Related Experiment Video
Updated: Jun 7, 2025
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
17.5K
Graph databases in systems biology: a systematic review
Ilya Mazein1, Adrien Rougny2, Alexander Mazein2
1Medical Informatics Laboratory, University Medicine Greifswald, Walther-Rathenau-Straße 48, Greifswald 17475, Germany.
Briefings in Bioinformatics
|November 20, 2024
Summary
Graph databases are vital for systems biology, managing complex biological data. Efficient graph database use will drive future knowledge discovery in this field.
Area of Science:
- Systems Biology
- Bioinformatics
- Data Science
Background:
- Graph databases are increasingly adopted in scientific fields for handling complex, interconnected data.
- Their application in systems biology is crucial for managing biological data repositories, ontologies, networks, and pathways.
Purpose of the Study:
- To review publications utilizing graph databases in systems biology.
- To analyze the application and advantages of specific graph databases and resources.
- To discuss standardization efforts and future prospects for knowledge generation.
Main Methods:
- Comprehensive literature search of PubMed and PubMed Central for publications mentioning graph databases.
- Categorization of publications by domain and application, focusing on pathway/network biology, ontologies, and tools.
- Analysis of top 16 graph databases and highlighted resources like UniProtKB, Disease Ontology, and Reactome.
Main Results:
- Identified widespread use of graph databases across systems biology applications.
- Highlighted the benefits of graph-based solutions from resources such as UniProtKB, Disease Ontology, and Reactome.
- Detailed various approaches and advantages of different graph databases.
Conclusions:
- Efficient design, querying, and maintenance of graph databases are essential for knowledge generation in systems biology.
- Graph databases facilitate communication between biological data repositories.
- Standardization and harmonization of knowledge graph creation are ongoing efforts in the systems biology community.
More Related Videos
Related Concept Videos
02:26Protein Networks
2.2K
2.2K
02:02Genomics
35.9K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.9K
03:21Phylogenetic Trees
45.2K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.2K
01:57Gene Families
8.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.8K
01:23Phylogeny
43.7K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
43.7K
02:21Globular and Fibrous Proteins
43.4K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
43.4K