SoyBase is a database created by the

United States Department of Agriculture The United States Department of Agriculture (USDA) is the federal executive department responsible for developing and executing federal laws related to farming, forestry, rural economic development, and food. It aims to meet the needs of com ...

. It contains genetic information about

soybeans The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu an ...

. It includes genetic maps, information about

Mendelian genetics Mendelian inheritance (also known as Mendelism) is a type of biological inheritance following the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 by Hugo de Vries and Carl Correns, and later popularized ...

and molecular data regarding genes and sequences. It was started in 1990 and is freely available to individuals and organizations worldwide.

History

SoyBase was instituted by the Corn Insects and Corn Genetics Research Unit (CICGRU) in

Ames, Iowa Ames () is a city in Story County, Iowa, United States, located approximately north of Des Moines in central Iowa. It is best known as the home of Iowa State University (ISU), with leading agriculture, design, engineering, and veterinary med ...

as a central repository for the soybean genetics community's published information. Originally, the database concentrated on genetic information such as

genetic linkage Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separ ...

maps and other Mendalian information. SoyBase genetic maps are a manually-curated composite of all published mapping and QTL studies, and thus provide a species level view of markers and QTL. In 2010 the soybean

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

sequence was released along with gene models and many other types of genome annotations that were integrated in to SoyBase. SoyBase genetic linkage maps were integral to the assembly of the soybean genome. In 2018 the database received approximately 63,000 page requests from 2,600 users per month from 130 countries. About 40 organizations in the United States and 82 foreign educational institutions access SoyBase yearly. SoyBase supplies data to U.S. and foreign government organizations and corporate entities.

Data submission and release policy

Data is accepted from the original source generators only. Users that independently identify data for inclusion into the database can contact SoyBase directly. A number Excel-based spreadsheet templates are available to facilitate the inclusion of data into SoyBase. All data in SoyBase are available without restrictions. A number of data sub-setting and download tools are provided, and when needed ad hoc subsets of the data can be requested from the SoyBase Curator.

Search tool

The SoyBase Database Search Tool uses a text entry box for queries. Results are returned as text and as displays. Results display soybean genetic (and genomic) data using

Generic Model Organism Database The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the Unit ...

(GMOD)

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Ope ...

. In addition to SoyBase, objects identified by exact lexical matches to the query term, the tool also uses a soybean-specific ontology to identify biologically-related SoyBase objects. Some SoyBase sequence data and annotations are available through an InterMine instance (SoyMine), which is a collaboration with the Legume Information System Project.

Graphical displays

Genetic maps contain information on markers ( SSR, RFLP, SNP, etc.), genes, and biparental and

Genome-wide Association Study In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any varian ...

(GWAS)

Quantitative Trait Loci A quantitative trait locus (QTL) is a locus (section of DNA) that correlates with variation of a quantitative trait in the phenotype of a population of organisms. QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs) ...

(QTL). Soybean genetic maps are displayed using the CMap comparative genetic map viewer. Soybean genomic sequence and gene model data are displayed using the GBrowse sequence viewer. Other genome annotations in this viewer include

epigenetic In biology, epigenetics is the study of stable phenotypic changes (known as ''marks'') that do not involve alterations in the DNA sequence. The Greek prefix '' epi-'' ( "over, outside of, around") in ''epigenetics'' implies features that are " ...

data such as

DNA methylation DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts ...

and

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. ...

data of various soybean strains subjected to different treatments and from different soybean tissues/cultivars.

Metabolic Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cel ...

data and biochemical pathway information is displayed using Pathway Tools. Soybean

metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical ...

information (SoyCyc) was inferred by the Plant Metabolic Network project and was used to populate PathwayTools displays.

References

{{reflist

External links

Plant Metabolic Network project

Generic Model Organism Database project

Legume Federation project

Legume Information System

United States Department of Agriculture

InterMine
Biological databases Model organism databases