MetaboLights is a data repository founded in 2012 for cross-

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

and cross-platform

metabolomic Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerpri ...

studies that provides primary research data and meta data for metabolomic studies as well as a knowledge base for properties of individual

metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

. The database is maintained by the European Bioinformatics Institute (EMBL-EBI) and the development is funded by

Biotechnology and Biological Sciences Research Council Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds science, scient ...

(BBSRC). As of July 2018, the MetaboLights browse functionality consists of 383 studies, two analytical platforms,

NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic f ...

and

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...

Semantic Semantics is the study of linguistic Meaning (philosophy), meaning. It examines what meaning is, how words get their meaning, and how the meaning of a complex expression depends on its parts. Part of this process involves the distinction betwee ...

annotation is based on various

ontologies In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to one, many, or all domains of discourse. More ...

and controlled vocabularies, including the BRENDA tissue ontology and the

NCBI The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is loca ...

taxonomy. The metabolite structure data is linked to chemical databases, including

ChemSpider ChemSpider is a freely accessible online chemical database, database of chemicals owned by the Royal Society of Chemistry. It contains information on more than 100 million molecules from over 270 data sources, each of them receiving a unique ...

PubChem PubChem is a database of Chemistry, chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which ...

, and

ChEBI Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on "small" chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinfor ...

. Links to metabolite databases, however, seem to be missing. MetaboLights consists of two components: * a ''repository'', that enables the metabolomic community to share experimental findings, data and protocols for any metabolomic study. (Fig. 1-2) * a ''reference layer'' of individual

metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

compounds and their reference spectra including additional information on their biological roles, locations, concentrations and

raw data Raw data, also known as primary data, are ''data'' (e.g., numbers, instrument readings, figures, etc.) collected from a source. In the context of examinations, the raw data might be described as a raw score (after test scores). If a scientist ...

from metabolomic experiments. (Fig. 3)

Scope and access

The data stored in MetaboLights is available for download from an FTP site and can be reused by the scientific community, where

data sharing Data sharing is the practice of making data used for scholarly research available to other investigators. Many funding agencies, institutions, and publication venues have policies regarding data sharing because transparency and openness are consid ...

is considered an integral part of the

scientific method The scientific method is an Empirical evidence, empirical method for acquiring knowledge that has been referred to while doing science since at least the 17th century. Historically, it was developed through the centuries from the ancient and ...

. Copyright and license information, however, is not easily identifiable. MetaboLights includes user tools for submission of experiments using the ISA-TAB format for

metadata Metadata (or metainformation) is "data that provides information about other data", but not the content of the data itself, such as the text of a message or the image itself. There are many distinct types of metadata, including: * Descriptive ...

tagging of all submissions. Submitted studies are automatically assigned a stable unique accession number (e.g. MTBLS1) that can be used as a publication reference; MetaboLights is one of the repositories recommended by several

scientific journal In academic publishing, a scientific journal is a periodical publication designed to further the progress of science by disseminating new research findings to the scientific community. These journals serve as a platform for researchers, schola ...

s, including

EMBO Journal ''The EMBO Journal'' is a semi-monthly peer-reviewed scientific journal focusing on full-length papers describing original research of general interest in molecular biology and related areas. The editor-in-chief is Facundo D. Batista (Harvard Medic ...

and

Nature Nature is an inherent character or constitution, particularly of the Ecosphere (planetary), ecosphere or the universe as a whole. In this general sense nature refers to the Scientific law, laws, elements and phenomenon, phenomena of the physic ...

Scientific Data Data ( , ) are a collection of discrete or continuous values that convey information, describing the quantity, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols that may be further interpreted formally ...

.Recommended Data Repositories, http://www.nature.com/sdata/data-policies/repositories There is also a guided submission process to help meet the Metabolomics Standards Initiative (MSI) recommendations for high quality data submissions for NMR and MS experiments.

References

{{reflist Metabolomic databases Science and technology in Cambridgeshire South Cambridgeshire District