The Allen Institute recently hosted two workshops on Cell Ontology & Taxonomy, which brought together scientists studying brain cell types with subject matter experts in ontology building. In my opinion, these workshop provided three useful outcomes: (1) it got people thinking about this topic, (2) it led to cell naming and organization convention that will be used for single cell RNA-sequencing data in our upcoming data release (stay tuned…), and (3) it highlighted some of out-standing questions and challenges that still need to be tackled moving forward. I will focus the remainder of this post on a subset of these questions and challenges.
- How do we name cell types in a systematic way? - Discussion revolved around how to balance the use of high-throughput gene expression information with canonical, generally morphologically-based names (e.g., Chandelier cells), or whether to use more generic cell type names (e.g., Neuron 12).
- How do we organize cell types? - In some brain regions, cell types can be hierarchically organized, while in others the organization is more complicated. One outcome of our first workshop was a proposal for how to put these cell types in a probabilistic framework, and how to map cells within this framework. Discussion at the second workshop focused on how to organize cell types into new or existing ontologies.
- To what extent can we take advantage of existing ontology work? - Several highly-used ontologies already exist in this space (e.g. cell ontology, gene ontology). Discussion revolved around situations where we could use or expand these existing tools, and situations where novel strategies would make more sense.
- How do we extend to multiple modalities or organ systems? - While the primary topic of discussion was related to gene expression in brain tissue, many people felt that an ontology system should allow inclusion of data from other organ systems (e.g., kidney or liver) or from other modalities (e.g., electrophysiology or morphology).
Whether you are a workshop attendee, an Allen Institute employee, a student, or any other interested scientist, I would encourage you to reply with any thoughts you have on this topic. I would also encourage you to Explore information related to cell taxonomy data and publications from the Allen Institute: http://portal.brain-map.org/explore/classes.