Browse and Search Data and Metadata
Browse and search data and metadata from experimental projects and studies, and search the Metabolite Database, which contains metabolite structures and annotations.
- Summary of all projects (groups of studies)
- Summary of all studies
- Bubble plots of studies by disease, sample source, species, pathway and metabolite class
Experimental Projects / Studies
- Data/metadata in experimental projects/studies
- Metabolite data/metadata in experimental studies and Metabolite Database
- Untargeted MS data with an m/z value
RefMet: A Reference list of Metabolite names
- Browse/Search/Download Refmet
- Convert metabolite names to RefMet nomenclature
- Help on RefMet The main objective of RefMet is to provide a standardized reference nomenclature for both discrete metabolite structures and metabolite species identified by spectroscopic techniques in metabolomics experiments. This is an essential prerequisite for the ability to compare and contrast metabolite data across different experiments and studies. The use of identifiers such as PubChem compound id's and InChiKeys offers only a partial solution because these identifiers will vary depending on parameters such as the salt form and degree of stereochemical detail. In addition, many metabolite species, especially lipids, are not reported by MS methods as discrete structures but rather as isobaric mixtures (such as PC(34:1) and TG(54:2)). To this end, a list of 42,000 names from a set of over 200 MS and NMR studies on the Metabolomics Workbench has been used as a starting point to generate a highly curated analytical chemistry-centric list of common names for metabolite structures and isobaric species. Additionally, the vast majority of these names have been linked to a metabolite classification system using a combination of LIPID MAPS and ClassyFire classification methods. A name-conversion user interface is provided where users can submit a list of metabolite names and map them to the corresponding Refmet names. This is a work-in-progress with the caveat that many metabolite names generated by metabolomics experiments will not currently map to RefMet identifiers. Nevertheless, RefMet has the ability to greatly increase the data-sharing potential of metabolomics experiments and facilitate "meta-analysis" and systems biology objectives for the majority of commonly encountered metabolite species.
- Use the Metabolomics Workbench REST service to retrieve different types of data The REST service enables access to a variety of data (including metabolite structures, study metadata and experimental results). These requests may be carried out using a web browser or may be embedded in 3rd party applications or scripts to enable rapid programmatic access.