Our results exhibit the advantages of community-scale integration compared to individual analysis. First, by matching biological states across datasets and technologies, the integrated reference can help to standardize cell ontologies and naming schemes (Fig. 4b,c). When observing previously assigned annotations derived from each study, we found that matched cell populations were often assigned slightly different names (Supplementary Fig. 5f). Unsupervised integration at this scale is a valuable tool for identifying these conflicts and can assist in the development of authoritative and standardized cell ontologies. We also identified cases where integrated annotations exhibited increased resolution compared to the original labels, and verified that our higher-resolution annotations were supported by the expression patterns of reproducible gene expression markers (Supplementary Fig. 5g).
