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Project: LiSyM

The LiSyM SEEK is one of the key Project Hubs building on the FAIRDOM-SEEK platform, serving the Liver Systems Medicine LiSyM network and its follow up project LiSyM-Cancer. Research results of both projects are collected and published on the LiSyM-SEEK platform.

LiSyM-Cancer is a multidisciplinary research network funded by the German Federal Ministry of Education and Research (BMBF). Molecular and cell biologists, clinical researchers and experts in mathematical modelling are jointly conducting research to investigate the development of liver cancer from pre-existing conditions such as steatotic liver disease or liver cirrhosis. The aim of the joint project is to identify relevant biomarkers to diagnose and prevent hepatocellular carcinoma at early stages.

Within the LiSyM-Cancer project SEEK integrates data derived from four different platforms which are in use for data storage and exchange depending on the needs of the network members: Nextcloud for short-term data exchange, REDCap for clinical data, openBIS for experimental raw data and its metadata and OMERO for image data.

Integrating these different platforms to easily transfer and connect the data and metadata between the different systems is a key task of the data management for LiSyM-Cancer.

LiSyM Cancer

LiSyM SEEK serves as

  • a private collaboration space for the LiSyM-Cancer network, for exchanging data (of any format), models and SOPs between partners
  • a FAIR public record of sharable results of any file format from the LiSyM-Cancer Network
  • a central registry for all publications derived from the LiSyM-Cancer Network
  • a registry for data deposited in specific data repositories e.g., GEO
  • an optional entry point to upload data to specific data repositories e.g., sequencing data to ENA via use of extended metadata
  • a platform for sharing standardised computational liver models

Features Include

  • ISA structure and data attribution
  • Extended metadata rich enough to capture the metadata of data items in openBIS, NextCloud, REDCap, OMERO, respectively
  • Registering remote data and storing data in one system
  • Association of publications and data, export of publications to websites LiSyM and LiSyM-Cancer.
  • Fine grained visibility control for single files or larger groups of files Support for storing, versioning, and running SBML models using JWS Online

Further Developments

  • Yellow pages describing researchers used as input for LiSyM-Cancer
  • More model types & file types (e.g. MulticellML, PEtab)
  • Publically available mover tools between SEEK and the other systems using the API

More Information

About project and related publications