PERSON: Fernanda Farinelli
This owl file represents the necessary entities of UBERON that are reused in OntONeo Ontology. This file was created using Ontofox and some intermediary entities were not imported.
UBERON subset applied to OntONeo ontology.
Uberon multi-species anatomy ontology
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
UBPROP:0000001
uberon
external_definition
1
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
Notes on the homology status of this class.
UBPROP:0000003
uberon
homology_notes
1
homology_notes
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_notes
Notes on the how instances of this class vary across species.
UBPROP:0000008
uberon
taxon_notes
1
taxon_notes
taxon_notes
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000012
uberon
external_ontology_notes
1
external_ontology_notes
external_ontology_notes
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
adult stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
WBls:0000041
XtroDO:0000084
fully formed animal stage
juvenile-adult stage
uberon
UBERON:0000066
fully formed stage
A stage that is part of the embryo stage.
embryonic stage part
uberon
UBERON:0000067
embryo stage part
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
End of the life of an organism.
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
EMAPA:16033
FBdv:00005288
HsapDv:0000001
PdumDv:0000100
VHOG:0000745
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote stage
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
BILS:0000107
BilaDO:0000006
EFO:0001290
FBdv:00000054
MESH:A16.254.270
MmusDv:0000004
OGES:000015
OGES:000020
PdumDv:0000200
XAO:1000004
ZFS:0000046
uberon
UBERON:0000107
cleavage stage
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
BILS:0000108
BilaDO:0000007
EFO:0001282
HsapDv:0000006
MmusDv:0000007
OGES:000003
OGES:000016
OGES:000021
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
WBls:0000005
XAO:1000003
ZFS:0000045
uberon
UBERON:0000108
blastula stage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
BILS:0000109
BilaDO:0000008
EFO:0001296
FBdv:00005317
HsapDv:0000010
MmusDv:0000013
OGES:000004
OGES:000019
WBls:0000010
XAO:1000005
ZFS:0000047
uberon
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
UBERON:0000109
gastrula stage
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
BILS:0000110
BilaDO:0000009
HsapDv:0000012
MmusDv:0000017
XAO:1000006
uberon
UBERON:0000110
neurula stage
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
uberon
segmentation stage
UBERON:0000111
organogenesis stage
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
BILS:0000112
BTO:0002168
EFO:0001300
EV:0300051
MmusDv:0000043
OGES:000009
XAO:1000010
XtroDO:0000083
ZFS:0000051
immature stage
juvenile stage
uberon
subadult stage
UBERON:0000112
sexually immature stage
The stage of being a sexually mature adult animal.
adult stage
BILS:0000113
EV:0300064
EV:0300070
MIAA:0000403
MmusDv:0000110
OGES:000026
OGES:000027
XAO:1000093
ZFS:0000044
uberon
UBERON:0000113
post-juvenile adult stage
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
BTO:0000068
CALOHA:TS-0034
ENVO:02000021
EV:0100123
FMA:305905
GAID:1155
MA:0002893
MESH:D000653
UMLS:C0002638
VHOG:0001267
uberon
acqua amnii
liquor amnii
UBERON:0000173
amniotic fluid
Anatomical cavity bounded by visceral and parietal peritoneum
The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
BTO:0001782
EHDAA2:0001446
EMAPA:16138
FMA:14704
GAID:24
MA:0000054
MESH:A01.047.025.600.678
UMLS:C1704247
VHOG:0000852
uberon
cavitas peritonealis
saccus serosus peritonei
UBERON:0001179
peritoneal cavity
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
mesenchymal
AAO:0010427
AEO:0000145
BTO:0001393
CALOHA:TS-0620
EHDAA2:0003145
EV:0100007
TAO:0000393
UMLS:C0162415
VHOG:0000170
XAO:0003046
ZFA:0000393
mesenchymal tissue
mesenchyme tissue
portion of mesenchymal tissue
portion of mesenchyme tissue
uberon
mesenchyma
UBERON:0003104
mesenchyme
A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]
TODO - check
EMAPA:26127
EMAPA:35925
Wharton's jelly
umbilical cord mesenchyme
uberon
UBERON:0003422
mesenchyme of umbilical cord
A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities.
Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)
DrerDO:0000052
EFO:0001310
OGES:000006
ZFS:0000050
phylotypic stage
uberon
pharyngula
UBERON:0004707
pharyngula stage
An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
EV:0300011
EVM:2990031
FBdv:00005333
FMA:63631
MIAA:0000399
MmusDv:0000031
OGES:000023
embryo late (growth) stage
fetal stage
fetus
fetus stage
uberon
embryo late growth stage
embryo late stage
UBERON:0007220
late embryonic stage
Of or pertaining to the period of time immediately following birth, or to the newborn.
consider splitting infant/newborn
BTO:0001762
EV:0300037
HsapDv:0000082
MmusDv:0000096
NIF_Organism:birnlex_695
OGES:000025
neonatal stage
fledgling stage
hatchling
hatchling stage
infant stage
nestling stage
pouch stage
puggle
puggle stage
uberon
newborn stage
UBERON:0007221
neonate stage
EV:0300123
HsapDv:0000093
NIF_Organism:birnlex_691
UMLS:C0001792
uberon
elderly
elderly stage
geriatric
geriatric stage
UBERON:0007222
late adult stage
XAO:1000011
XtroDO:0000006
ZFS:0000002
2-cell stage
two-cell stage
Cleavage:2-cell
NF stage 2 (2-cell)
uberon
UBERON:0007232
2 cell stage
XAO:1000013
XtroDO:0000007
ZFS:0000003
4-cell stage
four-cell stage
Cleavage:4-cell
NF stage 3 (4-cell)
uberon
UBERON:0007233
4 cell stage
XAO:1000014
XtroDO:0000008
ZFS:0000004
8-cell stage
eight-cell stage
Cleavage:8-cell
NF stage 4 (8-cell)
uberon
UBERON:0007236
8 cell stage
A head that is part of a embryo.
CALOHA:TS-0246
FBbt:00000155
FMA:293011
uberon
UBERON:0008816
embryonic head
One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta.
EMAPA:36493
allantoic vessel
umbilical cord blood vessel
umbilical vessel
uberon
umbilical cord blood vessels
umbilical vasculature
UBERON:0010260
umbilical blood vessel
The period spanning the range immediately before and after birth
In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes
paranatal stage
uberon
UBERON:0012101
perinatal stage
blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
BTO:0004053
CALOHA:TS-1079
EFO:0001942
MESH:D005312
uberon
cord blood
fetal blood
umbilical cord blood
UBERON:0012168
Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP]
umbilical cord blood
A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence.
uberon
adulthood stage
UBERON:0018241
prime adult stage
A mammalian developmental stage that covers the period from birth until weaning.
suckling stage
uberon
UBERON:0018685
nursing stage
The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity.
uberon
UBERON:0034919
juvenile stage
Nursing stage that follows the neonate stage in mammals and ends at weaning.
uberon
UBERON:0034920
infant stage
A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
uberon
UBERON:0035943
life cycle temporal boundary
A life cycle temporal boundary that marks the end of the life cycle of the organism.
end of life cycle
moment of death
time of death
uberon
death
end of life
UBERON:0035944
life-death temporal boundary
A life cycle temporal boundary that marks the start of the life cycle of the organism.
uberon
UBERON:0035945
start of life cycle
A life cycle temporal boundary that marks the start of the neonate stage of the organism.
moment of birth
time of birth
uberon
birth
UBERON:0035946
start of neonate stage
shorthand