You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Livestock Metabolome Database.

What is the LMDB?

Welcome to LMDB Version 1.0
The Livestock Metabolome Database (LMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in different livestock species. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database contains 1,202 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Each MetaboCard entry contains more than 100 data fields with information being devoted to chemical/clinical data and biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The LMDB database supports extensive text, sequence, chemical structure and relational query searches. Four additional databases, DrugBank, T3DB, SMPDB and FooDB are also part of the LMDB suite of databases. DrugBank contains equivalent information on ~1600 drug and drug metabolites, T3DB contains information on ~3600 common toxins and environmental pollutants, SMPDB contains pathway diagrams for ~700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

The simple text query (above) supports general text queries of the entire textual component of the database. Clicking on the Browse menu header (on the LMDB navigation panel above) generates a tabular synopsis of the LMDB's content. This browse view allows users to casually scroll through the database or re-sort its contents. Clicking on a given LMDB ID brings up the full data content for the corresponding metabolite. The Biofluids link in the Browse menu generates hyperlinked tables listing normal and abnormal concentrations of different metabolites for 23 different biofluids. In the Search menu, the ChemQuery Structure Search link allows users to draw (using a ChemSketch applet) or write (using a SMILES string) a chemical compound and to search LMDB for chemicals similar or identical to the query compound. The Text Query supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc.) of the text portion of LMDB. The Sequence Search allows users to conduct BLAST sequence searches of the over 0 gene and protein sequences contained in LMDB. Both single and multiple sequence BLAST queries are supported. The Advanced Search link opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The Advanced Search is the most sophisticated search tool for LMDB. The MS Search allows users to submit Mass spectral files (MoverZ format) that will be searched against the LMDB's library of MS/MS spectra. This allows the identification of metabolites from mixtures via MS/MS spectroscopy. The 1D and 2D NMR Searches allow users to submit peak lists from 1H or 13C NMR spectra (both pure and mixtures) or 2D TOCSY or 13C HSQC spectra, respectively, and to have these spectra compared to the NMR libraries contained in the LMDB. This allows the identification of metabolites from mixtures via NMR spectroscopy. The Downloads link provides links to collected sequence, image and text files associated with the LMDB. The HML Home button links to the Human Metabolome Library (HML) home page. The HML lists metabolites that can be ordered for a fee by researchers around the world. Finally, under the About menu there are links for LMDB Statistics, and information about the Data Sources used to assemble the LMDB.

Citing the LMDB

LMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (LMDB) and the original publication (see below). We ask that users who download significant portions of the database cite the LMDB paper in any resulting publications.

Please cite:

    Goldansaz SA, Guo AC, Sajed T, Steele MA, Plastow GS, Wishart DS (2017) Livestock metabolomics and the livestock metabolome: A systematic review. PLoS ONE 12(5): e0177675.