Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions.

ABSTRACT: The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation. Visualizing knowledge of biomolecular interactions increases comprehension and facilitates the development of new hypotheses. The rapidly changing landscape of high-content experimental results also presents a challenge for the maintenance of comprehensive knowledgebases. Distributing the responsibility for maintenance of a knowledgebase to a community of subject matter experts is an effective strategy for large, complex and rapidly changing knowledgebases. Cognoscente serves these needs by building visualizations for queries of biomolecular interactions on demand, by managing the complexity of those visualizations, and by crowdsourcing to promote the incorporation of current knowledge from the literature.

SUBMITTER: Vanburen V

PROVIDER: S-EPMC3527363 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions.

Vanburen Vincent V Chen Hailin H

Scientific reports 20121220

The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation. Visualizing knowledge of biomolecular interactions increases comprehension and facilitates the development of new hypotheses. The rapidly changing landscape of high-content experimental results also presents a challenge for the maintenance of comprehensive knowledgebases. Distributing the responsibility for maintenance of a knowledgebase to a community of subject matter experts ...[more]

PMID: 23264875

Similar Datasets

Standard biological parts knowledgebase.

Project description:We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

| S-EPMC3044748 | biostudies-literature

Switching specific biomolecular interactions on surfaces under complex biological conditions.

Project description:Herein, electrically switchable mixed self-assembled monolayers based on oligopeptides have been developed and investigated for their suitability in achieving control over biomolecular interactions in the presence of complex biological conditions. Our model system, a biotinylated oligopeptide tethered to gold within a background of tri(ethylene glycol) undecanethiol, is ubiquitous in both switching specific protein interactions in highly fouling media while still offering the non-specific protein-resistance to the surface. Furthermore, the work demonstrated that the performance of the switching on the electro-switchable oligopeptide is sensitive to the characteristics of the media, and in particular, its protein concentration and buffer composition, and thus such aspects should be considered and addressed to assure maximum switching performance. This study lays the foundation for developing more realistic dynamic extracellular matrix models and is certainly applicable in a wide variety of biological and medical applications.

| S-EPMC4184031 | biostudies-literature

Reactome: a knowledgebase of biological pathways.

Project description:Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.

| S-EPMC540026 | biostudies-literature

In situ characterization of nanoparticle biomolecular interactions in complex biological media by flow cytometry.

Project description:Nanoparticles interacting with, or derived from, living organisms are almost invariably coated in a variety of biomolecules presented in complex biological milieu, which produce a bio-interface or 'biomolecular corona' conferring a biological identity to the particle. Biomolecules at the surface of the nanoparticle-biomolecule complex present molecular fragments that may be recognized by receptors of cells or biological barriers, potentially engaging with different biological pathways. Here we demonstrate that using intense fluorescent reporter binders, in this case antibodies bound to quantum dots, we can map out the availability of such recognition fragments, allowing for a rapid and meaningful biological characterization. The application in microfluidic flow, in small detection volumes, with appropriate thresholding of the detection allows the study of even complex nanoparticles in realistic biological milieu, with the emerging prospect of making direct connection to conditions of cell level and in vivo experiments.

| S-EPMC5116075 | biostudies-literature

DECODING COMPLEXITY IN BIOMOLECULAR RECOGNITION OF DNA I-MOTIFS.

Project description:DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10,976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone, and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo , whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.

| S-EPMC10153190 | biostudies-literature

iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.

Project description:Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from their original location. Any registered data set can be searched and downloaded using a set of defined metadata for molecular dynamics and quantum mechanics and visualized through a dynamic Web interface.

| S-EPMC8489555 | biostudies-literature

Detecting biological network organization and functional gene orthologs.

Project description:SummaryWe developed a package TripletSearch to compute relationships within triplets of genes based on Roundup, an orthologous gene database containing >1500 genomes. These relationships, derived from the coevolution of genes, provide valuable information in the detection of biological network organization from the local to the system level, in the inference of protein functions and in the identification of functional orthologs. To run the computation, users need to provide the GI IDs of the genes of interest.Availabilityhttp://wall.hms.harvard.edu/sites/default/files/tripletSearch.tar.gzContactdpwall@hms.harvard.eduSupplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC3187654 | biostudies-literature

Interactions of NADP-reducing enzymes across varying environmental conditions: a model of biological complexity.

Project description:Interactions across biological networks are often quantified under a single set of conditions; however, cellular behaviors are dynamic and interactions can be expected to change in response to molecular context and environment. To determine the consistency of network interactions, we examined the enzyme network responsible for the reduction of nicotinamide adenine dinucleotide phosphate (NADP) to NADPH across three different conditions: oxidative stress, starvation, and desiccation. Synthetic, activity-variant alleles were used in Drosophila melanogaster for glucose-6-phosphate dehydrogenase (G6pd), cytosolic isocitrate dehydrogenase (Idh), and cytosolic malic enzyme (Men) along with seven different genetic backgrounds to lend biological relevance to the data. The responses of the NADP-reducing enzymes and two downstream phenotypes (lipid and glycogen concentration) were compared between the control and stress conditions. In general, responses in NADP-reducing enzymes were greater under conditions of oxidative stress, likely due to an increased demand for NADPH. Interactions between the enzymes were altered by environmental stress in directions and magnitudes that are consistent with differential contributions of the different enzymes to the NADPH pool: the contributions of G6PD and IDH seem to be accentuated by oxidative stress, and MEN by starvation. Overall, we find that biological network interactions are strongly influenced by environmental conditions, underscoring the importance of examining networks as dynamic entities.

| S-EPMC3516483 | biostudies-literature

Regimes of Biomolecular Ultrasmall Nanoparticle Interactions.

Project description:Ultrasmall nanoparticles (USNPs), usually defined as NPs with core in the size range 1-3 nm, are a class of nanomaterials which show unique physicochemical properties, often different from larger NPs of the same material. Moreover, there are also indications that USNPs might have distinct properties in their biological interactions. For example, recent in vivo experiments suggest that some USNPs escape the liver, spleen, and kidney, in contrast to larger NPs that are strongly accumulated in the liver. Here, we present a simple approach to study the biomolecular interactions at the USNPs bio-nanointerface, opening up the possibility to systematically link these observations to microscopic molecular principles.

| S-EPMC5485067 | biostudies-literature

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes.

Project description:In recent years, microRNAs have been shown to play important roles in physiological as well as malignant processes. The PhenomiR database http://mips.helmholtz-muenchen.de/phenomir provides data from 542 studies that investigate deregulation of microRNA expression in diseases and biological processes as a systematic, manually curated resource. Using the PhenomiR dataset, we could demonstrate that, depending on disease type, independent information from cell culture studies contrasts with conclusions drawn from patient studies.

| S-EPMC2847718 | 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