Closed NatalieZelenka closed 2 years ago
plasticfist
commented
3 years ago Adding comment that this isn't the only zero length subset file, there are others
you beat me to it. human-view.obo is zero length https://github.com/obophenotype/uberon/blob/master/subsets/human-view.obo
what is the best way to filter uberon for homo sapiens only? I was hoping this file would...
bgood-d4c
commented
3 years ago Yup same here.
matentzn
commented
3 years ago Sorry all, I was doing a lot of work on migrating the Uberon pipeline and I seem to have broke the mouse and human subsets - I have hotfixed this for now by uploading the last working version again, but will work on getting the updated subsets in asap. Thanks for noting, and big sorry for not seeing this earlier! Should you notice any other oddities in Uberon, please tag me directly if you remember :)
plasticfist
commented
3 years ago Thank you! @matentzn I'll go grab a copy, and I have a (noob?) question I hope you can help with. I've not been able to find a definition of what each subset is meant to include (and more importantly what they mean to exclude). e.g. organ_slim, uberon_slim, pheno_slim, but also other subsets like upper_level, non_informative, grouping_class. Also, how does human-view compare to the following (I found in a write up from ~5 years ago, I'm using it to filter in part, but it still includes non-human terms, like UBERON:0013078)
owltools --use-catalog ext.owl --reasoner elk --make-species-subset -t NCBITaxon:9606 --remove-dangling --assert-inferred-subclass-axioms --useIsInferred --remove-dangling --set-ontology-id human.owl -o human.owl
robot convert --input human.owl --output human.oboThanks @matentzn ! I'm just looking at the current hotfix file. I see there are 13341 subclasses of anatomical entity in the human_view versus 14034 in my other copy of the main ontology. human_view does seem to contain some non-human terms though, like 'fish scute' and 'bony plate'. Both have inferred 'part of' relations to Homo sapiens. I'm wondering if these inferences might be improved in the new version you are working on?
It looks like many of these are sourced from teleost anatomy.
matentzn
commented
3 years ago Note that the current "hotfixed" file is really just last years last release.. Some some variation in number of subclasses is expected.
The non-human terms sound more urgent - I will see that I take at least a look at these! Thanks for noticing :)
bgood-d4c
commented
3 years ago Right, I was comparing to the full ontology so I was happy that there were less ;).
BTW is there a uberon_human_view_ext version that includes the relevant CL terms ? I guess if not its easy to add the import.
plasticfist
commented
3 years ago @matentzn, I would second the request for uberon_human_view_ext, I am currently using ext.obo (for the CL terms), and then attempting to trim back down to human (9606 Homo Sapiens) only.
matentzn
commented
3 years ago Hey all, it seems to me that human-view.owl is already based on ext:
# run the reasoner, set to remove unsatisfiable classes (ie those not in the species specified in the context)
#ext-taxon-axioms.owl
subsets/%-view.owl: ext.owl contexts/context-%.owl
OWLTOOLS_MEMORY=14G owltools --use-catalog $< contexts/context-$*.owl --merge-support-ontologies --merge-imports-closure $(QELK) --set-ontology-id $(URIBASE)/$@ --run-reasoner -r elk -x -o -f ofn $@
.PRECIOUS: subsets/%-view.owlI am not that firm on the actual contents of Uberon, so perhaps I am wrong. In light of this: what exactly is it that you would like to have?
bgood-d4c
commented
3 years ago The main use case for the integrated cl + uberon for me is connecting cell types to body parts. It would be nice if the cell types contained in a human_view_ext were limited to human cells.
bgood-d4c
commented
3 years ago @matentzn how is it going with the new build of the subsets? Anything I might be able to help with?
matentzn
commented
3 years ago @bgood-d4c
Right now, I am only concerned with reviving the old human-view.owl; I think I have this, but I need some input from @cmungall on Monday to verify its all correct.
CL + Uberon: I can see CL and Uberon classes in the human-subset (which is based on ext); but the process here relies on taxon restrictions to actually exclude non-human classes also relies on taxon restrictions which are often missing from CL.
One way you could help me is look at the latest human-view.owl attempt and tell me everything that's wrong with it :)
https://www.dropbox.com/s/0nj2lpj48s32p0v/human-view.owl?dl=0
Talk soon!
matentzn
commented
3 years ago not to self
bgood-d4c
commented
3 years ago @matentzn at a quick glance there are a lot of fish specific terms in there. Terms with names that include one of the strings: 'fin', 'scute', 'tail', 'scale', 'gill', 'barbel' are starting points.
I found a bunch of them under the 'surface structure' group.
The definition for 'scale' includes a bunch of restrictions like - 'never in carnivora' . Pretty sure we could move that up the hierarchy a bit.
bgood-d4c
commented
3 years ago Also terms that include 'insect', 'tail', 'wing'
bgood-d4c
commented
3 years ago @matentzn here is a list for your convenience:
| pelvic fin lepidotrichium | UBERON:4000173 |
|---|---|
| caudal fin skeleton | UBERON:4000173 |
| dorsal fin basal cartilage (elasmobranchs) | UBERON:4000167 |
| dorsal fin proximal radial element 4 | UBERON:4300019 |
| anal fin distal radial bone | UBERON:2105381 |
| insect embryonic antennal segment | UBERON:2000646 |
| paired limb/fin field | UBERON:6000160 |
| forelimb wing bud mesenchyme | UBERON:0005732 |
| anal fin ray 6 | UBERON:4300231 |
| pelvic fin distal radial cartilage 2 | UBERON:2001774 |
| vinculum tendon of wing | UBERON:2201415 |
| scale | UBERON:0012119 |
| anterior dentation of dorsal fin spine 2 | UBERON:0002542 |
| dorsal fin proximal radial bone 7 | UBERON:2002004 |
| pectoral fin intermediate radial bone | UBERON:2005384 |
| dorsal fin proximal radial element 7 | UBERON:4200208 |
| posterior dentation of pectoral fin spine | UBERON:2105384 |
| pectoral fin base | UBERON:2002000 |
| tail blood vessel | UBERON:4300147 |
| tail blood vessel | UBERON:0003524 |
| basal scute | UBERON:0003524 |
| insect larval labral segment | UBERON:4200165 |
| dorsal fin proximal radial cartilage 8 | UBERON:6001734 |
| lateral ethmoid wing | UBERON:2205385 |
| insect embryonic/larval ocular segment sensillum | UBERON:2001616 |
| tail intervertebral disc | UBERON:6002642 |
| tail intervertebral disc | UBERON:0003449 |
| pelvic fin ray 2 | UBERON:0003449 |
| nail bed of finger | UBERON:2001777 |
| presumptive dorsal fin fold | UBERON:0005278 |
| dorsal fin proximal radial bone 5 | UBERON:2005104 |
| row of scales | UBERON:2005382 |
| elastoidin fin ray | UBERON:0012443 |
| posterior nasal barbel | UBERON:4400006 |
| dorsal fin distal radial cartilage 2 | UBERON:2001936 |
| scute | UBERON:2205373 |
| anal fin proximal radial bone | UBERON:0008201 |
| tail bud paraxial mesoderm | UBERON:2000268 |
| tail bud paraxial mesoderm | UBERON:0009620 |
| anal fin basal cartilage | UBERON:0009620 |
| nasal fin | UBERON:4300020 |
| caudal fin | UBERON:0009671 |
| pectoral fin proximal radial element | UBERON:4000164 |
| tail skin | UBERON:2101587 |
| tail skin | UBERON:0003534 |
| inner mental barbel | UBERON:0003534 |
| pancreas tail parenchyma | UBERON:2001969 |
| pancreas tail parenchyma | UBERON:0005224 |
| ganoid scale | UBERON:0005224 |
| pectoral fin endoskeletal disc | UBERON:4000052 |
| paired limb/fin segment | UBERON:2001456 |
| gill | UBERON:0010538 |
| insect larval head | UBERON:0002535 |
| anal fin distal radial element | UBERON:6001730 |
| dorsal fin distal radial element 3 | UBERON:2100646 |
| dorsal-fin stay | UBERON:2105374 |
| finished bone surface | UBERON:2001699 |
| dorsal fin distal radial element 4 | UBERON:4200232 |
| dorsal skin of finger | UBERON:2105375 |
| cosmoid scale | UBERON:0005276 |
| dorsal fin pterygiophore 6 | UBERON:4000081 |
| median fin | UBERON:2005369 |
| pharyngeal gill | UBERON:4000162 |
| pelvic fin actinotrichium | UBERON:0000206 |
| dorsal fin distal radial bone 1 | UBERON:2000596 |
| keratin-based scale | UBERON:2005372 |
| anal fin distal radial cartilage | UBERON:4000080 |
| branched pelvic fin ray | UBERON:2200646 |
| mesenchyme dorsal fin | UBERON:4300192 |
| median fin proximal radial cartilage | UBERON:2000788 |
| dorsal fin proximal radial bone 3 | UBERON:2205226 |
| pectoral fin ray 6 | UBERON:2005380 |
| caudal scute | UBERON:2001766 |
| scale primordium | UBERON:2001606 |
| pelvic fin distal radial bone 2 | UBERON:2002242 |
| pelvic fin | UBERON:2001415 |
| procumbent dorsal fin spine | UBERON:0000152 |
| dorsal fin proximal radial element | UBERON:4300175 |
| dorsal fin distal radial element 7 | UBERON:2100947 |
| cephalic dermal scale | UBERON:2105378 |
| pelvic fin basipterygial radial | UBERON:0018310 |
| fin hook | UBERON:1500009 |
| dorsal fin distal radial element | UBERON:4300284 |
| dorsal side of post-anal tail | UBERON:2100936 |
| dorsal side of post-anal tail | UBERON:0018692 |
| polypteroid scale | UBERON:0018692 |
| unbranched dorsal fin ray | UBERON:4000055 |
| dorsal fin proximal radial element 1 | UBERON:2001786 |
| dermal scale focus | UBERON:2101818 |
| posterior dorsal fin | UBERON:2002119 |
| internal gill | UBERON:4100014 |
| dorsal fin ray 2 | UBERON:0008892 |
| pectoral fin distal radial bone 3 | UBERON:2001755 |
| fin skeleton | UBERON:2002280 |
| dorsal fin actinotrichium | UBERON:0012353 |
| paired fin radial bone | UBERON:2000373 |
| anal fin hook | UBERON:1500006 |
| dorsal fin distal radial cartilage 7 | UBERON:2001948 |
| pectoral fin distal radial bone 1 | UBERON:2205378 |
| posterior dorsal fin basal cartilage (elasmobranchs) | UBERON:2002277 |
| dorsal tail fin | UBERON:4300032 |
| dorsal tail fin | UBERON:3010203 |
| dorsal tail fin | UBERON:3010203 |
| outer fin tissue | UBERON:3010203 |
| dorsal scute series | UBERON:3010380 |
| insect embryonic gnathal segment | UBERON:2001248 |
| dorsal fin pterygiophore 1 | UBERON:6000162 |
| median fin fold | UBERON:2002094 |
| anal fin lepidotrichium | UBERON:2000040 |
| dorsal fin distal radial cartilage 6 | UBERON:4000176 |
| pelvic fin middle radial bone | UBERON:2205377 |
| bony fin ray | UBERON:1500010 |
| mesenchyme median fin fold | UBERON:4300037 |
| dorsal fin proximal radial bone 8 | UBERON:2000912 |
| gill filament | UBERON:2005385 |
| blastema of regenerating fin/limb | UBERON:0009120 |
| mental barbel | UBERON:0012438 |
| dorsal fin distal radial bone 4 | UBERON:2002024 |
| insect larval head segment | UBERON:2005375 |
| scale pocket | UBERON:6001732 |
| anal fin middle radial bone | UBERON:4300004 |
| pelvic fin radial skeleton | UBERON:2001614 |
| dorsal fin musculature | UBERON:4440010 |
| insect visceral mesoderm | UBERON:2000648 |
| hypocercal tail | UBERON:6000130 |
| hypocercal tail | UBERON:4200056 |
| anal fin ray 7 | UBERON:4200056 |
| pelvic fin distal radial bone 3 | UBERON:2001775 |
| odontode scale | UBERON:2001416 |
| dorsal fin ceratotrichial spine (elasmobranchs) | UBERON:0000041 |
| scalenus medius | UBERON:4300101 |
| wing | UBERON:0001122 |
| rictal barbel | UBERON:0000023 |
| anal fin radial cartilage | UBERON:4300288 |
| unbranched anal fin ray | UBERON:2201671 |
| pectoral fin radial cartilage | UBERON:4300193 |
| insect imaginal precursor | UBERON:2201586 |
| dorsal fin distal radial cartilage 4 | UBERON:6005023 |
| triphycercal tail | UBERON:2205375 |
| triphycercal tail | UBERON:4200136 |
| limiting layer of elasmoid scale | UBERON:4200136 |
| pouch scale | UBERON:4000105 |
| bone of tail | UBERON:2002122 |
| bone of tail | UBERON:0006068 |
| branched caudal fin ray | UBERON:0006068 |
| pectoral fin proximal radial bone 1 | UBERON:2002062 |
| caudal-fin stay | UBERON:2002026 |
| distal epidermal cap of regenerating fin/limb | UBERON:2001700 |
| pectoral fin ray 5 | UBERON:2005149 |
| insect embryonic labial segment | UBERON:2001765 |
| post-anal tail bud | UBERON:6000165 |
| post-anal tail bud | UBERON:0002533 |
| lepidosteoid scale | UBERON:0002533 |
| median fin proximal radial bone | UBERON:4000051 |
| pectoral fin proximal radial cartilage 1 | UBERON:2005226 |
| anal fin spine 1 | UBERON:2202026 |
| anal fin radial bone | UBERON:4300097 |
| epidermal scale | UBERON:2001671 |
| pectoral fin distal radial bone | UBERON:0007381 |
| insect larval gnathal segment | UBERON:2001588 |
| dorsal fin spine 1 | UBERON:6001737 |
| dorsal fin ray | UBERON:2001789 |
| caudal fin blood vessel | UBERON:4300116 |
| branched pectoral fin ray | UBERON:2005304 |
| dorsal fin proximal radial cartilage 7 | UBERON:2001993 |
| homocercal tail | UBERON:2205384 |
| homocercal tail | UBERON:4200055 |
| pelvic fin distal radial bone | UBERON:4200055 |
| basal regeneration epithelium of regenerating fin/limb | UBERON:1500008 |
| pectoral fin hook | UBERON:2005150 |
| anterior definitive endoderm | UBERON:4300261 |
| pectoral fin radial element | UBERON:0004046 |
| gill membrane | UBERON:2101586 |
| pelvic fin ray 4 | UBERON:4300150 |
| insect mesoderm anlage | UBERON:2001779 |
| dorsal fin proximal radial cartilage 3 | UBERON:6000104 |
| anterior nasal barbel | UBERON:2205380 |
| paired fin | UBERON:2001937 |
| insect embryonic procephalic segment | UBERON:0002534 |
| proximal interphalangeal joint of little finger | UBERON:6000158 |
| dorsal fin middle radial element | UBERON:0016426 |
| ruffini nerve ending | UBERON:2101613 |
| scale sheath | UBERON:0012457 |
| dorsal fin proximal radial bone 1 | UBERON:4300234 |
| matrix part of tail of caudate nucleus | UBERON:2001818 |
| matrix part of tail of caudate nucleus | UBERON:0027246 |
| chromaffin system | UBERON:0027246 |
| insect gnathal segment | UBERON:0010074 |
| post-anal tail tip | UBERON:6000011 |
| post-anal tail tip | UBERON:0010162 |
| pectoral fin proximal radial element 3 | UBERON:0010162 |
| dorsal fin pterygiophore 5 | UBERON:2102028 |
| tail hair | UBERON:2005368 |
| tail hair | UBERON:0015148 |
| sphenoid lesser wing pre-cartilage condensation | UBERON:0015148 |
| dorsal fin distal radial bone 6 | UBERON:0010728 |
| dorsal fin proximal radial bone 2 | UBERON:2005377 |
| spinous region of dorsal fin | UBERON:2001819 |
| tip of tail | UBERON:4300120 |
| tip of tail | UBERON:7500035 |
| dorsal fin proximal radial element 6 | UBERON:7500035 |
| insect dorsal imaginal precursor | UBERON:2105383 |
| infranuchal scute | UBERON:6005831 |
| dorsal fin distal radial cartilage | UBERON:2001931 |
| dorsal fin proximal radial element 5 | UBERON:2200936 |
| anal fin proximal radial cartilage | UBERON:2105382 |
| suprabranchial fin | UBERON:2200268 |
| epicercal tail | UBERON:4000182 |
| epicercal tail | UBERON:4200061 |
| anal fin pterygiophore | UBERON:4200061 |
| dorsal fin middle radial bone | UBERON:2001420 |
| regenerating fin/limb | UBERON:2001613 |
| insect mesodermal crest | UBERON:2001269 |
| gill ray | UBERON:6000131 |
| anal fin musculature | UBERON:2001856 |
| epithelial mesenchymal boundary of regenerating fin/limb | UBERON:2001154 |
| insect larval sense organ | UBERON:2001388 |
| lateral line scale 6 | UBERON:6002639 |
| unbranched pelvic fin ray | UBERON:4300242 |
| tailgut | UBERON:4500011 |
| tailgut | UBERON:0004045 |
| pored lateral line scale | UBERON:0004045 |
| spinoid scale | UBERON:4300238 |
| insect ring gland | UBERON:4300235 |
| pectoral fin proximal radial element 4 | UBERON:6001722 |
| dorsal fin ray 5 | UBERON:2102029 |
| median fin proximal radial element | UBERON:2001758 |
| pectoral fin proximal radial cartilage 2 | UBERON:2105226 |
| tail vein | UBERON:2202027 |
| tail vein | UBERON:0003481 |
| tail fold of embryonic disc | UBERON:0003481 |
| tail fold of embryonic disc | UBERON:0009747 |
| pelvic fin distal radial element 1 | UBERON:0009747 |
| pelvic fin ray 6 | UBERON:2101417 |
| dorsal fin proximal radial element 3 | UBERON:2001781 |
| nonchromaffin paraganglion | UBERON:2105380 |
| bone of free limb or fin | UBERON:0034979 |
| caudal-fin organ | UBERON:0004375 |
| pectoral fin ray 2 | UBERON:2002125 |
| dorsal fin lepidotrichium | UBERON:2001762 |
| cheek scale | UBERON:4000177 |
| pectoral fin ray 7 | UBERON:0018312 |
| apical ectodermal ridge dorsal fin | UBERON:2001767 |
| anal fin radial skeleton | UBERON:2000090 |
| caudal fin dorsal procurrent ray | UBERON:4300143 |
| dorsal fin spine 2 | UBERON:2001829 |
| axilar scale | UBERON:2001790 |
| pectoral fin distal radial element 2 | UBERON:4300222 |
| anal fin ray 1 | UBERON:2102279 |
| apical ectodermal ridge median fin fold | UBERON:2001769 |
| tail fat pad | UBERON:2000717 |
| tail fat pad | UBERON:0018132 |
| presumptive ventral fin fold | UBERON:0018132 |
| dorsal fin ray 7 | UBERON:2005103 |
| rudimentary pectoral fin ray | UBERON:2001760 |
| tail base gland | UBERON:4300103 |
| tail base gland | UBERON:3010202 |
| caudal fin hook | UBERON:3010202 |
| unfinished bone surface | UBERON:2001949 |
| scale circulus | UBERON:4200231 |
| dorsal fin proximal radial bone 4 | UBERON:2002051 |
| lateral line scale | UBERON:2005381 |
| axillary tail of breast | UBERON:2001824 |
| axillary tail of breast | UBERON:0035289 |
| pelvic fin ray 3 | UBERON:0035289 |
| abdominal scute | UBERON:2001778 |
| apical ectodermal ridge pelvic fin | UBERON:2001547 |
| postcleithral scale | UBERON:2001450 |
| pectoral fin | UBERON:4300102 |
| finger fringes | UBERON:0000151 |
| post-anal tail | UBERON:3010123 |
| post-anal tail | UBERON:0007812 |
| dorsal fin ray 1 | UBERON:0007812 |
| caudal fin lower lobe | UBERON:2001754 |
| dorsal fin distal radial element 2 | UBERON:2001594 |
| predorsal scute | UBERON:2105373 |
| pelvic fin spine | UBERON:4200113 |
| predorsal scale | UBERON:2002270 |
| gill opening | UBERON:4500003 |
| insect mesodermal crest of segment t3 | UBERON:2002057 |
| dorsal fin proximal radial cartilage 6 | UBERON:6000132 |
| pectoral fin proximal radial cartilage 4 | UBERON:2205383 |
| finger glands | UBERON:2202029 |
| pelvic fin distal radial element 3 | UBERON:3010178 |
| embryonic post-anal tail | UBERON:2101416 |
| embryonic post-anal tail | UBERON:0007144 |
| post-anal tail muscle | UBERON:0007144 |
| post-anal tail muscle | UBERON:0003665 |
| insect labial segment | UBERON:0003665 |
| barbel | UBERON:6000014 |
| dorsal fin distal radial element 8 | UBERON:2000622 |
| pectoral fin distal radial cartilage 1 | UBERON:2105379 |
| paired fin lepidotrichium | UBERON:2202277 |
| insect embryonic/larval head sense organ | UBERON:4440011 |
| anal fin spine 2 | UBERON:6007280 |
| elasmoid scale | UBERON:4300098 |
| caudal fin lepidotrichium | UBERON:4000070 |
| pectoral fin distal radial element | UBERON:4000174 |
| pelvic fin ray 1 | UBERON:2101588 |
| chromaffin paraganglion | UBERON:2001776 |
| pectoral fin proximal radial element 2 | UBERON:0012279 |
| gill raker | UBERON:2102027 |
| adipose fin skeleton | UBERON:2000356 |
| anal fin pterygiophore 1 | UBERON:4500004 |
| presumptive median fin fold | UBERON:4300096 |
| nasal barbel | UBERON:2005102 |
| tail somite | UBERON:4300287 |
| tail somite | UBERON:0009621 |
| anterior dentation of pectoral fin spine | UBERON:0009621 |
| pharyngeal gill precursor | UBERON:2002001 |
| anal fin ray 5 | UBERON:0008894 |
| fin spine | UBERON:2001773 |
| dorsal scute | UBERON:4200075 |
| insect ocular segment | UBERON:2001160 |
| dorsal fin hook | UBERON:6000005 |
| dorsal fin pterygiophore 8 | UBERON:4300281 |
| gill raker row | UBERON:2005371 |
| pectoral fin ray 1 | UBERON:2001994 |
| dorsal fin fold | UBERON:2001761 |
| tail of pancreas | UBERON:2000102 |
| tail of pancreas | UBERON:0001151 |
| guard scale | UBERON:0001151 |
| pectoral fin distal radial bone 2 | UBERON:4200093 |
| dorsal fin pterygiophore 3 | UBERON:2002279 |
| median fin spine | UBERON:2005366 |
| maxillary barbel | UBERON:4200070 |
| outer mental barbel | UBERON:2001938 |
| dorsal fin distal radial bone 7 | UBERON:2001968 |
| dorsal fin distal radial bone 3 | UBERON:2005378 |
| pectoral fin ray 3 | UBERON:2005374 |
| paired fin radial element | UBERON:2001763 |
| median fin radial element | UBERON:1600006 |
| dorsal fin proximal radial cartilage 2 | UBERON:2105225 |
| dorsal fin proximal radial bone | UBERON:2201819 |
| median fin cartilage | UBERON:2000947 |
| fin taste bud | UBERON:2001535 |
| pelvic fin distal radial element | UBERON:0034723 |
| anal fin ray 2 | UBERON:1600008 |
| dorsal fin distal radial element 1 | UBERON:2001770 |
| anal fin middle radial cartilage | UBERON:2105372 |
| adipose fin | UBERON:2201614 |
| ovary growing follicle | UBERON:2000251 |
| insect trunk mesoderm derivative | UBERON:0012186 |
| gill lamella | UBERON:6026000 |
| pelvic fin ray 7 | UBERON:2000211 |
| dorsal fin proximal radial cartilage 4 | UBERON:2001782 |
| paired limb/fin | UBERON:2205381 |
| cycloid scale | UBERON:0004708 |
| caudal-fin ray pump | UBERON:2002285 |
| pectoral fin radial bone | UBERON:2002126 |
| unbranched pectoral fin ray | UBERON:2001586 |
| insect larval ocular segment | UBERON:4500010 |
| fin bone | UBERON:6001731 |
| pectoral fin proximal radial bone 4 | UBERON:0004376 |
| dorsal fin skeleton | UBERON:2002029 |
| pectoral fin distal radial cartilage 2 | UBERON:4000168 |
| dorsal fin radial bone | UBERON:2202279 |
| insect larval procephalic segment | UBERON:2001672 |
| dorsal fin proximal radial element 2 | UBERON:6001733 |
| anal fin ray | UBERON:2101819 |
| dorsal fin distal radial bone 5 | UBERON:4500006 |
| caudal fin radial element | UBERON:2005376 |
| archipterygial fin | UBERON:0018325 |
| definitive endoderm | UBERON:4200003 |
| paired limb/fin skeleton | UBERON:0005439 |
| caudal fin ventral procurrent ray | UBERON:0011582 |
| dorsal fin distal radial bone 8 | UBERON:2001830 |
| pelvic fin distal radial cartilage 1 | UBERON:2005379 |
| tail external integument structure | UBERON:2201417 |
| tail external integument structure | UBERON:3000982 |
| pectoral fin spine | UBERON:3000982 |
| anal fin skeleton | UBERON:2001787 |
| caudal fin actinotrichium | UBERON:4000166 |
| adipose fin ray | UBERON:2000437 |
| lateral mesethmoid wing | UBERON:4300274 |
| dorsal fin middle radial cartilage | UBERON:2001747 |
| pectoral fin distal radial cartilage 3 | UBERON:2201613 |
| fin ray | UBERON:2202280 |
| central figure of scute | UBERON:4400005 |
| median fin radial cartilage | UBERON:0018309 |
| paired fin spine | UBERON:2205225 |
| pectoral fin proximal radial element 1 | UBERON:4500009 |
| fascia of tail | UBERON:2102026 |
| fascia of tail | UBERON:0035096 |
| caudal fin lymph vessel | UBERON:0035096 |
| diphycercal tail | UBERON:2005303 |
| diphycercal tail | UBERON:4200053 |
| caudal fin vasculature | UBERON:4200053 |
| dorsal fin pterygiophore 4 | UBERON:2005097 |
| lobe of tail | UBERON:2005367 |
| lobe of tail | UBERON:0013131 |
| tail vasculature | UBERON:0013131 |
| tail vasculature | UBERON:0010204 |
| pectoral fin fold | UBERON:0010204 |
| dorsal fin ray 3 | UBERON:2005317 |
| pectoral fin ray | UBERON:2001756 |
| paired limb/fin cartilage | UBERON:4500007 |
| anal-fin stay | UBERON:0007389 |
| dorsal fin distal radial cartilage 1 | UBERON:2001698 |
| pectoral fin actinotrichium | UBERON:2205372 |
| dorsal fin pterygiophore 7 | UBERON:2000544 |
| mesomere (fin) | UBERON:2005370 |
| pectoral fin ray 4 | UBERON:4200160 |
| median fin skeleton | UBERON:2001764 |
| scalenus anterior | UBERON:4000170 |
| tail connective tissue | UBERON:0008622 |
| tail connective tissue | UBERON:0003599 |
| pelvic fin ray | UBERON:0003599 |
| paired fin radial cartilage | UBERON:4300117 |
| heterocercal tail | UBERON:1700006 |
| heterocercal tail | UBERON:4200054 |
| pelvic fin radial bone | UBERON:4200054 |
| pectoral fin skeleton | UBERON:2000508 |
| dorsal tail tubercle | UBERON:0010710 |
| dorsal tail tubercle | UBERON:3010201 |
| dorsal fin radial element | UBERON:3010201 |
| pelvic fin distal radial cartilage 3 | UBERON:2101672 |
| pectoral fin proximal radial bone 2 | UBERON:2201416 |
| anal fin actinotrichium | UBERON:2002027 |
| dorsal fin proximal radial element 8 | UBERON:2000375 |
| dorsal fin proximal radial cartilage 1 | UBERON:2105385 |
| pelvic fin middle radial element | UBERON:2201818 |
| insect visceral mesoderm derivative | UBERON:1600010 |
| pelvic fin distal radial bone 1 | UBERON:6026002 |
| anal fin radial element | UBERON:2001417 |
| dorsal fin | UBERON:2101671 |
| fin radial skeleton | UBERON:0003097 |
| paired limb/fin bud mesenchyme | UBERON:4440008 |
| insect larval labial segment | UBERON:0010329 |
| dorsal fin pterygiophore 2 | UBERON:6001740 |
| dorsal fin spine | UBERON:2005365 |
| skin of forelimb wing | UBERON:2002261 |
| dorsal fin pterygiophore | UBERON:0010855 |
| caudal scute series | UBERON:2001419 |
| pelvic fin skeleton | UBERON:2001605 |
| pelvic fin bud mesenchyme | UBERON:0010711 |
| ventral tail fin | UBERON:4300229 |
| ventral tail fin | UBERON:3010204 |
| ventral tail fin | UBERON:3010204 |
| dermal scale | UBERON:3010204 |
| paired fin radial skeleton | UBERON:0007380 |
| posterior dentation of dorsal fin spine 2 | UBERON:4300013 |
| paired limb/fin bud | UBERON:2002003 |
| anal fin middle radial element | UBERON:0004357 |
| dorsal fin distal radial cartilage 3 | UBERON:2101614 |
| dorsal fin distal radial element 5 | UBERON:2205374 |
| mesenchyme pectoral fin | UBERON:2105376 |
| scalenus posterior | UBERON:0003934 |
| fin | UBERON:0001123 |
| dorsal fin distal radial element 6 | UBERON:0008897 |
| ventral fin fold | UBERON:2105377 |
| regeneration epithelium of fin/limb | UBERON:2001069 |
| insect larval segment | UBERON:2001389 |
| transforming ctenoid scale | UBERON:6001729 |
| fringe on postaxial edge of finger iv | UBERON:2002274 |
| insect cardiogenic mesoderm | UBERON:3010127 |
| pectoral fin distal radial cartilage | UBERON:6005541 |
| paired fin skeleton | UBERON:2201588 |
| external gill | UBERON:0010713 |
| pectoral fin distal radial element 1 | UBERON:0008891 |
| anal fin proximal radial element | UBERON:2102277 |
| terminal scale | UBERON:2100268 |
| ventral side of post-anal tail | UBERON:4300188 |
| ventral side of post-anal tail | UBERON:0018691 |
| fin fold pectoral fin bud | UBERON:0018691 |
| fin field | UBERON:2005316 |
| pelvic fin ray 5 | UBERON:0005731 |
| pectoral fin distal radial element 3 | UBERON:2001780 |
| median fin radial bone | UBERON:2102280 |
| tail of caudate nucleus | UBERON:2005225 |
| tail of caudate nucleus | UBERON:0002628 |
| pharyngeal arch derived gill | UBERON:0002628 |
| fin web | UBERON:0011150 |
| pectoral fin proximal radial cartilage 3 | UBERON:4300031 |
| anterior dorsal fin basal cartilage (elasmobranchs) | UBERON:2202028 |
| extrinsic post-anal tail muscle | UBERON:4300033 |
| extrinsic post-anal tail muscle | UBERON:0035091 |
| insect external sensory organ | UBERON:0035091 |
| tail | UBERON:6005168 |
| tail | UBERON:0002415 |
| pelvic fin bud | UBERON:0002415 |
| caudal fin musculature | UBERON:4300173 |
| dorsal fin distal radial bone | UBERON:2000628 |
| palaeoniscoid scale | UBERON:2000936 |
| scale row | UBERON:4000074 |
| abdominal scute series | UBERON:4300006 |
| dorsal fin proximal radial cartilage | UBERON:2001254 |
| dorsal fin proximal radial cartilage 5 | UBERON:2200947 |
| dorsal fin distal radial cartilage 5 | UBERON:2205382 |
| dorsal fin distal radial bone 2 | UBERON:2205376 |
| dorsal fin distal radial cartilage 8 | UBERON:2005373 |
| pelvic fin distal radial element 2 | UBERON:2205379 |
| branched anal fin ray | UBERON:2101415 |
| roofing cartilage | UBERON:2001992 |
| caudal fin upper lobe | UBERON:2001172 |
| pelvic fin distal radial cartilage | UBERON:2001593 |
| barbel taste bud | UBERON:4500020 |
| adipose fin actinotrichium | UBERON:0034718 |
| pelvic fin radial element | UBERON:2000460 |
| pectoral fin proximal radial bone 3 | UBERON:2100508 |
| pectoral fin proximal radial cartilage | UBERON:2002028 |
| anal fin ray 3 | UBERON:2201587 |
| fish scute | UBERON:2001771 |
| prepelvic fin spine | UBERON:2002294 |
| barbel primordium | UBERON:4200111 |
| lateral line scale series | UBERON:2005119 |
| forelimb wing bud | UBERON:2002099 |
| inner fin tissue | UBERON:4300230 |
| paired fin bud | UBERON:3010379 |
| scale radius | UBERON:0002531 |
| forelimb wing | UBERON:2002118 |
| anterior dorsal fin | UBERON:0000024 |
| dorsal fin radial cartilage | UBERON:4200023 |
| insect trunk mesoderm anlage | UBERON:2201672 |
| pectoral fin radial skeleton | UBERON:6005436 |
| mesenchyme pelvic fin | UBERON:4440009 |
| pectoral fin bud | UBERON:0003935 |
| dorsal fin ray 4 | UBERON:4300172 |
| branched dorsal fin ray | UBERON:2001757 |
| anal fin spine | UBERON:2001785 |
| scalene muscle | UBERON:2002262 |
| anal fin ray 4 | UBERON:0008611 |
| ctenoid scale | UBERON:2001772 |
| anterior distal serration of pectoral fin spine | UBERON:2002273 |
| insect trunk mesoderm | UBERON:2002002 |
| pelvic fin hook | UBERON:6000128 |
| pectoral fin bud mesenchyme | UBERON:4300262 |
| pectoral fin lepidotrichium | UBERON:4300228 |
| anal fin | UBERON:4000175 |
| insect larval antennal segment | UBERON:4000163 |
| dorsal fin proximal radial bone 6 | UBERON:6001735 |
| cheek scale row | UBERON:2005383 |
| median fin lepidotrichium | UBERON:0018313 |
| pectoral fin proximal radial bone | UBERON:4500008 |
| dorsal fin ray 6 | UBERON:2001587 |
| UBERON:2001759 |
plasticfist
commented
3 years ago snake parts...
[Term] id: UBERON:0013078 name: venom-injecting tooth def: "A fang that is used to inject venom into prey, through either a tube or a groove" [https://orcid.org/0000-0002-6601-2165] synonym: "fang" RELATED [] synonym: "grooved fang" RELATED [] synonym: "tubular fang" RELATED [] synonym: "tubular tooth" RELATED [] is_a: UBERON:0001091 ! calcareous tooth
[Term] id: UBERON:0013113 name: angular/surangular bone def: "Bone formed from the fusion of angular and surangular bones. Found in snakes" [ISBN:0073040584] is_a: UBERON:0008907 ! dermal bone relationship: has_fused_element UBERON:0011079 ! angular bone relationship: has_fused_element UBERON:0011636 ! surangular bone relationship: part_of UBERON:0003113 ! dermatocranium
[Term] id: UBERON:0013115 name: pterygoideus glandulae muscle is_a: UBERON:0001630 ! muscle organ relationship: part_of UBERON:0013116 ! venom gland musculature
[Term] id: UBERON:0013116 name: venom gland musculature is_a: UBERON:0008229 ! craniocervical region musculature relationship: part_of UBERON:0000033 ! head
cmungall
commented
3 years ago Hi all,
I think @matentzn's job here should be to restore the file and ensure it is built using the correct procedure:
Now when this task is done, there will still be fishy terms and other non-human terms in the human-view. This reflects the fact that TCs are incompletely, in particular for ontologies like CL.
We actually have a whole github project dedicated to improving TCs: https://github.com/orgs/obophenotype/projects/2
I suggest we still keep this ticket open, and some of us (hopefully @wdahdul can help, as well as CL editors @nicolevasilevsky) can add necessary taxon constraints. I think many of the ones reported here can be excluded with assertions far enough up the existential graph.
Some observations:
historically uberon was managed as separate edit modules which made it harder to have unified curation practice (including TCs) but these have either been merged or are being merged into one, so this will rapidly improve TC coverage
In particular
I think this will take care of the majority but we will keep iterating we can keep this ticket open to coordinate this if convenient
btw, the report above has tail | UBERON:6005168 but UBERON:6005168 is actually "insect external sensory organ"
(which nevertheless should be excluded)
cmungall
commented
3 years ago Additionally, CL has historically lacked TCs, but I have added some high level ones recently
We will soon see influxes of species-specific CL terms specifically from scSeq, some can be determined by the ensembl ID, but this shouldn't be necessary. See some of the linked tickets in CL in this GH project.
paolaroncaglia
commented
3 years ago Hi @cmungall , @matentzn , @nicolevasilevsky et al,
The Human Cell Atlas (HCA) is interested in a human-centric (or mammalian-applicable) Uberon slim, for import into the HCA application ontology. So we’re very keen on keeping the ball rolling and I could help with improving/adding some taxon constraints to Uberon if you’d like. Would we need to arrange a meeting with representatives from Uberon/CL/GO to outline an optimal strategy and assign tasks? Or can we start from what’s already detailed in this ticket and in the project board https://github.com/orgs/obophenotype/projects/2?
Many thanks,
Paola
paolaroncaglia
commented
3 years ago @bgood-d4c (and FYI @matentzn ) The list you very kindly provided in https://github.com/obophenotype/uberon/issues/1824#issuecomment-816985001 seems to have some formatting or rendering issues. There are duplicate labels which are not, in fact, duplicate terms, and the last line is incomplete. Would it be possible to have the list as a tab-delimited file or Google spreadsheet please? Thanks!
bgood-d4c
commented
3 years ago It looks like the labels were shifted down. Here is a tab-delimited version. Note that this is really just a sample - collected through string matching some key non-human signals in labels. Thanks!
non-human-uberon-sample.txt
matentzn
commented
3 years ago @paolaroncaglia This is great!
I will help with the technical parts. I would say you can start with a Google sheet with @bgood-d4c suggestions, and start adding NCBI taxon ids to them - we can then import those using ROBOT template. Note that if you have
A subclassOf Band
B only in taxon Tyou don't need to say anything about A - so basically just have Uberon open and find the most general class you can assign taxon ids to..
paolaroncaglia
commented
3 years ago Thanks @bgood-d4c and @matentzn . I'll keep you posted.
paolaroncaglia
commented
3 years ago To start with, here's the spreadsheet with @bgood-d4c 's suggestions, with duplicate lines removed, and sorted by Uberon ID.
matentzn
commented
3 years ago before you go to far @paolaroncaglia lets make sure with @cmungall that "never in taxon" annotations are good here. I will ping him on slack.
nicolevasilevsky
commented
3 years ago @paolaroncaglia I'd love to have a meeting to outline the tasks and assign tasks. Could you let me know when you are ready to get started and we can arrange to meet? Thanks!
balhoff
commented
3 years ago You all may find my OBO taxon constraints plugin for Protégé useful in seeing what effective taxon constraint the reasoner knows about for the selected term (and you can get explanations). Just keep in mind that it can be SLOW. :-)
cmungall
commented
3 years ago Yes, never_in_taxon annotations are good.
But remember these need to be expanded to be seen by the reasoner. Note there are multiple alternative logical representations:
Form 1 is the most explicit but is outside EL
Form 2 should be deprecated. It is an awkward way to say 3. However we adopted it a while ago to accommodate manchester syntax limitations in the old shortcut expansion method that is deprecated
Both 2 and 3 rely on axioms injected into NCBITaxon
I fear due to my negligence we may have lost the expansions from the annotation form to any expanded form... more later....
paolaroncaglia
commented
3 years ago Hi @nicolevasilevsky ,
@paolaroncaglia I'd love to have a meeting to outline the tasks and assign tasks. Could you let me know when you are ready to get started and we can arrange to meet? Thanks!
Sure! I'll message you on Slack. Thank you.
paolaroncaglia
commented
3 years ago Hi @matentzn and others, Following up on this ticket, in summary:
We've added ~1800 taxon restrictions in Uberon which will be visible in the next release; Those taxon restrictions will feed into an updated version of a Uberon slim applicable to Euarchontoglires (i.e. primates incl. human, rodents incl. mouse/rat, and rabbits), it should be ready soon; We have plans to build a similar slim for CL; I will now remove my assignment from this ticket, and leave it to @matentzn please to review any pending action item, then the ticket may be closed. For those interested in the work and tasks summarized above, please feel free to follow https://github.com/obophenotype/uberon/issues/2050#, https://github.com/obophenotype/uberon/issues/2127, https://github.com/obophenotype/cell-ontology/issues/1113.
Thanks! Paola P.S. Most of the terms suggested by @bgood-d4c now have taxon rules, but I'll make a note to double-check any remaining ones.
paolaroncaglia
commented
3 years ago @shawntanzk (cc @matentzn and other colleagues on the technical Support Board) Please see this comment for required action item at your next meeting. Many thanks!
paolaroncaglia
commented
2 years ago Hi @shawntanzk , Wrt my previous post
Please see this comment for required action item at your next meeting. Many thanks!
GitHub displays the linked comment funnily, and I can see now why you were confused. I meant to refer to the comment that actually precedes the comment with the list of curation tasks, i.e. "Now that the ~1772 taxon constraints added in #2050 are in Uberon, could someone please re-build the Euarch slim? (The old one was at https://github.com/obophenotype/uberon/blob/v2021-07-27/subsets/euarchontoglires-basic.owl.) Many thanks!"
Please let me know if you need more specs. If it helps, I had a 1:1 meeting with David yesterday and he noted "We now have a fix (Jim diagnosed the problem and reported back on the call last night.) I'll ping Nico and see if we have a timeline for the new release.". I haven't read all GitHub notifications that came meanwhile, so I might be missing some very recent update. :-)
shawntanzk
commented
2 years ago ah ok! so basically I think running a release would solve it. There still are some issues atm that I think we won't want out in a release, but we are fixing it atm :)
Action item for tech group:
shawntanzk
commented
2 years ago @paolaroncaglia release has been done and the human and eunach slime should be rebuilt - it is not empty now. Could you check, and if there is any issues, could you make new tickets for them please? Thanks
paolaroncaglia
commented
2 years ago @shawntanzk thanks!! I'll check tomorrow (downloading the release now).
Bug description This file in the repo seems empty, it's linked from this page of the website (under taxon subsets).