biology

SoyBase Database

SoyBase Database is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand SoyBase Database rather than just read about it. In short: SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans.

Key takeaways

SoyBase Database belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect SoyBase Database to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of SoyBase Database from memory before moving on to harder problems.

Reference excerpt

SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans. It includes genetic maps, information about Mendelian genetics 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 as a central repository for the soybean genetics community's published information. Originally, the database concentrated on genetic information such as genetic linkage 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 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 (GMOD) open-source software. 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 (GWAS) Quantitative Trait Loci (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 data such as DNA methylation and gene expression data of various soybean strains subjected to different treatments and from different soybean tissues/cultivars. Metabolic data and biochemical pathway information is displayed using Pathway Tools. Soybean metabolic pathway information (SoyCyc) was inferred by the Plant Metabolic Network project and was used to populate PathwayTools displays.

References

External links Plant Metabolic Network project Generic Model Organism Database project Legume Federation project Legume Information System United States Department of Agriculture InterMine

Worked examples

Example 1 — a first encounter with SoyBase Database

Start with the simplest possible case. Write down what SoyBase Database claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to SoyBase Database before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about SoyBase Database ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of SoyBase Database

In research: SoyBase Database appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses SoyBase Database in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: SoyBase Database is common in secondary-school and first-year university syllabi. It links to neighbouring topics Model organism databases, so understanding it makes those chapters shorter.
In everyday life: Look for SoyBase Database outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study SoyBase Database in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SoyBase Database means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain SoyBase Database out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SoyBase Database in simple terms?

SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans.

Why does SoyBase Database matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study SoyBase Database?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on SoyBase Database.