Related Experiment Video
Updated: Sep 23, 2025
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
15.6K
rbioapi: user-friendly R interface to biologic web services' API
Moosa Rezwani1, Ali Akbar Pourfathollah1, Farshid Noorbakhsh2
1Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
Bioinformatics (Oxford, England)
|May 13, 2022
Summary
The rbioapi R package offers a unified interface for biological and medical databases and web services, addressing challenges of single-service packages for improved consistency and scalability in bioinformatics research.
Area of Science:
- Bioinformatics
- Computational Biology
- Data Science
Background:
- Existing R packages often provide a one-to-one interface with specific databases or web services.
- This fragmented approach leads to user inconsistencies and developer scalability issues in bioinformatics data access.
- A unified framework is needed to streamline interactions with diverse biological and medical data resources.
Purpose of the Study:
- To develop a novel R package, rbioapi, serving as a consistent and scalable framework.
- To facilitate the implementation of Application Programming Interface (API) resources for biological and medical data within the R environment.
- To enhance user-friendliness and interoperability for accessing various bioinformatics databases and web services.
Main Methods:
- Development of the rbioapi R package as a versatile interface.
- Implementation of support for multiple biological and medical databases and web services.
- Ensuring a consistent, user-friendly, and scalable design for the package.
Main Results:
- rbioapi provides a unified interface for accessing biological and medical databases and web services.
- The package currently supports key resources including Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt.
- rbioapi is designed for consistency, user-friendliness, and scalability, overcoming limitations of single-service packages.
Conclusions:
- rbioapi offers a significant advancement for R users accessing biological and medical data.
- The package promotes consistency and scalability, simplifying complex data integration tasks.
- Future expansion of supported services aims to make rbioapi a comprehensive resource for the bioinformatics community.
Related Concept Videos
01:11Introduction to R
1.2K
R is a powerful software environment for statistical computing and graphics. Originating as an implementation of the S language, developed at Bell Laboratories, R has evolved into a robust, open-source statistical software favored by statisticians and data scientists worldwide. Its comprehensive suite includes data manipulation, calculation, and graphical display capabilities, making it versatile for data analysis and visualization. Its programming language is at the core of R's...
1.2K
01:29Protein Folding Quality Check in the RER
3.9K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.9K
01:22Interpreting R Charts
120
R chart, or range chart, is a fundamental tool in statistical process control used to monitor the variability within a process. It complements the X-bar (x̄) chart by focusing on the range of the data, rather than individual values, providing a clear picture of the process dispersion over time.
An R chart plots the range of subsets of measurements collected from a process. Each point on the chart represents the range—defined as the difference between the maximum and minimum...
An R chart plots the range of subsets of measurements collected from a process. Each point on the chart represents the range—defined as the difference between the maximum and minimum...
120
02:04Protein-Protein Interfaces
3.9K
3.9K
02:24Ribosome Profiling
3.7K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.7K
01:26Protein Modifications in the RER
5.7K
Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
5.7K