TogoMedium is a database of microbial culture media that is based solely on Semantic Web technology.
There exist hundreds of microbial culture collections that are maintained by biological resource centers (BRCs) around the world. Currently, 787 culture collections are listed in Culture Collections Information Worldwide (CCINFO) provided by the World Data Centre for Microorganisms (WDCM). These culture collections are not only essential infrastructure for conducting microbial research but also serve as valuable sources of rich information, including microbial physiological and phenotypic information that is described in the accompanying metadata of each microorganism. Through our collaborative efforts with BioResource Research Center, Riken, and Biological Resource Center, National Institute of Technology and Evaluation (NITE), the metadata of their culture collections, namely JCM and NBRC, have been converted into RDF datasets. Both datasets are available on the NBDC RDF portal.
Each metadata record includes the minimum data set description defined by the World Federation of Culture Collections (WFCC) Global Catalogue of Microorganisms (GCM), which includes one or more links to web documents that describe how to prepare growth media for the corresponding microorganism. Along with the development of the RDF datasets mentioned above, we have also independently developed an RDF dataset that focuses on the ingredients of microbial growth media whose recipes are provided by JCM and NBRC.
Initially, we developed RDF data of growth media provided by JCM and NBRC, and then we started to collect media recipes for microorganisms whose genome sequences are available but not included in either JCM or NBRC. As of March 2023, our database contains 2,834 growth media (of which 749 are from NBRC, 1,376 from JCM, and 709 from manual collection from research papers and the web). The database system is implemented using the OpenLink Virtuoso triple store, SPARQList API, and TogoStanza. One characteristic feature of the RDF data is that all ingredients are described using the Growth Medium Ontology (GMO). Different BRCs, or even a single BRC, sometimes use different names for the same ingredients, which hinders the integrated use of growth media data. The TogoMeidum RDF will enable us to carry out integrated analyses, such as aligning ingredients and designing a similarity measure between growth media.