Classes not in UBERON, or bad definitions

[bionicjules]

not_in_UBERON.txt

These are all classes that I use in my ontology of biomimetics. Some appear in annotations in UBERON, but I propose that they are sufficiently significant to be independent classes.

[cmungall]

Thanks! I have turned your list into grouped checkboxes. We will triage these to other ontologies and work through core uberon relevant ones ASAP. We may need to call on you for definitions/explanation of some

Plant parts

In scope for PO:

Planteome/plant-ontology#677

• plane of abscission
• plane of dehiscence
• line of dehiscence

Mollusc

CEPH is becoming MOLO: obophenotype/cephalopod-ontology#4

• byssus
• byssus thread
• abductin-like part of byssus thread
• collagen-like part of byssus thread
• elastin-like part of byssus thread
• silk-like part of byssus thread
• bivalve shell
• mollusc shell material
• crossed lamellar shell material
• bivalve hinge ligament
• conch shell
• aragonite hard lens
• calcite hard lens

Arthropod

@dosumis - what should our strategy be here? Generalize the insect module? I think many of these are in the insect module in any case

• part of exoskeleton. UBERON:0006611 ! exoskeleton We don't create part-of-X terms
• cuticular hair
• cuticular hinge [several types]
• elastic cuticular hinge
• soft cuticular hinge
• arthropod eye. we wouldn't make a class like this unless there is a non-taxonomic differentia
• ommatidium (single) . UBERON:0000971
• ommatidium hard lens
• cuticular fracture line
• ecdysial line of an arthropod exoskeleton

Similar definitions needing to be revised

• chitin-based cuticle. (Why is protein-based cuticle obsolete?) CJM: see GO:0007592
• cuticle - (can contain 40% Ca salts, so wrong to say non-mineral)

Insecta

All are being taken care of here: obophenotype/insect-anatomy-ontology#4

• insect cuticle
• shell of insect egg
• insect cuticular structure
• respiratory plastron
• chorionic plastron
• cuticular plastron
• moth cocoon silk
• insect head appendage
• insect proboscis
• lepidopterous proboscis (NOT a sucking device)
• mandible of insect
• mandible of locust
• hind-wing of beetle
• hind-wing of dermapteran
• insect foot
• part of insect foot we don't make part-of-Xs
• arolium (currently only for Hymenoptera)
• locust wing hinge ligament
• comb and strigil
• insect tymbal
• tymbal of a cicada
• strepsipteran haltere (reduced forewing)
• insect tympanum
• maggot
• chrysalis
• life cycle of insect
• life cycle of endopterygote insect
• life cycle of orthoperoid insect
• campaniform sensillum
• lyriform sensillum
• insect penis
• fracture line of a fly puparium

Arachnida

File these here: https://github.com/obophenotype/spider-ontology/issues

• spider head appendage
• mandible of spider

Crustacea

• calcified exoskeleton
• crustacean cuticle
• cyprinid larval stage Why is this under crustacea? ~~cjm

Annelida

• worm head appendage
• mandible of worm

Vertebrata

• vertebrate eye UBERON:0000019 ! camera-type eye
• bony endoskeleton - can you provide definition, cc @wdahdul
• tooth - UBERON:0001091 ! calcareous tooth

Gnathostomata

• egg-case of dogfish
• hagfish mucin
• cartilagenous endoskeleton
• cartilagenous bone - cc @wdahdul we have UBERON:0007844 ! cartilage element
• mirror eye

Amphibia

• amphibian bony endoskeleton we wouldn't make a class like this, you can post-compose

Sauropsida

• shell of bird egg
• alula feather
• wing of bird
• wing of pterosaur - cc @wdahdul should we have this?
• ballistic tongue
• Chameleon tongue elastic propulsion mechanism
• ecdysial line of skin of a snake

Mammalia

• hedgehog spine (NOT “keratin-coated” -it’s ALL keratin)
• porcupine quill (as above)
• under-fur
• wing of bat
• heel pad
• mammalian dermal cell
  pelt
• snake skin ready to slough
• avian bony endoskeleton
• mammalian brain won't add - see above
• human brain won't add - see above

Onychophora

• Peripatus mucin

Echinodermata

• echinoderm test

General zoology

• collagen fibre
• egg protection
• nematode body wall
• intermediate filament mucin
• nuclear membrane GO:0031965 ! nuclear membrane
• head appendage
• locomotory appendage
• lateral locomotory appendage
• leg for digging we wouldn't add these
• leg for jumping
• leg for running
• leg for swimming
• lateral locomotory appendage part
• median locomotory appendage tentacle
• tentacle of coral polyp
• tentacle of jellyfish
• counter-current system - https://github.com/obophenotype/porifera-ontology/issues/
• dermal element - UBERON:0004756 ! dermal skeletal element
• epidermis UBERON:0001003 and the more general UBERON:0007376 ! outer epithelium
• skin - we have skin, do you need a more generic term? How would this be defined?
• electrical discharge organ
• gas exchange organ
• hydrostatic skeleton
• luminescent organ
• lantern - what is this? We have aristotle's lantern
• mesogloea -
• myomere - same as UBERON:0003082 ! myotome?
• nervous system
• brain
• nerve cell
• nerve axon
• nerve cell body - GO:0043025 ! neuronal cell body
• acceleration sensor
• chemical sensor
• flow sensor
• magnetosensor
• proprioceptor
• stretch sensor
• touch sensor
• vibration sensor
• part of ear - we don't create part-of-X classes
• tympanum
• part of eye - we don't create part-of-X classes
• lens
• hard lens
• part of male reproductive system - we don't create part-of-X classes
• euspermatozoon - https://github.com/obophenotype/cell-ontology/issues/new
• paraspermatozoon - https://github.com/obophenotype/cell-ontology/issues/new

BFO:0000027

• swarm - https://github.com/PopulationAndCommunityOntology/pco/issues or https://github.com/obophenotype/sibo/issues

BFO:0000034

• sensing mode
• sensing heat
• sensing light
• sensing smell
• part of organ of special sense
• sensing sound
• sensing loudness
• sensing pitch
• sensing strain
• sensing taste
• sensing touch
• adult stage
• imaginal stage
• egg stage

NCBITaxon not available

NOTE FROM CJM: We aren't responsible for the species taxonomy, see http://obofoundry.org/ontology/ncbitaxon.html -- these can be requested from NCBI. But check spelling first. E.g. Sepia nemoralis --> NCBITaxon:28835 ! Cepaea nemoralis

Glaphyrella trebouxiodes
Neomeris annulata
Notomegabalanus algicola
Machilinus casasecai
Machilinus spinifrontis
Petrobius maritimus
Rufocephalus sp.
Cyclochila australasiae
Entimus imperialis
Myathropa florea
Mallophora ruficauda
Baryscapus galactopus
Opisthobranchia
Sepia nemoralis
Acropora reticulata
Antipathes salix

[gouttegd]

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.