In viewing a projection of annotated scRNA-seq data with cell type assignments, the user observes that a particular cell type is broken up into several smaller clusters in the visualization, indicating that the assignment could be refined. The user wants to find other datasets where the cell type is present to see if that is the case in other datasets.
The user launches a “Find cell type in HuBMAP” query directly from the projection view in Vitessce and specifies that all other data types in addition to scRNA-seq should be included in the search. The resulting datasets are retrieved and can be viewed directly in Vitessce.
While it would be possible to launch such a query outside Vitessce and then to open the returned data sets one by one, the integration of the query interface into the visualization tool would make this process much more efficient and make it more likely that the user actually retrieves and navigates to additional datasets.
Bringing such functionality into Vitessce would complement the abstract query capabilities that the Common Coordinate Framework (CCF) and HuBMAP Knowledge Graph will enable. In particular until the community has generated more generalizable knowledge about the cell-level organization of human tissues, querying the primary data will be a critical need. Wherever possible, e.g., to define filters on the tissues or structures to be searched, we will interface with the CCF.
Needs
[ ] Ability to launch advanced query directly from Vitessce with pre-set conditions from current dataset.
[ ] Ability to select more filters/choices for output (e.g. all data types in addition to current data type of dataset)
[ ] Output from advanced query will return related datasets and have ability to be viewed directly in Vitessce
[ ] If dataset can be visualized with CCF, CCF interface will also be available.
In viewing a projection of annotated scRNA-seq data with cell type assignments, the user observes that a particular cell type is broken up into several smaller clusters in the visualization, indicating that the assignment could be refined. The user wants to find other datasets where the cell type is present to see if that is the case in other datasets.
The user launches a “Find cell type in HuBMAP” query directly from the projection view in Vitessce and specifies that all other data types in addition to scRNA-seq should be included in the search. The resulting datasets are retrieved and can be viewed directly in Vitessce.
While it would be possible to launch such a query outside Vitessce and then to open the returned data sets one by one, the integration of the query interface into the visualization tool would make this process much more efficient and make it more likely that the user actually retrieves and navigates to additional datasets.
Bringing such functionality into Vitessce would complement the abstract query capabilities that the Common Coordinate Framework (CCF) and HuBMAP Knowledge Graph will enable. In particular until the community has generated more generalizable knowledge about the cell-level organization of human tissues, querying the primary data will be a critical need. Wherever possible, e.g., to define filters on the tissues or structures to be searched, we will interface with the CCF.
Needs