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obsolete terms that are in the deprecated subset #1878

Open Clare72 opened 2 weeks ago

Clare72 commented 2 weeks ago

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
SianGramates commented 2 weeks ago

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.

epipharynx primordium aorta primordium
Clare72 commented 2 weeks ago

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!)

Clare72 commented 2 weeks ago

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