MetaboLights is a data repository founded in 2012 for cross-

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...

and cross-platform metabolomic 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, ...

. The database is maintained by the European Bioinformatics Institute (EMBL-EBI) and the development is funded by Biotechnology and Biological Sciences Research Council (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 to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fie ...

and mass spectrometry. Semantic annotation is based on various

ontologies In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...

and controlled vocabularies, including the

BRENDA tissue ontology The BTOGremse, M., Chang, A., Schomburg, I., Grote, A., Scheer, M., Ebeling, C., Schomburg, D. (2011): �The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources��, ''Nucleic Acids Res.'', 39 (Databas ...

and the

NCBI The National Center for Biotechnology Information (NCBI) is part of the United States 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 ...

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

ChemSpider ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry. Database The database contains information on more than 100 million molecules from over 270 data sources including: * EPA DSSTox * U.S. Food and D ...

PubChem PubChem is a database of 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 is part of ...

, 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 Bioinf ...

. 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 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 method for acquiring knowledge that has characterized the development of science since at least the 17th century (with notable practitioners in previous centuries; see the article history of scientific ...

. Copyright and license information, however, is not easily identifiable. MetaboLights includes user tools for submission of experiments using the ISA-TAB format for metadata 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 journals, 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, in the broadest sense, is the physical world or universe. "Nature" can refer to the phenomena of the physical world, and also to life in general. The study of nature is a large, if not the only, part of science. Although humans are ...

Scientific Data In the pursuit of knowledge, data (; ) is a collection of discrete values that convey information, describing quantity, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols that may be further interpr ...

.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 Biological databases Science and technology in Cambridgeshire Scientific databases South Cambridgeshire District