Blog

MaSyMoS

We are pleased to announce that we have added a new data source to CovidGraph: The MaSyMoS database 

Management System for Models and Simulations” is a Neo4J based database for SBML and CellML Models as well as simulation descriptions in SED-ML format. In addition, MaSyMoS contains bio-ontologies that are most frequently used for the annotation of models, i.e., GO, ChEBI, SBO, KiSAO.”

Essentially MaSyMoS stores simulation models and these can now be easily explored via the Visual Graph Explorer, which is available publicly for free for everyone. At the moment the MaSyMoS data is only available in our staging environment and we are working on getting it migrated into the live graph.

Simulation models help to understand the function of biological and biomedical systems. MaSyMoS connects simulation models from two major model repositories, BioModels and PMR2. Models are represented in standard formats like SBML, the Systems Biology Markup Language.

Most importantly, models are linked in the knowledge graph to associated data including publications and terms from bio-ontologies, such as the Gene Ontology. In addition to systems biology models, MaSyMoS stores curated COVID-19 models from BioModels.

MaSyMos models in the Visual Graph Explorer

Researchers can use the Visual Graph Explorer to navigate the rich network of data available in our knowledge graph. An intuitive user interface helps them to find and load selected papers, patents, authors, genes and now simulation models. This enables them to understand how ostensibly disconnected entities actually relate to each other in the real world.

The Explorer allows for nodes like papers or genes to be iteratively loaded onto a blank canvas. These can then be right clicked and additional, related nodes can be added to the canvas. Double clicking anywhere on the canvas will enable the bulk selection tool and you can simply drag a net around the nodes you want to select and click once more to finalise the selection. Right clicking on any of the selected nodes will open the menu. Nodes can also be removed from the view. For publications the abstracts and full-text can be seen directly in the sidebar of the Explorer. 

This approach allows users to build up a custom view of the data they are interested in and it is possible to easily see how nodes are related and to make intuitive jumps to new parts of the graph. Users can even get the underlying Cypher query that allows the same set of nodes to be selected directly from the Neo4j browser. (See our Documentation for more information about connecting to the Neo4j browsers of either the live or development knowledge graphs.)

To search for MaSyMoS models, species, compartments or reactions select any of the SBML options from the dropdown menu next to the search bar. This will set a starting point for exploring the graph. It is now also possible to explore models that are referenced in a publication and to display associated reactions and species in the visual graph explorer, as well as the name and author of a model.

Selecting MaSyMos Nodes

 

Adding and integrating these COVID-19 models into the CovidGraph helps to bridge the gap between biomedical research and systems biology and we are enormously pleased to have the  MaSyMoS data incorporated into our ecosystem.

 

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