Development of a Web-Based CellCards Knowledgebase for Categorization and Analysis of Individual Cells and Cell Connectomes – UROP Symposium

Development of a Web-Based CellCards Knowledgebase for Categorization and Analysis of Individual Cells and Cell Connectomes

Fatima Oudeif

Research Mentor(s): Yongqun He
Research Mentor School/College/Department: Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology
Presentation Date: 08/03/2022
Presentation Type: Poster
Poster Number: 52
Session: Session II: 1:30 – 2:20pm
Room: League Ballroom
Authors: Fatima Oudeif, Yongqun He

Abstract

The human body is a complex network composed of many diverse cells which are distributed across tissues and harbor various genes. As the units of human body organization, these cells have their own functions and work collaboratively with other cells to form connectomes with various specific functions such as renal corpuscle connectome for blood filtering. In order to develop a thorough understanding of how cellular interactions and hierarchy effects human health and function, it is crucial to efficiently categorize, map, and visualize the cells and their associated material entities and functions. However, as the human body is a very complex system of countless interactions and connections, mapping the human body at the cellular level is a difficult task. In response to this bottleneck, we are developing a cell-centered knowledgebase called CellCards (https://cellcards.org), which defines, classifies, and categorizes cells to support hierarchy and organization of data. To achieve this goal, data is gathered from existing web resources (e.g., HubMAP ASCT+B resource) and publications and stored at the database level. Formal ontologies are being used as a vital tool for data classification. Using the podocyte cell card as an example, we have developed a MySQL database to store the data. We have also developed an automatic PHP program that extracts related data from the Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables and store the data in our MySQL database. An additional PHP program is being developed to automatically extract data from the database and systematically generate informational cards for cells and connectomes on our website. Our effective ontology-backed knowledgebase will have bypassed the difficulty of storing hierarchical data, as is the nature of the structure of the human body. The CellCards project holds many benefits – ultimately, it will form a convenient source of knowledge for the biomedical field and for the general public alike, as unifying cell data and mapping their connections and interactions with one another will greatly support our understanding of the human body as we know it. Additionally, cell cards such as dendritic cells that are important for vaccine development are being generated, thus supporting future quests for knowledge in different fields in medicine.

 

 

 

 

 

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