Application for a specialised information service in Systems Medicine

Involved Partners: Nicole Radde (Universität Stuttgart), Dagmar Waltemath (Universitätsmedizin Greifswald), Christian Winterhalter (Universitätsbibliothek Greifswald)

Participation opportunities

Survey on the Needs of the Systems Medicine Community

Until September 13, you can still participate in our survey on the currently used services and tools for research in systems medicine. The contact person for inquiries is Hilke Beelich.

Workshop at GMDS 2023 in Heilbronn on September 19, 2023, from 2:00 PM to 3:30 PM

As part of the workshop at GMDS 2023, we aim to gather specific needs, requirements, and potential preliminary work for the establishment of the specialized information service. The planned FID is intended to build on existing work and create an information portal for unified access to semantically well-described standard formats, metadata models, guidelines, services, domain-specific services, educational offerings, and curated example datasets. We want to discuss in this session what such an FID should look like, what information it should include, and what functionalities it should offer to users.

 

Workshopplan (tentative)
Time slotGoalWhat?Who?
14:00-14:10 UhrSetting the sceneWhat is a specialised information service? What is „Systems Medicine“?Dagmar Waltemath
14:20-15:10 UhrWorld CafeNeeds at the FID SysMedtba
15:10-15:25 UhrWrap-UpResults of the work groupstba
15:25-15:30 UhrNächste SchritteInformation about the application procedureDagmar Waltemath

Context

The adherence to the FAIR data principles ensures that the data produced within the context of a scientific project is Findable, Accessible, Interoperable, and Reusable (FAIR). The implementation of FAIR principles leads to a more transparent data management, thereby promoting the use and reuse of data in the scientific community.

In the context of a systems medicine research question, the focus is typically on a simulation model that, under various conditions, examines the effects of different biochemical interventions, therapies, medication decisions, or the impact of prophylactic measures and generates computer-assisted predictions.

The increasing complexity of models and the rapidly growing number of simulation studies have underscored the need for structured knowledge representation in this field. Among the existing community-driven solutions are:

  • COMBINE, a global network for standardizing and harmonizing data representation formats and metadata for model description, visualization, and simulation.
  • BioModels Database, an open repository for computer-assisted models operated by EMBL-EBI.
  • Center for Reproducible Biomodeling for training in sustainable systems medicine and a collection of modeling and simulation tools.

These resources are freely available but are currently challenging to find. While individual actors are well-connected, these networks and communication channels are not easily recognizable for users. Additionally, publications with guidelines, specifications, and assistance for working with simulation models have been released but are not adequately linked to the respective networks or research groups.

On the other hand, there is a clear need for reusable simulation studies in the context of the reproducibility crisis (Höpfl et al., 2023). For example, BioModels has reported this rate to be approximately 50% - these are the already curated systems medicine models (Tiwari et al., 2021). Reproducibility Cards (Tiwari et al., 2021a) and position papers (Niarakis et al., 2022, Papin et al., 2020) have also drawn attention to the problems of the lack of availability of good metadata, correctly implemented standards, and high-quality repositories.

The planned FID aims to build on existing work and establish an information portal for unified access to semantically well-described standard formats, metadata models, guidelines, services, domain-specific services, educational offerings, and curated example datasets. In various participation formats, we are currently gathering the specific needs, requirements, and possible preliminary work for the application to establish a specialized information service.