Workshop: Standards and Tooling for Whole Brain Cell Type Taxonomies

Workshop on standards and tooling for whole brain cell type taxonomies

Large scale efforts are underway to use multimodal single cell transcriptomics technologies to generate complete atlases of brain cell types, their locations and properties, and to map these cell types between species. Integrated analysis of these results to produce a coherent picture of brain cell-types across species, their classification, properties, and locations will require robust, scalable standards for recording these relationships that are easy to author, interpret and re-use. The goal of this workshop is to present and solicit feedback on a new draft standard that aims to solve these problems, building on lessons learned in development of a mini-atlas of cell types in the mouse motor cortex, and to plan the tool development needed to make this standard easy to author and use.

Thursday, September 22, 2022
8am-1pm Pacific Time

Virtual meeting login information will be sent to registered attendees.


Registration is free. Please contact with questions.

In preparation for this workshop, we have developed a draft successor to the CCN that addresses these problems, supports annotation with ontologies directly and includes clear standards for recording cell location, bridging between modalities, and recording the provenance and evidence to support mappings. The aim of this workshop is to solicit feedback on this draft standard to ensure it meets community needs and to garner community input on the tooling we will build to make the resulting data structures easy to author and use.

Full workshop announcement     Agenda     Organizers


Workshop agenda is subject to change.



Time: Eastern

Time: Pacific

Zoom webinar opens to participants




Welcome and housekeeping

David Osumi-Sutherland, introduction and overview of workshop goals



Brain cell types and associated taxonomy standards

Moderator: Shawn Tan

Mike Hawrylycz: Defining and characterizing cell types in primary motor cortex: BICCN mini-atlas project (15 minutes)

Jeremy Miller: Cell type taxonomy standards and the Allen Institute informatics structure (10 minutes)

David Osumi-Sutherland: Principles of data management applied for scalable linking and FAIR data sharing (10 minutes)

Raymond Sanchez: Putting it all together: Cell Type Knowledge Explorer demo (5 minutes)



Break   11:50am-12:00pm 8:50-9:00am

Invited talks: Taxonomy author use cases and challenges

Moderator: Jeremy Miller

Zizhen Yao: Challenges of authoring whole brain taxonomies - lessons from mouse

Fenna Krienen: Challenges of authoring cross-species taxonomies

Aparna Bhaduri: Representing development in cell type taxonomies

Brian Kalmbach: Challenges of annotating patch-seq data and integrating it into cell-type taxonomies

12:00-1:10pm 9:00-10:10am

Invited talks: Taxonomy consumer use cases

Moderator: Patrick Ray

David Fischer: Use of ontologies and cell type taxonomies as inputs to analysis

Sten Linnarsson: Cell type taxonomies and analysis

1:10-1:30pm 10:10-10:30am
Break   1:30-2:00pm 10:30-11:00am

Extending taxonomy standards: challenges and potential solutions

Shawn Tan, Proposed taxonomy standards 2.0 to address challenges encountered while building Cell Type Knowledge Explorer (15 minutes)

Breakout rooms (45 minutes): see below for details

2:00-3:00pm 11:00am-12:00pm
Break   3:00-3:10pm 12:00-12:10pm

Report back and planning for future work and testing

Breakout room report back (30 minutes)

David Osumi-Sutherland, General discussion on integrating solutions into a path forward (15 minutes)

Mike Hawrylycz, closing remarks (5 minutes)

3:10-4:00pm 12:10-1:00pm


Breakout rooms:



Taxonomy Structure and Classifications

This breakout group will review and critique the proposed data-structures, workflows and tooling for the proposed new taxonomy standard, including linking taxonomies across species.
Representing Patch-seq This breakout group looks at how we structure, package, annotate, and link patch-seq data and predicted cell types to transcriptomically-defined taxonomies.
Representing Spatial Transcriptomics This breakout group looks at how we record the spatial location of transcripomically defined cell types and how we record evidence for it.
Representing Development This breakout group looks at how we can annotate transcriptomic data analysis indicating continuous change during development (e.g. developmental trajectories) and across space. It will also discuss the importance of integrating developmental information to cell typing in the adult.
Downstream Uses of Taxonomy This breakout group aims to solicit uses-cases and their requirements for downstream uses of the taxonomy

Workshop organizers

  • Mike Hawrylycz, Allen Institute for Brain Science

  • Huseyin Kir, European Bioinformatics Institute (EMBL-EBI)

  • Jeremy Miller, Allen Institute for Brain Science

  • David Osumi-Sutherland, European Bioinformatics Institute (EMBL-EBI)

  • Patrick Ray, Allen Institute for Brain Science

  • Raymond Sanchez, Allen Institute for Brain Science

  • Shawn Tan, European Bioinformatics Institute (EMBL-EBI)

Workshop support

  • NIH BRAIN Initiative grant, RFA-MH-19-146, A Community Framework for Data-driven Brain Transcriptomic Cell Type Definition, Ontology, and Nomenclature, 1RF1MH123220-01

  • NIH BRAIN Initiative Brain Cell Data Center (BCDC), RFA-MH-17-215, A Community Resource for Single Cell Data in the Brain, 1U24MH114827-01

  • Allen Institute for Brain Science