Standards Used/Developed in CellCards
This page introduces the standards that are used / developed in our CellCards project. These standards include our new developed cell card schema and many community-based interoperable ontologies.
A Cell Card Schema standard supported by LinkML is being developed to support the cellcards project.
The LinkML modeling language will be used to design schemas that are easily shared across many platforms and communities. We will leverage the modeling features of LinkML to define the minimum information standards, the structure of the cell cards, and mappings between cell card fields and ontology terms. This will allow us to validate data that goes into the cell cards and disseminate documentation to the community about the information standards required to produce CellCards. We will also use LinkML to drive the CellCards user interface. This will standardize the workflows, making it easier for other groups to use and ensuring rigor and reproducibility. We will leverage the knowledge base created in other resources such as ASCT+B2.
More information about the Cell Card Schema:
- CellCard Schema GitHub (https://github.com/CellCards/CellCard-Schema):
- Schema cellcard.yaml: https://github.com/CellCards/CellCard-Schema/blob/main/src/linkml/cellcard.yaml
- Data example (podocyte): https://github.com/CellCards/CellCard-Schema/blob/main/src/data/examples/podocyte-001.yaml
- Jupyter notebook example (podocyte): https://github.com/CellCards/CellCard-Schema/blob/main/notebooks/podocyte-linkml-example.ipynb
- Schema Documentation:
- CellCard Schema Documentation: https://cellcards.github.io/CellCard-Schema/CellCard/
- Linkml tutorial: https://linkml.io/linkml/intro/tutorial.html
- See more in our Tutorial page.
Ontologes be used in CellCards:
- Cell Ontology (CL): https://github.com/obophenotype/cell-ontology
- Cell Line Ontology (CLO): https://github.com/CLO-ontology/CLO
- Human Phenotype Ontology (HP): https://github.com/obophenotype/human-phenotype-ontology
- Uber-anatomy ontology (Uberon): http://uberon.org
- more ontologies to add later ...
More information will be added. Stay tuned ...