Short description 

Microbiologists and researchers working with microbial strains often struggle to effectively compare their own results with existing scientific information. The burden of resolving strain-based information from different platforms falls on the individual, which can be time-consuming and cumbersome.

To make this process easier, StrainInfo is a service being developed to provide a one-stop shop for strain identity information. Strain identifiers represent a universal language for working with strains and can be found throughout literature, databases, and culture collection catalogs. The most widely used strain identifiers for microorganisms are culture collection numbers (CCNo) like DSM 20083 or LMG 10502, which are assigned by culture collection centers during strain deposition. The variety of primary sources for CCNo and the absence of a centralized resource impede the finding that DSM 20083 and LMG 10502 represent the very same strain.

Resolving these identifiers facilitates the discovery of corresponding strains and the gathering of additional strain information. This is the prerequisite for microbiologists to compare their own results with other scientific information and integrate this data into their own analysis. StrainInfo provides culture collection numbers, their relations, and associated information on taxonomy, sequence accessions, and literature to help researchers in their work with microbial strains.

Graphical abstract

Graphical abstract “Use Case Strain-ID” by Lorenz Reimer with visual adaptation by Thomas Clavel is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

How you can contribute 

You are a … 

• microbiologist trying to identify and match CCNo to a given strain:
  Use the service StrainInfo and provide feedback
• microbiologist with cultures prior to their deposition:
  Register your strain designation, get a persistent strain identifier, and provide feedback using the built-in feedback (future service in the year 2024/25)

Planned output 

For researchers

• Resolving CCNo and strain designation, and their relations to sequences, species names, and literature
• Using the API to synchronize or update your data, or retrieve new culture data
• Register your strain designation prior to deposition, and receive a persistent identifier (PID) starting in the year 2024/25

Infrastructure output

• Created and testing the beta version of StrainInfo database
• Gathering feedback on functions and user experience of strain identifier service
• Providing a central registry/ resolution database for CCNo and strain designation

Achievements

• StrainInfo webpage: https://straininfo.dsmz.de/
• Developed an API for automated retrieval of strain identifier information
  Video tutorial for API search on StrainInfo: https://youtu.be/utcq5G9xtbk?feature=shared&t=58
  written explanations for API requests in Python: https://straininfo.dsmz.de/doc#manual_vd_anc_1
• Assigned unique StrainInfo ID (SI-ID) and a DOI to each strain and keep an archive for different versions of the strain data
• Integrated strain identifier search on the central NFDI4Microbiota webportal