However, to date, it is unknown what gain in precision and workflow quality can be expected. In this article we synthesize workflows by annotating GIS tools with these types, specifying a range of common analytical tasks taken from an urban livability scenario. We measure the quality of automatically synthesized workflows against a benchmark generated from common data types. Results show that CCD concepts significantly improve the precision of workflow synthesis.

| S-EPMC7983927 | biostudies-literature

The neuroscience of advanced scientific concepts.

Project description:Cognitive neuroscience methods can identify the fMRI-measured neural representation of familiar individual concepts, such as apple, and decompose them into meaningful neural and semantic components. This approach was applied here to determine the neural representations and underlying dimensions of representation of far more abstract physics concepts related to matter and energy, such as fermion and dark matter, in the brains of 10 Carnegie Mellon physics faculty members who thought about the main properties of each of the concepts. One novel dimension coded the measurability vs. immeasurability of a concept. Another novel dimension of representation evoked particularly by post-classical concepts was associated with four types of cognitive processes, each linked to particular brain regions: (1) Reasoning about intangibles, taking into account their separation from direct experience and observability; (2) Assessing consilience with other, firmer knowledge; (3) Causal reasoning about relations that are not apparent or observable; and (4) Knowledge management of a large knowledge organization consisting of a multi-level structure of other concepts. Two other underlying dimensions, previously found in physics students, periodicity, and mathematical formulation, were also present in this faculty sample. The data were analyzed using factor analysis of stably responding voxels, a Gaussian-naïve Bayes machine-learning classification of the activation patterns associated with each concept, and a regression model that predicted activation patterns associated with each concept based on independent ratings of the dimensions of the concepts. The findings indicate that the human brain systematically organizes novel scientific concepts in terms of new dimensions of neural representation.

| S-EPMC8505455 | biostudies-literature

Uncertainty Visualization: Concepts, Methods, and Applications in Biological Data Visualization.

Project description:This paper provides an overview of uncertainty visualization in general, along with specific examples of applications in bioinformatics. Starting from a processing and interaction pipeline of visualization, components are discussed that are relevant for handling and visualizing uncertainty introduced with the original data and at later stages in the pipeline, which shows the importance of making the stages of the pipeline aware of uncertainty and allowing them to propagate uncertainty. We detail concepts and methods for visual mappings of uncertainty, distinguishing between explicit and implict representations of distributions, different ways to show summary statistics, and combined or hybrid visualizations. The basic concepts are illustrated for several examples of graph visualization under uncertainty. Finally, this review paper discusses implications for the visualization of biological data and future research directions.

| S-EPMC9580861 | biostudies-literature

Mobile augmented reality based indoor map for improving geo-visualization.

Project description:Unlike traditional visualization methods, augmented reality (AR) inserts virtual objects and information directly into digital representations of the real world, which makes these objects and data more easily understood and interactive. The integration of AR and GIS is a promising way to display spatial information in context. However, most existing AR-GIS applications only provide local spatial information in a fixed location, which is exposed to a set of problems, limited legibility, information clutter and the incomplete spatial relationships. In addition, the indoor space structure is complex and GPS is unavailable, so that indoor AR systems are further impeded by the limited capacity of these systems to detect and display location and semantic information. To address this problem, the localization technique for tracking the camera positions was fused by Bluetooth low energy (BLE) and pedestrian dead reckoning (PDR). The multi-sensor fusion-based algorithm employs a particle filter. Based on the direction and position of the phone, the spatial information is automatically registered onto a live camera view. The proposed algorithm extracts and matches a bounding box of the indoor map to a real world scene. Finally, the indoor map and semantic information were rendered into the real world, based on the real-time computed spatial relationship between the indoor map and live camera view. Experimental results demonstrate that the average positioning error of our approach is 1.47 m, and 80% of proposed method error is within approximately 1.8 m. The positioning result can effectively support that AR and indoor map fusion technique links rich indoor spatial information to real world scenes. The method is not only suitable for traditional tasks related to indoor navigation, but it is also promising method for crowdsourcing data collection and indoor map reconstruction.

| S-EPMC8444080 | biostudies-literature

BPG: Seamless, automated and interactive visualization of scientific data.

Project description:BackgroundWe introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment.ResultsThis open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines.ConclusionBPG provides a new approach for linking interactive and scripted data visualization and is available at http://labs.oicr.on.ca/boutros-lab/software/bpg or via CRAN at https://cran.r-project.org/web/packages/BoutrosLab.plotting.general.

| S-EPMC6341661 | biostudies-literature

xiSPEC: web-based visualization, analysis and sharing of proteomics data.

Project description:We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.

| S-EPMC6030980 | biostudies-literature

The 3D hype: Evaluating the potential of real 3D visualization in geo-related applications.

Project description:The use of 3D visualization technologies has increased rapidly in many applied fields, including geovisualization, and has been researched from many different perspectives. However, the findings for the benefits of 3D visualization, especially in stereoscopic 3D forms, remain inconclusive and disputed. Stereoscopic "real" 3D visualization was proposed as encouraging the visual perception of shapes and volume of displayed content yet criticised as problematic and limited in a number of ways, particularly in visual discomfort and increased response time in tasks. In order to assess the potential of real 3D visualization for geo-applications, 91 participants were engaged in this study to work with digital terrain models in different 3D settings. The researchers examined the effectivity of stereoscopic real 3D visualization compared to monoscopic 3D (or pseudo 3D) visualization under static and interactive conditions and applied three tasks with experimental stimuli representing different geo-related phenomena, i.e. objects in the terrain, flat areas marked in the terrain and terrain elevation profiles. The authors explored the significant effects of real 3D visualization and interactivity factors in terms of response time and correctness. Researchers observed that the option to interact (t = -10.849, p < 0.001) with a virtual terrain and its depiction with real 3D visualization (t = 4.64, p < 0.001) extended the participants' response times. Counterintuitively, the data demonstrated that the static condition increased response correctness (z = 5.38, p < 0.001). Regarding detailed analysis of data, an interactivity factor was proposed as a potential substitute for real 3D visualization in 3D geographical tasks.

| S-EPMC7241704 | biostudies-literature

Data sharing practices and data availability upon request differ across scientific disciplines.

Project description:Data sharing is one of the cornerstones of modern science that enables large-scale analyses and reproducibility. We evaluated data availability in research articles across nine disciplines in Nature and Science magazines and recorded corresponding authors' concerns, requests and reasons for declining data sharing. Although data sharing has improved in the last decade and particularly in recent years, data availability and willingness to share data still differ greatly among disciplines. We observed that statements of data availability upon (reasonable) request are inefficient and should not be allowed by journals. To improve data sharing at the time of manuscript acceptance, researchers should be better motivated to release their data with real benefits such as recognition, or bonus points in grant and job applications. We recommend that data management costs should be covered by funding agencies; publicly available research data ought to be included in the evaluation of applications; and surveillance of data sharing should be enforced by both academic publishers and funders. These cross-discipline survey data are available from the plutoF repository.

| S-EPMC8381906 | biostudies-literature

MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context.

Project description:Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.

| S-EPMC7383707 | biostudies-literature

Effective image visualization for publications - a workflow using open access tools and concepts.

Project description:Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization. Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible "cheat sheet"-style format, enabling wide distribution, use, and adoption to more specific needs.

| S-EPMC7931257 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data