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