biology

MatrixDB

MatrixDB 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 MatrixDB rather than just read about it. In short: MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides. MatrixDB takes into account the multimeric nature of the extracellular proteins (for example, collagens, laminins and thrombospondins are multimers).

Key takeaways

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

Reference excerpt

MatrixDB is a biological database focused on molecular interactions between extracellular proteins and polysaccharides. MatrixDB takes into account the multimeric nature of the extracellular proteins (for example, collagens, laminins and thrombospondins are multimers). The database was initially released in 2009 and is maintained by the research group of Sylvie Ricard-Blum at UMR5246, Claude Bernard University Lyon 1. MatrixDB is linked with UniGene and the Human Protein Atlas. It also allows users to build customised tissue- and disease-specific interaction networks, which can be further analysed and visualised using Cytoscape or Medusa. MatrixDB is an active member of the International Molecular Exchange Consortium (IMEx), a group of the major public providers of interaction data. Other participating databases include the Biomolecular Interaction Network Database (BIND), IntAct, the Molecular Interaction Database (MINT), MIPS, MPact, and BioGRID. The databases of IMEx work together to prevent duplications of effort, collecting data from non-overlapping sources and sharing the curated interaction data. The IMEx consortium also worked to develop the HUPO-PSI-MI XML standard format for annotating and exchanging interaction data. MatrixDB includes interaction data extracted from the literature by manual curation and offers access to relevant data involving extracellular proteins provided by IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database.

References

External links http://matrixdb.univ-lyon1.fr http://www.icbms.fr/aspe

Worked examples

Example 1 — a first encounter with MatrixDB

Start with the simplest possible case. Write down what MatrixDB 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 MatrixDB 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 MatrixDB 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 MatrixDB

In research: MatrixDB 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 MatrixDB 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: MatrixDB is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biological databases, Polysaccharides, so understanding it makes those chapters shorter.
In everyday life: Look for MatrixDB 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 MatrixDB in 20 minutes

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

Frequently asked questions

What is MatrixDB in simple terms?

Why does MatrixDB 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 MatrixDB?

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 MatrixDB.