Brain Data Standards - A method for building data-driven cell-type ontologies

Abstract

Large-scale single-cell ‘omics profiling is being used to define a complete catalogue of brain cell types, something that traditional methods struggle with due to the diversity and complexity of the brain. But this poses a problem: How do we organise such a catalogue - providing a standard way to refer to the cell types discovered, linking their classification and properties to supporting data? Cell ontologies provide a partial solution to these problems, but no existing ontology schemas support the definition of cell types by direct reference to supporting data, classification of cell types using classifications derived directly from data, or links from cell types to marker sets along with confidence scores. Here we describe a generally applicable schema that solves these problems and its application in a semi-automated pipeline to build a data-linked extension to the Cell Ontology representing cell types in the Primary Motor Cortex of humans, mice and marmosets. The methods and resulting ontology are designed to be scalable and applicable to similar whole-brain atlases currently in preparation.

A concerted neuron–astrocyte program declines in ageing and schizophrenia

“…Feature plots for neuronal subtypes (Supplementary Figs. 2 and 3 ) were generated using markers from the repository in https://bioportal.bioontology.org/ontologies/PCL (v1.0, 2020-04-26) 75 , 76 , 78 , specifically those for neuronal subtypes from MTG.…”

“…Feature plots for astrocyte subtypes previously described in both the MTG and M1 75 , 76 (Extended Data Fig. 9 ) were generated using markers from the repository at https://bioportal.bioontology.org/ontologies/PCL (v.1.0, 2020-04-26) 75 , 76 , 78 . Leiden clusters were assigned to one of three astrocyte subtypes on the basis of expression of these subtype markers.…”

Concerted neuron-astrocyte gene expression declines in aging and schizophrenia

“…4 and Extended Data Fig. 5) were generated using markers from the repository in https://bioportal.bioontology.org/ontologies/PCL (v1.0, 2020-04-26) 75,76,78 , specifically those for neuronal subtypes from MTG.…”

“…Feature plots for astrocyte subtypes previously described in both MTG and M1 75,76 (Extended Data Fig. 17) were generated using markers from the repository in https://bioportal.bioontology.org/ontologies/PCL (v1.0, 2020-04-26) 75,76,78 . Leiden clusters were assigned to one of three astrocyte subtypes on the basis of expression of these subtype markers.…”

Publication, Funding, and Experimental Data in Support of Human Reference Atlas Construction and Usage

“…Each month, 88,777 papers are published in PubMed making it difficult to keep track of expertise, methods, data, code. Scientific Data papers typically focus on ontologies [10][11][12] or experimental data [13][14][15] while science of science studies commonly focus on authors, their publications, and possibly the funding that supports the research 16 . The construction of a HRA benefits from interlinking expertise, publication, funding, and experimental datasets.…”