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obophenotype / asct-b_validation

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Review Eye v1.0 table #1

Open emquardokus opened 3 years ago

emquardokus commented 3 years ago

Eye_AS_has_part_CT_log.tsv

n s slabel user_slabel o olabel user_olabel
1 CL:0000561 amacrine cell Amacrine Cells UBERON:0001791 inner nuclear layer of retina inner nuclear layer
n s slabel user_slabel o olabel user_olabel
2 CL:0000748 retinal bipolar neuron ON Bipolar Cells UBERON:0001791 inner nuclear layer of retina inner nuclear layer

Eye_AS_CT_strict_log.tsv

n s slabel user_slabel o olabel user_olabel
1 CL:0000561 amacrine cell Amacrine Cells UBERON:0001791 inner nuclear layer of retina inner nuclear layer
emquardokus commented 3 years ago

Eye_AS_has_part_CT_log.tsv Issue 1 amacrine cells are found in the inner nuclear layer of retina; https://en.wikipedia.org/wiki/Inner_nuclear_layer Issue 2 CCF_Tool problem retinal bipolar neuron vs ON Bipolar cell; it appears that there is a CT/1/NOTES column that is likely splitting up the correct information found in table that DOES show ON Bipolar Cells|ON Bipolar Cells|CL:0000749 Rows 21, 26,27,29, 30, 31, in ASCT+B table

anitacaron commented 2 years ago

These two logs are valid relationships. They're only to filter the type of relationship. In the case of __AS_has_part_CT__ they're different from the expected part of.

Image

The only file with no valid relationship is class_{organ}_log.tsv

emquardokus commented 2 years ago

Eye_v1.2_DRAFT

  1. Corrected 1 instance of obsolete CL ID mapping for Muller glia CL_0011107 - Muller glia This one is the obsolete Muller cell Updated mapping to current CL ID CL:0000636 Mueller cell. This cell had been mapped to an obsolete cell in CL CL:0011107
  2. Removed Glycinergic amacrine cell of retina FMA:62362 used; however subclass added to CL:4030028 'glycinergic amacrine cell' https://github.com/obophenotype/asct-b_validation/issues/61; I did NOT add new CL term because it's not active yet and this would also throw a flag in the 4th release pipeline. Will add for 5th release tables.