science

TreeBASE

TreeBASE is a science 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 TreeBASE rather than just read about it. In short: TreeBASE was a repository of phylogenetic data published in scientific journals. In phylogenetic studies, research data are collected or generated, such as comparative observations (e.g. character state matrices or multiple sequence alignments) made on a set of taxa, metadata about these taxa, and the phylogenetic trees that are inferred to best describe the evolutionary relationships between the taxa.

Key takeaways

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

Reference excerpt

TreeBASE was a repository of phylogenetic data published in scientific journals. In phylogenetic studies, research data are collected or generated, such as comparative observations (e.g. character state matrices or multiple sequence alignments) made on a set of taxa, metadata about these taxa, and the phylogenetic trees that are inferred to best describe the evolutionary relationships between the taxa.

Mission The purpose of the TreeBASE project was to provide stable records and identifiers for these data, so that other workers can refer to their deposited data in their publication, and other scientists can locate the data and use them to verify the original research or to include or extend them in further analyses.

History and funding The project was started in 1994, with funding from the US National Science Foundation. After this prototype, a redesign was initiated under the CIPRES project. This new version was released in March 2010 and has been supported by, among others, the pPOD project, which funded the addition of a RESTful web service interface with CQL search facilities, and National Evolutionary Synthesis Center (NESCent), which hosted the database and web server. Starting in Winter 2010, TreeBASE was reorganized and became associated with the Phyloinformatics Research Foundation In 2022, TreeBASE was taken offline due to security issues which were unable to be fixed with project resources; the future of the database is uncertain.

References

Worked examples

Example 1 — a first encounter with TreeBASE

Start with the simplest possible case. Write down what TreeBASE claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, 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 TreeBASE 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 TreeBASE 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 TreeBASE

In research: TreeBASE appears in science 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 TreeBASE 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: TreeBASE is common in secondary-school and first-year university syllabi. It links to neighbouring topics Academic publishing, Bibliographic databases and indexes, Database stubs, so understanding it makes those chapters shorter.
In everyday life: Look for TreeBASE 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 TreeBASE in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what TreeBASE 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 TreeBASE out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is TreeBASE in simple terms?

Why does TreeBASE matter?

Because it connects several science 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 TreeBASE?

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 TreeBASE.