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

Autor: Tan SZK; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Kir H; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Aevermann BD; J. Craig Venter Institute (JCVI), La Jolla, CA, USA., Gillespie T; University of California San Diego, La Jolla, CA, USA., Harris N; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Hawrylycz MJ; Allen Institute for Brain Science, Seattle, WA, USA., Jorstad NL; Allen Institute for Brain Science, Seattle, WA, USA., Lein ES; Allen Institute for Brain Science, Seattle, WA, USA., Matentzoglu N; Semanticly Ltd, Athens, United Kingdom., Miller JA; Allen Institute for Brain Science, Seattle, WA, USA., Mollenkopf TS; Allen Institute for Brain Science, Seattle, WA, USA., Mungall CJ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Ray PL; Allen Institute for Brain Science, Seattle, WA, USA., Sanchez REA; Allen Institute for Brain Science, Seattle, WA, USA., Staats B; Allen Institute for Brain Science, Seattle, WA, USA., Vermillion J; Allen Institute for Brain Science, Seattle, WA, USA., Yadav A; Allen Institute for Brain Science, Seattle, WA, USA., Zhang Y; J. Craig Venter Institute (JCVI), La Jolla, CA, USA., Scheuermann RH; J. Craig Venter Institute (JCVI), La Jolla, CA, USA.; University of California San Diego, La Jolla, CA, USA., Osumi-Sutherland D; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. davidos@ebi.ac.uk.
Jazyk: angličtina
Zdroj: Scientific data [Sci Data] 2023 Jan 24; Vol. 10 (1), pp. 50. Date of Electronic Publication: 2023 Jan 24.
DOI: 10.1038/s41597-022-01886-2
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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