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

Workshop organizers




- The mini-atlas and the CCN - lessons learned

- Principles of data management required for scalable linking and FAIR data sharing

- Taxonomies and the Allen Institute informatics structure

- CCN 2.0 outline




Use cases (invited talks):

- Taxonomy author use cases and challenges

- Taxonomy consumer use cases

David Fischer, Tooling for snRNA-seq annotation

Fenna Krienen, Cross-species taxonomies

Aparna Bhaduri, Use of CCN in brain development studies



- Authoring

- Consuming

- Representing development


Report back and planning for future work and testing


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