Transcriptomics-based classification and nomenclature of neocortical cell types

Cell Taxonomies
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In a recent submission to arXiv several prominent investigators of brain cell types (from the Allen Institute and across the world) presented a position piece that proposes to use a transcriptomics-based system for cell type classification and nomenclature in neocortex. Do you have any thoughts about this topic? If so, please post here!

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@jeremyinseattle quite an interesting article, thank you for sharing!

I like very much the paragraph that says:
“A more flexible way to organize our knowledge and understanding of cell types would be as a living, updatable framework, one allowing reference, query and inference. One example of an appropriate datastructure for such a community platform is a ‘knowledge graph’, a widely used tool in the tech industry and computer science as a platform for data aggregation”

I totally agree, I feel that the bio community has lots to gain by embracing knowledge graphs.

I feel, however, that a “committee of experts representing the breadth of approaches and disciplines in the field.” would have a hard time coping with so many changes in the field.

I feel that extremely open approaches, like Wikidata, are a good shot. If not Wikidata per se, an equally open Wikibase. I am obviously biased, because modeling cell types on Wikidata is exactly what I do every day.

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@lubianat. Thanks for sharing, I was unaware of this Wikidata option. I will me sure to share this with the people building the knowledge graph in case it is something they could use. Regarding the committee of experts, there is always a balance to strike between building something quickly, building something correctly, building something useful to the public, and building something that various stakeholders are happy with. The committee of experts was intended to help with this task, but there are certainly other ways to achieve that goal in parallel.

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Sure, the challenge of weighing pros and cons is massive. One committee-based approach that is halfway between Wikipedia and a super centralized structure is Stanford’s Encyclopedia of Philosophy (https://plato.stanford.edu/), in which entries are authored by experts, and there are regular releases, but articles are not petrified, and things can be updated from time to time. The OBO Foundry ontologies mostly work on that way too, I guess.

In any case, Wikidata is a nice way to reach more people and could complement expert-based efforts. It is a good platform for biologists (like me) to get started with classification/structured knowledge. I’ve recently reconciled PanglaoDB’s cell type markers to Wikidata, enabling queries like “Which cell types are marked by genes related to neurogenesis?”(https://w.wiki/oKs). As a 1st year PhD student in Brazil, I feel the most straightforward way for people outside the “main circuit” to contribute are these super open systems.

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