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Printable Handouts
Navigable Slide Index
- Introduction
- Development of metabolomics
- The phenome-exposome conundrum
- Reaction times following external change
- Metabolome: molecular phenotype
- Metabolomics on the rise
- Phenome centres founded all over the world
- Big data analytics
- How do you make sense of all that data?
- Open data
- F-A-I-R
- The scientific methods
- The importance of data sharing
- FAIR data in metabolomics
- International data centres in biology
- European Bioinformatics Institute (EBI)
- What do the EBI databases do?
- MetaboLights database: Overview
- MetaboLights database: Usage
- Prerequisites for FAIR data exchange
- Data submission to MetaboLights
- Controlled vocabularies & ontologies
- The Metabolomics Standards Initiative (MSI)
- Using MetaboLights in everyday life
- MetaboLights database usage example
- Easily accessible data
- Data growth in EBI data repositories
- A new type of publication: Data descriptor
- Ideal dataset preparation: LIMS
- Global standards and data exchange
- The COSMOS coordination action
- NMR markup language: nmrML
- MetabolomeXchange 2014
- MetabolomeXchange's databases
- Data growth in MetabolomeXchange
- Summary
Topics Covered
- Introduction to metabolomics, phenome and exposome
- Metabolomics on the rise
- Phenome centres
- Data sharing and FAIR data
- MetaboLights database
- ISA toolkit
- COSMOS
- MetabolomeXchange
Links
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Talk Citation
Steinbeck, C. (2017, October 31). FAIR data in metabolomics [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 3, 2024, from https://doi.org/10.69645/BRDR5376.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Dr. Christoph Steinbeck has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
Other Talks in the Series: Bioinformatics for Metabolomics
Transcript
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0:00
Hello, everyone. My name is Christoph Steinbeck.
I'm a professor for Analytical Chemistry,
Cheminformatics and Chemometrics at the Friedrich Schiller University in Jena,
in Germany, and I'm also a visiting faculty
at the European Bioinformatics Institute in Cambridge,
in the United Kingdom.
Today, I'm going to speak about FAIR data in metabolomics.
This talk is part of a whole series of lectures on computational metabolomics,
and in order to understand it best,
I would encourage you to listen to the introductory talks on metabolomics beforehand.
0:40
Metabolomics is one of an ever growing number of -omes.
It is one of the youngest of those -omes and
many aspects which are already well-established in
other omics technologies are still under development in
metabolomics such as aspects of standards,
development, and data sharing.
Metabolomics complements information from genomics and proteomics.
Since the metabolism can be seen as an end point
of information processing in biomolecular systems,
the metabolome is at least partly influenced by the genome and gene expression.
Many of its aspects, however,
are directly influenced by external stimuli such as the food we eat and much more.
1:27
This is what I like to call the phenome-exposome conundrum.
The metabolome is a molecular phenotype which
reflects a very large number of external influences under which an organism develops.
These external influences include lifestyle,
what we eat, the fact that we age,
how we exercise or don't,
the diseases that we get,
the drugs we take, and,
of course, our inherited genetics.
Those external influences are nowadays subsumed under the name exposome.