obsolete terms that are in the deprecated subset
Clare72 opened this issue · 3 comments
I don't have any information about this subset, but it looks as though there was at some stage a plan to obsolete these terms as they have been added to a subset called 'deprecated' and they have a comment saying 'DEPRECATION WARNING'. Looking at the terms it seems as though they are overly specific stage terms (except for the 3 optic lobe terms), where it might be better to use FBdv for curation.
The stage terms seem to have mostly been used to annotate images.
In some cases (mainly embryo cycles, pupal and adult substages) these terms are either not used or an appropriate FBdv term is already also used - I think these terms can just be obsoleted now.
In other cases an appropriate FBdv term will need adding.
The embryonic optic lobe terms do not have definitions, but comments say that they are duplicates of the respective 'primordium' terms, so these should just be merged.
| ID | label |
|---|---|
| FBbt:00005304 | blastoderm embryo |
| FBbt:00000054 | cleavage stage embryo |
| FBbt:00005292 | cycle 1 embryo |
| FBbt:00005303 | cycle 10 embryo |
| FBbt:00005307 | cycle 11 embryo |
| FBbt:00005308 | cycle 12 embryo |
| FBbt:00005309 | cycle 13 embryo |
| FBbt:00005312 | cycle 14 embryo |
| FBbt:00005313 | cycle 14A embryo |
| FBbt:00005314 | cycle 14B embryo |
| FBbt:00005315 | cycle 15 embryo |
| FBbt:00005316 | cycle 16 embryo |
| FBbt:00005294 | cycle 2 embryo |
| FBbt:00005295 | cycle 3 embryo |
| FBbt:00005296 | cycle 4 embryo |
| FBbt:00005297 | cycle 5 embryo |
| FBbt:00005298 | cycle 6 embryo |
| FBbt:00005299 | cycle 7 embryo |
| FBbt:00005300 | cycle 8 embryo |
| FBbt:00005302 | cycle 9 embryo |
| FBbt:00005331 | dorsal closure embryo |
| FBbt:00005660 | embryonic inner optic lobe |
| FBbt:00005659 | embryonic optic lobe |
| FBbt:00005661 | embryonic outer optic lobe |
| FBbt:00005321 | extended germ band embryo |
| FBbt:00005337 | first instar larva |
| FBbt:00005317 | gastrula embryo |
| FBbt:00005333 | late embryo |
| FBbt:00005290 | pre-blastoderm embryo |
| FBbt:00005338 | second instar larva |
| FBbt:00005291 | stage 1 embryo |
| FBbt:00005340 | stage 1 third instar larva |
| FBbt:00005324 | stage 10 embryo |
| FBbt:00005325 | stage 11 embryo |
| FBbt:00005327 | stage 12 embryo |
| FBbt:00005328 | stage 13 embryo |
| FBbt:00005330 | stage 14 embryo |
| FBbt:00005332 | stage 15 embryo |
| FBbt:00005334 | stage 16 embryo |
| FBbt:00005335 | stage 17 embryo |
| FBbt:00005293 | stage 2 embryo |
| FBbt:00005341 | stage 2 third instar larva |
| FBbt:00005301 | stage 3 embryo |
| FBbt:00005306 | stage 4 embryo |
| FBbt:00005311 | stage 5 embryo |
| FBbt:00005318 | stage 6 embryo |
| FBbt:00005319 | stage 7 embryo |
| FBbt:00005322 | stage 8 embryo |
| FBbt:00005323 | stage 9 embryo |
| FBbt:00005370 | stage A1 adult |
| FBbt:00005371 | stage A2 adult |
| FBbt:00006012 | stage A3 adult |
| FBbt:00005343 | stage P1 prepupa |
| FBbt:00005357 | stage P10 pharate adult |
| FBbt:00005358 | stage P11 pharate adult |
| FBbt:00005359 | stage P11(i) pharate adult |
| FBbt:00005360 | stage P11(ii) pharate adult |
| FBbt:00005361 | stage P12 pharate adult |
| FBbt:00005362 | stage P12(i) pharate adult |
| FBbt:00005363 | stage P12(ii) pharate adult |
| FBbt:00005364 | stage P13 pharate adult |
| FBbt:00005365 | stage P14 pharate adult |
| FBbt:00005366 | stage P15 pharate adult |
| FBbt:00005367 | stage P15(i) pharate adult |
| FBbt:00005368 | stage P15(ii) pharate adult |
| FBbt:00005344 | stage P2 prepupa |
| FBbt:00005345 | stage P3 prepupa |
| FBbt:00005346 | stage P4 prepupa |
| FBbt:00005347 | stage P4(i) prepupa |
| FBbt:00005348 | stage P4(ii) prepupa |
| FBbt:00005350 | stage P5 pupa |
| FBbt:00005351 | stage P5(i) pupa |
| FBbt:00005352 | stage P5(ii) pupa |
| FBbt:00005353 | stage P6 pupa |
| FBbt:00005354 | stage P7 pupa |
| FBbt:00005355 | stage P8 pharate adult |
| FBbt:00005356 | stage P9 pharate adult |
| FBbt:00005305 | syncytial blastoderm embryo |
| FBbt:00005339 | third instar larva |
I think we should NOT deprecate the collective embryonic terms (blastoderm embryo, gastrula embryo, dorsal closure embryo, extended germ band embryo, late embryo). They are part_of parents to many developing structure terms, and useful to curators trying to decide which of several terms in a developmental sequence to use (some of the developing structure definitions include stage information, but many do not). So while we don't attach data TO them, we definitely curate WITH them.
There is a bit of an ontological problem with some of these part_of relationships, but a proper solution is complicated, so we can leave them for now (probably several years!)
I have split the terms to keep out into a new ticket - #1882
and also split out embryonic optic lobe merges to new ticket - #1881
Remaining stage terms to be obsoleted (when curation updated to use FBdv):
| ID | label |
|---|---|
| FBbt:00005292 | cycle 1 embryo |
| FBbt:00005303 | cycle 10 embryo |
| FBbt:00005307 | cycle 11 embryo |
| FBbt:00005308 | cycle 12 embryo |
| FBbt:00005309 | cycle 13 embryo |
| FBbt:00005312 | cycle 14 embryo |
| FBbt:00005313 | cycle 14A embryo |
| FBbt:00005314 | cycle 14B embryo |
| FBbt:00005315 | cycle 15 embryo |
| FBbt:00005316 | cycle 16 embryo |
| FBbt:00005294 | cycle 2 embryo |
| FBbt:00005295 | cycle 3 embryo |
| FBbt:00005296 | cycle 4 embryo |
| FBbt:00005297 | cycle 5 embryo |
| FBbt:00005298 | cycle 6 embryo |
| FBbt:00005299 | cycle 7 embryo |
| FBbt:00005300 | cycle 8 embryo |
| FBbt:00005302 | cycle 9 embryo |
| FBbt:00005337 | first instar larva |
| FBbt:00005338 | second instar larva |
| FBbt:00005291 | stage 1 embryo |
| FBbt:00005340 | stage 1 third instar larva |
| FBbt:00005324 | stage 10 embryo |
| FBbt:00005325 | stage 11 embryo |
| FBbt:00005327 | stage 12 embryo |
| FBbt:00005328 | stage 13 embryo |
| FBbt:00005330 | stage 14 embryo |
| FBbt:00005332 | stage 15 embryo |
| FBbt:00005334 | stage 16 embryo |
| FBbt:00005335 | stage 17 embryo |
| FBbt:00005293 | stage 2 embryo |
| FBbt:00005341 | stage 2 third instar larva |
| FBbt:00005301 | stage 3 embryo |
| FBbt:00005306 | stage 4 embryo |
| FBbt:00005311 | stage 5 embryo |
| FBbt:00005318 | stage 6 embryo |
| FBbt:00005319 | stage 7 embryo |
| FBbt:00005322 | stage 8 embryo |
| FBbt:00005323 | stage 9 embryo |
| FBbt:00005370 | stage A1 adult |
| FBbt:00005371 | stage A2 adult |
| FBbt:00006012 | stage A3 adult |
| FBbt:00005343 | stage P1 prepupa |
| FBbt:00005357 | stage P10 pharate adult |
| FBbt:00005358 | stage P11 pharate adult |
| FBbt:00005359 | stage P11(i) pharate adult |
| FBbt:00005360 | stage P11(ii) pharate adult |
| FBbt:00005361 | stage P12 pharate adult |
| FBbt:00005362 | stage P12(i) pharate adult |
| FBbt:00005363 | stage P12(ii) pharate adult |
| FBbt:00005364 | stage P13 pharate adult |
| FBbt:00005365 | stage P14 pharate adult |
| FBbt:00005366 | stage P15 pharate adult |
| FBbt:00005367 | stage P15(i) pharate adult |
| FBbt:00005368 | stage P15(ii) pharate adult |
| FBbt:00005344 | stage P2 prepupa |
| FBbt:00005345 | stage P3 prepupa |
| FBbt:00005346 | stage P4 prepupa |
| FBbt:00005347 | stage P4(i) prepupa |
| FBbt:00005348 | stage P4(ii) prepupa |
| FBbt:00005350 | stage P5 pupa |
| FBbt:00005351 | stage P5(i) pupa |
| FBbt:00005352 | stage P5(ii) pupa |
| FBbt:00005353 | stage P6 pupa |
| FBbt:00005354 | stage P7 pupa |
| FBbt:00005355 | stage P8 pharate adult |
| FBbt:00005356 | stage P9 pharate adult |
| FBbt:00005305 | syncytial blastoderm embryo |
| FBbt:00005339 | third instar larva |