MetaboLights: a resource evolving in response to the needs of its scientific community
By Kenneth Haug, Keeva Cochrane, V. Nainala, Mark Williams, Jiakang Chang, Kalai Vanii Jayaseelan, C. O’Donovan. Nucleic Acids Res., 2019
579 citations recorded by the source corpus.
Abstract MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological roles and locations. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information. In this article, we describe the significant updates that we have made over the last two years to the resource to respond to the increasing amount and diversity of data being submitted by the metabolomics community. We refreshed the website and most importantly, our submission process was completely overhauled to enable us to deliver a far more user-friendly submission process and to facilitate the growing demand for reproducibility and integration with other ‘omics. Metabolomics resources and data are available under the EMBL-EBI’s Terms of Use via the web at https://www.ebi.ac.uk/metabolights and under Apache 2.0 at Github (https://github.com/EBI-Metabolights/).
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6a4e68e98ab8913dd49bb553d73d6dd2e6222f19
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Citations in the corpus
- MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, background): “With the availability of public metabolomics repositories (26,27), there is a growing interest in data mining and meta-analysis.”
- MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data (2023, unknown): “Using the accession numbers provided in the original paper, we downloaded raw sequencing data from the NCBI Sequence Read Archi v e (SRA) database, and the metabolite concentration table from the MetaboLights ( 47 ).”
- MetaboLights: open data repository for metabolomics (2023, background): “Registered accounts span 97 countries across Europe (32), Oceania (4), Americas (14), Asia (33) and Africa (13).”
- Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, methodology): “Single-omic repositories include MetaboLights [36] and Metabolomics Workbench [37] for metabolome data, the PRoteomics IDEntifications Database [38] for proteome data, Gene Expression Omnibus [39] and Sequence Read Archive [40] for genomic data, the Encyclopedia of DNA Elements [41] for functional e”