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Ubergraph

Matches in Ubergraph for { ?s <http://purl.obolibrary.org/obo/UBPROP_0000012> ?o ?g. }

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UBERON_0000003 UBPROP_0000012 "we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure" @default.
UBERON_0000014 UBPROP_0000012 "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive" @default.
UBERON_0000019 UBPROP_0000012 "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" @default.
UBERON_0000042 UBPROP_0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." @default.
UBERON_0000043 UBPROP_0000012 "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" @default.
UBERON_0000044 UBPROP_0000012 "MA and EMAPA introduce distinct classes for what appears to be the same thing" @default.
UBERON_0000058 UBPROP_0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." @default.
UBERON_0000060 UBPROP_0000012 "in FMA, serosa is a wall" @default.
UBERON_0000062 UBPROP_0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" @default.
UBERON_0000071 UBPROP_0000012 "ncit:Death is an outcome" @default.
UBERON_0000072 UBPROP_0000012 "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole" @default.
UBERON_0000074 UBPROP_0000012 "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" @default.
UBERON_0000085 UBPROP_0000012 "EHDAA2 has embryo starting later" @default.
UBERON_0000095 UBPROP_0000012 "ZFA treats this as a subtype of NC." @default.
UBERON_0000105 UBPROP_0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" @default.
UBERON_0000105 UBPROP_0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" @default.
UBERON_0000117 UBPROP_0000012 "in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)" @default.
UBERON_0000121 UBPROP_0000012 "consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer)" @default.
UBERON_0000125 UBPROP_0000012 "Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate." @default.
UBERON_0000127 UBPROP_0000012 "FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus." @default.
UBERON_0000161 UBPROP_0000012 "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" @default.
UBERON_0000165 UBPROP_0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" @default.
UBERON_0000177 UBPROP_0000012 "biospecimen in NCIT" @default.
UBERON_0000204 UBPROP_0000012 "BTO term refers specifically to the avian structure" @default.
UBERON_0000211 UBPROP_0000012 "this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament" @default.
UBERON_0000303 UBPROP_0000012 "definition generalized to accommodate AAO class - 'Originates on the iliac portion of the ventral iliac rim and inserts on the lateral surface of the M. adductor magnus.' [AAO:0010034]" @default.
UBERON_0000309 UBPROP_0000012 "the BTO class refers to earthworms." @default.
UBERON_0000333 UBPROP_0000012 "Note that some sources treat 'intestinal gland' as synonymous with crypts" @default.
UBERON_0000344 UBPROP_0000012 "FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately" @default.
UBERON_0000346 UBPROP_0000012 "BTO has def The multilamellar myelin membrane is a specisalised lipid-rich domain of the glial cell plasma membrane. FMA has primary term name Myelinated plasma membrane of Schwann cell" @default.
UBERON_0000353 UBPROP_0000012 "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" @default.
UBERON_0000370 UBPROP_0000012 "Definition generalized to accommodate AAO class - 'Origin by two heads that are separated by a ventral tendon of the M. semitendinosus. One head originates from the ventral border of the pubic portion of the pelvic rim. The other head originates from the ischiatic border of the pelvic rim. The ventral head fuses with accessory head from the M. semitendinosus and inserts along the ventro-medial border of the femur. The dorsal belly merges with the ventral and accessory heads and inserts along the medial surface of the femur.' [AAO:0010040]" @default.
UBERON_0000373 UBPROP_0000012 "not to be confused with BTO:0001350 or GO:0048655-tapetal layer morphogenesis" @default.
UBERON_0000383 UBPROP_0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" @default.
UBERON_0000391 UBPROP_0000012 "in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular" @default.
UBERON_0000412 UBPROP_0000012 "ncit has 'hair papilla' as part of hypodermis" @default.
UBERON_0000456 UBPROP_0000012 "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions" @default.
UBERON_0000922 UBPROP_0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" @default.
UBERON_0000936 UBPROP_0000012 "part_of brainstem in MA; midbrain tectum in NIF" @default.
UBERON_0000941 UBPROP_0000012 "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" @default.
UBERON_0000977 UBPROP_0000012 "In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86" @default.
UBERON_0000983 UBPROP_0000012 "mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton" @default.
UBERON_0000991 UBPROP_0000012 "FMA xref is a 'general anatomical term'" @default.
UBERON_0001007 UBPROP_0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" @default.
UBERON_0001013 UBPROP_0000012 "in FMA this is dense irregular connective tissue" @default.
UBERON_0001015 UBPROP_0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." @default.
UBERON_0001031 UBPROP_0000012 "FMA def is 'Neural tissue which consists of Schwann cells' which does not fit, but we still use 'neural tissue' here. WP def specifically states Schwann cells, which would restrict it to PNS" @default.
UBERON_0001032 UBPROP_0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" @default.
UBERON_0001033 UBPROP_0000012 "in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes" @default.
UBERON_0001035 UBPROP_0000012 "MA classifies this as a cartilaginous joint" @default.
UBERON_0001042 UBPROP_0000012 "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme" @default.
UBERON_0001043 UBPROP_0000012 "esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)" @default.
UBERON_0001045 UBPROP_0000012 "in FMA this represents an embryonic region." @default.
UBERON_0001046 UBPROP_0000012 "in FMA this class has no children. In MA it has a single child hindgut epithelium" @default.
UBERON_0001053 UBPROP_0000012 "currently intended for invert structure; alt definitions include: organs in which intimate relationships between axons and terminal blood vessels are established" @default.
UBERON_0001063 UBPROP_0000012 "flocculus is an exact label for two distinct classes in NIF." @default.
UBERON_0001074 UBPROP_0000012 "check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)" @default.
UBERON_0001075 UBPROP_0000012 "VSAO definition states it surrounds notochord but not applicable to post-natal." @default.
UBERON_0001095 UBPROP_0000012 "we deliberately merge the MA classes as we believe them equivalent" @default.
UBERON_0001105 UBPROP_0000012 "FMA and MA differ in whether they consider this part of the shoulder" @default.
UBERON_0001107 UBPROP_0000012 "Note that as defined here, this structure attaches to the sternum, which is a tetrapod structure. TAO has class 'sternohyoid' as part of mandibular muscle, but no sternum, so excluded here. The TAO/ZFA class has no definition, but the dictionary of icthyology states: 'a large muscle originating on the ventral spine of the postcleithrum and inserting on the sides of the urohyal. It functions in rapid opening of the jaw and expanding the buccal cavity' - a generic way of grouping these is via a hyoid - girdle connection" @default.
UBERON_0001140 UBPROP_0000012 "in EHDAA2, the renal vein is part of the kidney" @default.
UBERON_0001156 UBPROP_0000012 "in MA, this is a subclass of colon" @default.
UBERON_0001180 UBPROP_0000012 "classified as a cavity in EHDAA2, organ segment in FMA. We hedge and use a union" @default.
UBERON_0001211 UBPROP_0000012 "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" @default.
UBERON_0001211 UBPROP_0000012 "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" @default.
UBERON_0001213 UBPROP_0000012 "the BTO class refers to a generic villous" @default.
UBERON_0001214 UBPROP_0000012 "see also MA:0002165 ! lieno-pancreatic vein" @default.
UBERON_0001231 UBPROP_0000012 "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" @default.
UBERON_0001232 UBPROP_0000012 "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" @default.
UBERON_0001247 UBPROP_0000012 "in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament" @default.
UBERON_0001251 UBPROP_0000012 "WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line." @default.
UBERON_0001254 UBPROP_0000012 "MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium" @default.
UBERON_0001269 UBPROP_0000012 "whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface." @default.
UBERON_0001270 UBPROP_0000012 "in FMA, this is part of the axial skeletal system" @default.
UBERON_0001272 UBPROP_0000012 "in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra." @default.
UBERON_0001273 UBPROP_0000012 "this is_a hip bone in MA." @default.
UBERON_0001274 UBPROP_0000012 "this is_a hip bone in MA; in FMA it is a zone of bone organ." @default.
UBERON_0001275 UBPROP_0000012 "isa bone zone in FMA" @default.
UBERON_0001276 UBPROP_0000012 "in FMA this is classified as simple columnar, MA divides this into squamous and glandular" @default.
UBERON_0001295 UBPROP_0000012 "in FMA this is subdivided into basal and outer" @default.
UBERON_0001336 UBPROP_0000012 "MA class sex-neutral" @default.
UBERON_0001338 UBPROP_0000012 "NCIT:C12339 paraurethral gland belongs here" @default.
UBERON_0001341 UBPROP_0000012 "classified as a cavity in EHDAA2, so this truly corresponds to FMA 'Cavity of lesser sac' - we hedge for now; todo - treat same as greater sac" @default.
UBERON_0001344 UBPROP_0000012 "FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)" @default.
UBERON_0001352 UBPROP_0000012 "subdivision of head in FMA." @default.
UBERON_0001359 UBPROP_0000012 "EHDAA2 models this as developing from CP, which is wrong" @default.
UBERON_0001359 UBPROP_0000012 "the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations." @default.
UBERON_0001368 UBPROP_0000012 "the definition generalized to accommodate the AAO class - 'Originates on the ventro-lateral pelvic rim and inserts on the ventral aspect of the femur, medial to the insertion of the pectineus.' [AAO:0010043]" @default.
UBERON_0001369 UBPROP_0000012 "AAO has iliacus major and minor, both of which attach to ilium and femur - consider grouping these somehow" @default.
UBERON_0001382 UBPROP_0000012 "Definition generalized to accommodate AAO class - 'Originates on the lateral border of the ilium and the anterior margin of the pubis. It inserts on the ventral surface of the femoral shaft.' [AAO:0010036]" @default.
UBERON_0001410 UBPROP_0000012 "the MA term, even though plural, represents the singular, as it is an isa child of artery" @default.
UBERON_0001434 UBPROP_0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" @default.
UBERON_0001464 UBPROP_0000012 "See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint" @default.
UBERON_0001467 UBPROP_0000012 "In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone" @default.
UBERON_0001468 UBPROP_0000012 "FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra" @default.
UBERON_0001470 UBPROP_0000012 "in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle" @default.
UBERON_0001483 UBPROP_0000012 "in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon" @default.
UBERON_0001484 UBPROP_0000012 "check ncita" @default.
UBERON_0001491 UBPROP_0000012 "in FMA this includes radio-carpal and radio-ulnar *ligaments*" @default.