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obophenotype / brain_data_standards_ontologies

A repository for co-ordinating work on ontologies for the Brain Data Standards Project
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Differences in description groupings #20

Closed shawntanzk closed 3 years ago

shawntanzk commented 3 years ago

I'm trying to write the summary for each cell type and have started my base starting point on the extended tables with neuron descriptions in the "Phenotypic variation of transcriptomic cell types in mouse motor cortex" paper. I have noticed a few differences or things I'm not clear about between the patch-seq groupings in the "A multimodal cell census and atlas of the mammalian primary motor cortex" paper vs the extended tables with neuron descriptions in the "Phenotypic variation of transcriptomic cell types in mouse motor cortex" paper. For ease of reference, I will call them the biorxiv paper and the nature paper accordingly. I do understand that the Nature paper wasn't grouping them per se, but the difference in description grouping is something I struggled with. Anyway, below I write some issues related to this:

Vip Sncg - should this be under Vip or Sncg subclass? Dendogram in Biorxiv paper puts it under Sncg, but nature paper puts it under Vip and describes Sncg subclass as "mostly Vip- and strongly Cck+). Or should it be shared parent?

Sncg Npy2r - this should be under 'Large Cck Basket cells' right? Dendogram in Biorxiv paper is quite vague with this, the line does not seem to extend to it.

Vip Serpinf 1_1 and Vip Serpinf 1_2 grouped together which Vip Serpinf 1_3 and Vip Htr1f grouped together in description in Nature paper, compared to Vip Serpinf 1_1-3 grouped together with Vip Htr1f grouped separately. Also given the names (L5/6 CCK cell & L5 Vip cell), was wondering how to resolve that Nature paper suggests Vip Serpinf1_3 and Vip Htr1f is also found in L2/3

L2/3 Vip Bipolar cells seem quite varied in description, and groupings in description in nature paper are quite different. I can try to find the common points in the groupings and put it that way?

There are two groups of 'L5 T Martinotti Cell' in the Biorvix paper that has a gap for Sst Htr1a - could I check that this is just to exclude Sst Htr1a from the grouping?

Pvalb Gabrg1 placed under L6 FS cell w/ large sag, while Pvalb Egfem1 under Lower FS Basket Cell in Biorvix paper, whereas Nature paper clusters them with the same description (that seems to cover L6 FS cell w/ large sag)

shawntanzk commented 3 years ago

I've also made a draft of the summaries and some issues on there that relate to the above on this google doc. Happy to hear any comments on them, do please track changes so I can see and learn what should be done. Thanks!

jeremymiller commented 3 years ago

I don't know the answers to any of these questions, but I really appreciate you laying all of these differences out. Let me reach out to the domain experts and I'll post the responses in this thread once I have them.

shawntanzk commented 3 years ago

these are either solved or we will base it on information we get from nomenclature file - stagnant ticket, closing it