YMDB 2.0: a significantly expanded version of the yeast metabolome database

Abstract

YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae. Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important changes include a 7-fold increase in the number of compounds in the database (from 2007 to 16 042), a 430-fold increase in the number of metabolic and signaling pathway diagrams (from 66 to 28 734), a 16-fold increase in the number of compounds linked to pathways (from 742 to 12 733), a 17-fold increase in the numbers of compounds with nuclear magnetic resonance or MS spectra (from 783 to 13 173) and an increase in both the number of data fields and the number of links to external databases. In addition to these database expansions, a number of improvements to YMDB's web interface and its data visualization tools have been made. These additions and improvements should greatly improve the ease, the speed and the quantity of data that can be extracted, searched or viewed within YMDB. Overall, we believe these improvements should not only improve the understanding of the metabolism of S. cerevisiae, but also allow more in-depth exploration of its extensive metabolic networks, signaling pathways and biochemistry.

Defining the RNA interactome by total RNA ‐associated protein purification

“…Consistent with this, we observed significant enrichment for proteins annotated with GO term “small molecule metabolic process” (Fig B). Furthermore, 377 proteins enriched in TRAPP were annotated in the Yeast Metabolome Database (YMDB) (Ramirez‐Gaona et al , ) to be enzymes or transporters associated with pathways of intermediary metabolism (Fig D). In particular, the majority of enzymes involved in glycolysis and/or gluconeogenesis were identified in TRAPP (Fig EV5) with average enrichment of more than fourfold.…”

“…Amongst the 23 proteins showing > 2‐fold increased RNA association following sorbic acid, eleven were enzymes participating in intermediary metabolism annotated in the YMDB (Ramirez‐Gaona et al , ). In contrast, only two such enzymes were identified amongst the 100 proteins showing > 2‐fold decreased RNA binding.…”

“…We utilized The Yeast Metabolome Database (Ramirez‐Gaona et al , ) and The E. coli Metabolome Database (Sajed et al , ) to identify proteins involved in intermediary metabolism. The analysis of enrichment of proteins belonging to the GO terms in Figs B and C, B, B and C, B and C, and B was performed with Perseus software (Tyanova et al , ).…”

The BRENDA enzyme information system–From a database to an expert system

“…Examples are SMPDB (The Small Molecule Pathway Database) for human enzymes (Jewison et al, 2014). The Yeast Metabolome Database (YMDB) is a manually curated database for small molecule metabolites found in or produced by Saccharomyces cerevisiae (Ramirez-Gaona et al, 2017).…”

Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification

“…Three open metabolome databases, including PubChem 35 , the Human Metabolome Database (HMDB) 36 , and the Yeast Metabolome Database (YMDB) 37 , were used for formula and structure databases. All three databases (PubChem, HMDB, and YMDB) in XML format were downloaded, and processed by an in-house script to extract metadata associated with each metabolite, including ID, formula, InChI key, InChI string, SMILES, IUPAC, and monoisotopic mass.…”