chemistry

Human Metabolome Database

Human Metabolome Database is a chemistry 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 Human Metabolome Database rather than just read about it. In short: The Human Metabolome Database (HMDB) is a comprehensive online database of small molecule metabolites found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada and is one of the first dedicated metabolomics databases.

Key takeaways

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

Reference excerpt

The Human Metabolome Database (HMDB) is a comprehensive online database of small molecule metabolites found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada and is one of the first dedicated metabolomics databases. The HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data (Fig. 1–3). The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra. The clinical data includes information on >10,000 metabolite-biofluid concentrations and metabolite concentration information on more than 600 different human diseases. The biochemical data includes 5,688 protein (and DNA) sequences and more than 5,000 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the HMDB contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, MetaCyc, PubChem, Protein Data Bank, ChEBI, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches. It has been widely used in metabolomics, clinical chemistry, biomarker discovery and general biochemistry education. Four additional databases, DrugBank, toxin database, SMPDB and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1,600 drug and drug metabolites, T3DB contains information on 3,100 common toxins and environmental pollutants, SMPDB contains pathway diagrams for 700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

Version history The first version of HMDB was released on January 1, 2007, followed by two subsequent versions on January 1, 2009 (version 2.0), August 1, 2009 (version 2.5), September 18, 2012 (version 3.0) and Jan. 1, 2013 (version 3.5), 2017 (version 4.0). 2022 (version 5.0). Details for each of the major HMDB versions (up to version 5.0) is provided in Table 1.

Scope and access All data in HMDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. HMDB data is available through a public web interface and downloads.

See also KEGG DrugBank SMPDB MetaCyc Bovine Metabolome Database Metabolome Metabolomics List of biological databases

References

Worked examples

Example 1 — a first encounter with Human Metabolome Database

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

In research: Human Metabolome Database appears in chemistry 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 Human Metabolome 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: Human Metabolome Database is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biochemistry databases, Food databases, Human metabolites, so understanding it makes those chapters shorter.
In everyday life: Look for Human Metabolome 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 Human Metabolome Database in 20 minutes

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

Frequently asked questions

What is Human Metabolome Database in simple terms?

Why does Human Metabolome Database matter?

Because it connects several chemistry 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 Human Metabolome 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 Human Metabolome Database.