INCF Working Group on Neuroinformatics for cell types
Maryann Martone, UC San Diego
Tom Gillespie, UC San Diego
This Working Group coordinates common efforts for defining and describing cell types across neuroscience, to reduce duplicate efforts and to improve interoperability and reuse of cell type-specific data collected across groups. The key focus is facilitating interactions between groups collecting large-scale datasets used to define novel cell types (such as single-cell transcriptomics) and ontologists and tool developers who have considerable experience curating cell type-specific data, with the goal to reduce duplicate efforts and to improve interoperability and reuse of cell type-specific data collected across groups.
The coordination of this effort has now moved to the Allen Institute, as part of their work on cell nomenclatures which began with the Cell Type Ontology Workshop held at the Allen Institute in Seattle in 2019. The outcome of the workshop was a framework for developing nomenclature: the Common Cell Type Nomenclature, or CCN. It was initially applied to brain cells and types, and intended to encompass existing naming strategies used in publications across diverse research teams, to allow tracking of many different taxonomies across diverse areas of bioscience. The CCN is described in this 2020 paper in eLife. To learn more about the current activities of the CCN, visit: https://portal.brain-map.org/explore/classes/nomenclature.
Thomas H Gillespie, University of California, San Diego
Francoise Mohammed Sy, Blue Brain Project & EPFL
Maryann E Martone, University of California, San Diego
Sean L Hill, Blue Brain Project, CAMH, EPFL & Psychiatry
This Working Group aims to provide a venue for the open and inclusive development of shared terminologies for describing cell types in neuroscience. The group develops best practices for defining new cell types based on novel measurement techniques, compiles various cell type use cases and works to connect them to existing and newly developed ontological tools. They also make suggestions for how shared terminologies can be used to guide experiments for bridging between cell types defined by orthogonal modalities.