Introduction
CellCards is an ontology-backed knowledgebase of individual cells and cell connectomes. This is a collaborative project co-developed by researchers from six universities.
The ideas behind CellCards have been discussed for many years by organizations such as the BRAIN Initiative Cell Census Network (BICCN) and Allen Brain Atlas initiative and in meetings such as a previous joint HuBMAP-HCA meeting. However, how to define and generate different cell cards is still unclear. Inspired by the GeneCards program and various community discussions, we aim to develop the cell-centered CellCards knowledgebase using strong ontology support. The cells will be linked to other cells, tissues, and biomarkers, and annotated with various types of knowledge and using the semantic relations defined in interoperable ontologies.
CellCards systematically defines and classifies two types of cell cards: (i) cards for individual cell types, and (ii) cards for cell connectomes or functional tissue units. Our prototype design of the cell card tool uses the podocyte as an example. Each cell card will include various types of information. For example, different cell types will be represented with CL, cell lines with the CLO ontology, anatomic locations with Uberon terms and biological processes in GO terms. HuBMAP specific datasets such as gene expression datasets or biomarkers will be interlinked from the CellCards website as well.
In recent years the concept of a "connectome" has been introduced to describe the network of connections between neurons in the nervous system, which has proved to be a valuable approach to understanding brain function in health and disease. We aim to extend the approach of studying connected functional cellular units within other organs, tissues, and cell types. Two general patterns of cell connectomes are envisioned: (i) cells that are in direct or proximate contact and work together as a functional unit, such as the renal corpuscle connectome for blood filtering, and (ii) cells that are functionally connected via networks of messaging molecules (e.g., hormones and cytokines or ligands and receptors), such as the cells of the Renin-Angiotensin-Aldosterone System (RAAS), which act as a functional unit to regulate blood pressure. Some cell types, such as the granular cells producing renin and endothelial cells, are part of both connectomes.
We are also developing an ontology-supported Cell Annotation Pipeline (CAP) - Literature Mining program, named as "CAP-LM", to support cell card knowledge text mining. We have developed the first example page "Podoctye LM" to support the mining of podocyte-related biomelecular knowledge from the literature. More features from the program will be generated later.
Cells are the units of life. Different cell types have their own features, functions, and expression profiles. The integrative collection and views of these cells are expected to make CellCards transformative in unifying cell knowledge. Our CellCards program is novel in its systematic knowledge collection, annotation, and representation of various types of information about individual cell types and cell connectomes. Using our ontology-driven approaches, CellCards will be semantically enabled and integrated into various programs.
Suggestions, comments, and collaborations are welcome. Thank you!
