openworm/PyOpenWorm

I can weigh in on this discussion with firsthand knowledge. The annotations in Wormbase are often wrong. In building the NeuroPAL (a strain with landmarks for complete neural ID for the purposes of ID'ing gene expression & neural activity), I've now injected nearly 100 promoters which I would consider to have high-fidelity papers backing the ID (e.g., good markers and/or dye-fill were used, I trust the lab doing the IDs, other precautions were taken, ...). Despite this care, I've found the data to have many mistakes. This sentiment is echoed by many people in our lab including those who completed the IDs for the glutamatergic, cholinergic, & GABAergic neurons (Esther, Laura, & Marie's work; most of these IDs use multiple markers to validate expression -- these are the only IDs I really trust given how much care was taken in validating the expression). The errors in past publication are likely due to the complexity of the task, the variability seen in reporter lines (many genes change their expression at different larval stages, in response to environmental insults such as starvation, and, generally, there are often a lot of weakly expressing cells that are difficult to ID so they're usually ignored). The single-cell transcriptomic work being done now by several labs is likely to fill in the gap with more solid work. For this reason, it might pay to forego the current Wormbase annotations in favor of aggregate consensus from different labs' single-cell transcriptomic work. With regards to specific MNs (e.g., AS1), I'm not sure that we have good markers for many of these (obviously this is necessary if you want to get this kind of cell specificity). I've recently seen a few of FLPs & other genes that target MN subtypes (e.g., VA11/12). Paschalis Kratsios is focused on this specific work and can provide further details and data. Hope that's helpful!