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The home of the Drosophila anatomy ontology
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brain lineage/neuroblast nomenclature #1799

Closed Clare72 closed 3 months ago

Clare72 commented 5 months ago

We currently have a mixture of Hartenstein and Ito/Lee nomenclature used in labels, it would be good to standardise this.

Both sets of nomenclature are still in use in publications. Ito/Lee tends to be mainly used for secondary neurons, whereas the Hartenstein nomenclature has been used at all stages of development.

In the VNC, the NB1-1, NB1-2 etc nomenclature is used for stage neutral and primary terms, whereas lineage 0, 1, 2 etc. is used for secondary terms. We could implement a similar scheme for brain neuroblasts, using Hartenstein nomenclature for neutral (including the neuroblasts themselves) and primary and Ito/Lee for secondary.

We could also make different synonym types to represent the different nomenclature schemes e.g. label: 'neuroblast BLD3' synonym: "neuroblast BLD3" EXACT HARTENSTEIN_LINEAGE [doi:10.1101/2023.06.27.546055] synonym: "neuroblast VLPl4" EXACT ITO_LEE_LINEAGE [doi:10.1101/2023.06.27.546055] (this will give us warnings for the duplicate_label_synonym check but might be the best way to provide both sets of nomenclature if a user does not know in advance which one will be the label).

Clare72 commented 4 months ago

mainly done, could do with making a lineage clone pattern (and maybe an INP pattern? - only 2 terms right now)