Microbial culture collections around the world provide valuable information resources about microorganisms, but their metadata are independently maintained. To enhance the interoperability of such resources, we have developed RDF datasets from the metadata of two culture collections in Japan. Among the efforts, here, we report the RDFized microbial growth media information and a new database of growth media . Currently, the database includes 1,644 media and available at http://growthmedium.org/.
Initially, we have developed RDF data of growth media provided by the JCM and NBRC, and then we also started to collect media recipes for microorganisms of which genome sequences are available and not included in both JCM and NBRC. As of October 2019, our database contains 1644 growth media (of which 649 are from NBRC, 843 from JCM, 152 by the manual collection from research papers and the Web). The database system was implemented using OpenLink Virtuoso triple store, SPARQList API, TogoStanza, and TogoDB. One of the useful features of the RDF data is that all ingredients are described using the Growth Medium Ontology (GMO). Different BRCs or even single BRC sometimes use different naming for the same ingredients that hinders the integrated use of the growth media data. The new RDF will enable us to carry out integrated analyses such as an alignment of ingredients and design a similarity measure between growth media. Figure 1 shows a TogoStaza application to visualize the alignment of ingredients of growth media used for the specified microorganisms. We have a plan to implement a functionality for retrieving similar media to a userspecified medium.