Update uberon mappings #1346
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Update uberon mappings #1346
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Uberon's 'anatomical group' (UBERON:0000480) has a definition that makes it incompatible with FBbt's 'anatomical group' (FBbt:00007016), despite the identical label. The correct equivalent term in Uberon is 'disconnected anatomical group' (UBERON:0034923).
FBbt's 'gonadal sheath' (FBbt:00004859) was mapped to Uberon's 'epithelium of gonad' (UBERON:0004909), which is incorrect because the gonadal sheath in Drosophila is not a simple epithelium but also contains a muscular layer. Use 'gonadal sheath epithelium' (FBbt:00047208) at our end of the mapping instead.
Uberon's 'ganglion' (UBERON:0000045) is a 'cell cluster organ' (UBERON:0010001), which does not fit well with FBbt's classification of 'ventral nerve cord' (FBbt:00005097) as a 'organ system subdivision' (FBbt:00007330, UBERON:0011216), because both FBbt and Uberon consider 'organ system subdivision' to be disjoint with 'cell cluster organ'. Remove the mapping between FBbt's 'ganglion' and Uberon's 'ganglion' for now.
The mapping between FBbt's 'cuboidal/columnar epithelium' and Uberon's 'simple columnar epithelium' is fine, despite the fact the definition of the FBbt term does not include the distinction between unilaminar and stratified epithelia. Given that there are seemingly no stratified cuboidal/columnar epithelia in Drosophila, it is correct to state this mapping as "exact".
FBbt's 'larval ventral nerve cord' was mapped to Uberon's 'ventral nerve cord'. Update the mapping so that the FBbt side points to the stage-neutral 'ventral nerve cord'.
FBbt's 'circulatory system' should point to Uberon's 'open circulatory system', instead of the more general 'circulatory system'.
Mapping between FBbt's 'symmetrical commissure' and Uberon's 'nervous system commissure' causes some problem when applying taxon constraints, due to the Uberon term being linked to the concept of white matter. Remove the mapping as per Chris Mungall's suggestion in obophenotype/uberon#325.
Use stage-neutral term 'anus' to map to Uberon's 'anus'.
As we currently do not have terms for actual muscles, our muscle cell terms (both visceral and somatic) should point to the equivalent terms in CL rather to the muscle terms in Uberon. Mapping to Uberon muscle terms can be reinstated when we'll have proper terms for muscles in FBbt.
FBbt's 'ventral neurectoderm' was mapped to Uberon's 'neurectoderm', despite the FBbt term being more specific. The correct FBbt equivalent to Uberon's 'neurectoderm' is 'neurogenic region' (which is the parent class to 'ventral neurectoderm'). FBbt's 'neurogenic region' was already mapped to Uberon's 'insect neurogenic region', but that term is of dubious use and should probably be removed from Uberon.
The mapping between FBbt's 'exocuticle' and the identical term in Uberon was marked as potentially dubious because the FBbt term is pupal-specific, which the Uberon term is not. However, given that the FBbt term is more specific than the Uberon term and not the other way round, the mapping is still correct (a FBbt exocuticle is a Uberon exocuticle that is part of some Drosophila, and that also happens to only exist in the pupae).
FBbt's 'neuromere' was mapped to Uberon's 'segmental subdivision of nervous system' (!), due to a typo. The correct Uberon term is 'neuromere', which has ID UBERON:0004732 while 'segmental subdivision of nervous system' is UBERON:0004731.
FBbt's 'testis sheath' refers to a structure containing both an epithelium and a muscle layer, and therefore should not be mapped to Uberon's 'epithelium of testis'. Likewise for 'ovarian sheath'. There is already a mapping between the sex-neutral terms 'gonadal sheath epithelium' and 'epithelium of gonad', so that will do for now. If we add sex-specific terms for 'testis epithelium' and 'ovarian epithelium', we could map them back to the corresponding Uberon terms.
Remove mapping of FBbt's 'somatic muscle cell' with Uberon's 'muscle'. The FBbt term is already mapped to CL's 'somatic muscle cell'.
FBbt's 'adult heart' was mapped to both Uberon's 'primary circulatory organ' and 'dorsal vessel heart'. In Uberon, 'dorsal vessel heart' is a subclass of 'primary circulatory organ', so there is no need for the FBbt term to be mapped to both Uberon terms. By mapping it to 'dorsal vessel heart', it is automtically classified as a 'primary circulatory organ'. Also use tge stage-neutral term 'dorsal vessel' instead of 'adult dorsal vessel' to map to Uberon's 'circulatory system dorsal vessel.
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@dosumis Do you wish to review the proposed changes to the mappings? The most important ones (related to #201) have been discussed, and I believe the others should be uncontroversial. Of note, with those changes applied (especially the removal of the |
I think this is because it has a step that strips out disjoints. |
I forgot that a lot of issues were simply hidden under the rug by that step… ^^' Yes, those mapping changes do not fix all the incompatibilities between FBbt and Uberon, far from it. But they at least fix those that can be fixed simply by playing on the mappings themselves, without requiring deeper changes to either FBbt or Uberon. |
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@dosumis As discussed in the VFB/FlyBase ontologies call of 26 January, this PR addresses the most easily solvable issues in the Uberon/FBbt bridge (that is, issues that can be solved just by updating the mapping themselves, without requiring any further changes to the underlying ontologies). If you have no objection, I’d like to have that merged before starting to address the other, not-as-easily-solvable issues. |
dosumis
requested changes
Feb 7, 2022
src/ontology/mappings.tsv
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| FBbt:00004974 UBERON:0003202 exact endocuticle Conflicting definition (inner layer in Uberon; middle layer in FBbt) | ||
| FBbt:00004507 UBERON:0003211 exact medial ocellus Uberon term should be under ‘dorsal ocellus’ (CL:0003161) | ||
| FBbt:00005159 UBERON:0003212 exact gustatory sensory organ | ||
| FBbt:00007474 UBERON:0003914 exact epithelial tube | ||
| FBbt:00005066 UBERON:0003917 exact fat body Uberon definition makes it a single gland localized dorsally to the gut; FBbt definition makes it distributed throughout the body; and not sure it's correct to define it as a gland | ||
| FBbt:00025998 UBERON:0004120 exact mesodermal derivative | ||
| FBbt:00025990 UBERON:0004121 exact ectodermal derivative | ||
| FBbt:00005140 UBERON:0004732 exact neuromere Should point to neuromere (Uberon:0004731)? | ||
| FBbt:00005140 UBERON:0004731 exact neuromere |
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I think uberon needs a more abstract 'segmental subdivision of the nervous system as parent to both current Uberon and FBbt neuromere.
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OK, then I’ll remove that mapping for now and add it to the list of “mappings that may need deeper changes in either FBbt or Uberon”.
src/ontology/mappings.tsv
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| FBbt:00004859 UBERON:0004909 exact gonadal sheath Source term should be ‘gonadal sheath epithelium’ (FBbt:00047208) | ||
| FBbt:00004955 UBERON:0004910 exact testis sheath The FBbt term does not refer to an epithelium (the testis sheath contains an epithelial layer but also a muscular layer); maybe FBbt should have a 'male gonadal sheath epithelium'? | ||
| FBbt:00004896 UBERON:0004911 exact ovarian sheath Likewise | ||
| FBbt:00047208 UBERON:0004909 exact gonadal sheath epithelium |
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Equivalence may be too strong here. Note also Uberon term looks dodgy to me. Its text def says epithelium surrounding a gonad. Its logical def covers all epithelia of gonad. Not clear that all are on surface (see granulosa cell layer) and anyway there are bound to be species where this doesn't apply.
Remove mapping between FBbt’s `neuromere` and Uberon’s `neuromere`, on the grounds that Uberon could use a more abstract `segmental subdivision of the nervous system`. Remove mapping between FBbt’s `gonadal sheath epithelium` and Uberon’s `epithelium of gonad`. The Uberon term has a logical definition that covers all epithelia of gonad, not necessarily only an epithelium at the surface of it (despite what the text definition says).
Update mappings to reflect newly added terms in Uberon (see obophenotype/uberon#2272).
As some point this will have to be automated in the Makefile, but I’d rather have that done upstream in the ODK rather than in FBbt, so let’s keep doing it “manually” for now.
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This PR fixes some of the problems with the current mappings between FBbt and Uberon, notably some highlighted in #201.
It focuses on issues that can be addressed solely by editing the mappings themselves, without requiring any changes to FBbt or Uberon terms (including addition of new terms).
The following changes have been discussed in #201:
anatomical groupto Uberon’sdisconnected anatomical group(instead ofanatomical group, which has a definition that makes it incompatible with the FBbt term despite the identical label).epithelium of gonadto FBbt’s recently addedgonadal sheath epithelium( instead ofgonadal sheath, which refers to a structure containing a muscular layer in addition to an epithelium).ganglionand Uberon’sganglion, which have incompatible classifications (multi-tissue structurein FBbt,cell cluster organin Uberon).Other changes include:
ventral nerve cordto FBbt’sventral nerve cordinstead oflarval ventral nerve cord, or Uberon’scirculatory system dorsal vesselto FBbt’sdorsal vesselinstead ofadult dorsal vessel).circulatory systemto Uberon’sopen circulatory system(instead of the more generalcirculatory system).symmetrical commissureand Uberon’snervous system commissure(problematic due to the Uberon term being linked to the concept of white matter; removal of the mapping suggested by Chris Mungall in the discussion about brain commissures, white matter and non-vertebrates obophenotype/uberon#325).neurectodermto FBbt’sneurogenic region(instead of the more specificventral neurectoderm).neuromereto Uberon’sneuromere(instead ofsegmental division of nervous system, to which it was previously mapped – most likely as a result of a typo, the two Uberon terms having consecutive IDs).testis sheathand Uberon’sepithelium of male gonad(the FBbt term refers to a structure containing a muscular layer; we currently do not have a term to refer solely to the epithelium of the male gonad, so better to remove the mapping for now). Likewise for for the mapping between FBbt’sovarian sheathandepithelium of female gonad.adult heartand Uberon’sprimary circulatory organ(the FBbt term is already mapped to Uberon’sdorsal vessel heart, which is a subclass ofprimary circulatory organ).