avidaR:一个R库,可以在数字生物体的基于本体学的数据库上执行复杂的查询
Raúl Ortega1, Miguel Angel Fortuna1
1Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Seville, Spain.
PeerJ. Computer science
|October 9, 2023
概括
一个新的数据库,avidaDB和R包,avidaR,提供了来自进化实验的数字生物的全面数据. 这个工具有助于数字进化研究,增强生物研究.
科学领域:
- 人工生命的人工生命
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
背景情况:
- 数字进化研究的是自我复制的计算机程序 (数字生物),这些程序在计算环境中发生突变和进化.
- 现有的资源缺乏来自进化实验的数字生物的全面,最新的数据库,阻碍了研究.
- 数字进化领域为生物原理提供了宝贵的见解.
研究的目的:
- 开发一个基于本体学的语义数据库 (avidaDB) 和一个用户友好的R包 (avidaR) 来访问数字进化数据.
- 为研究人员提供复杂的数据查询,而不需要对语义网络技术 (SPARQL,RDF) 的专业知识.
- 支持对关键进化概念的研究,如强度,可进化性和复杂性.
主要方法:
- 开发avidaDB,一个基于本体学的语义数据库,用于存储数字生物数据.
- 创建了avidaR,这是一个R包,旨在轻松查询avidaDB.
- 为了可访问性,avidaR与CRAN (综合R档案网络) 的集成.
主要成果:
- avidaDB托管了超过一百万个数字生物的数据,包括基因组,表型和转录组.
- 通过avidaR,研究人员可以对强度,可变性,复杂性等进行复杂的分析.
- 现在可以在CRAN上使用avidaR包,确保R社区能够广泛访问.
结论:
- avidaDB和avidaR为数字进化研究社区提供了有价值的,可访问的资源.
- 这些工具使生物学家能够探索复杂的进化动态和基因组架构.
- 综合数据和用户友好的工具的可用性将推动数字演变领域的发展.
相关概念视频
Ligand Binding Sites
12.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.9K
Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
Anatomical Terminology
12.7K
Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...
12.7K
Antibody Structure and Classes
939
Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
939
Affinity and Avidity
36.2K
Overview
36.2K
Synthetic Biology
4.8K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.8K


