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commit 0a19f706db218802c3b0fe38557a748bb4bab3c7 1 parent 279172d
@cmungall cmungall authored
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11 Makefile
@@ -487,6 +487,9 @@ newterms-fma-mouse.obo:
newterms-mouse-wpanat.obo:
obol -u onto_grep onto-3-way-align -r wpanat -r mouse_anatomy -r uberon -ont1 wikipedia -ont2 adult_mouse_anatomy.gxd -ont3 uberon > $@
+newterms-fma-wpanat.obo:
+ obol -u onto_grep onto-3-way-align -r wpanat -r fma3 -i fma3-latin.obo -r uberon -ont1 dbpedia -ont2 fma -ont3 uberon > $@
+
newterms-fma-envo.obo:
obol -u onto_grep onto-3-way-align -r envo -r fma -i fma3-latin.obo -r uberon -ont1 ENVO -ont2 fma -ont3 uberon > $@
@@ -805,8 +808,14 @@ dbpedia_all_AnatomicalStructure.pro:
dbpedia_all_Embryology.pro:
blip ontol-sparql-remote "SELECT * WHERE { ?x rdf:type <http://dbpedia.org/ontology/Embryology> }" -write_prolog > $@.tmp && sort -u $@.tmp > $@
+dbpedia_all_Animal_anatomy.pro:
+ blip ontol-sparql-remote "SELECT * WHERE { ?x <http://purl.org/dc/terms/subject> <http://dbpedia.org/resource/Category:Animal_anatomy> }" -write_prolog > $@.tmp && sort -u $@.tmp > $@
+
+dbpedia_subjects.pro:
+ sort -u dbpedia_all_*.pro > $@
+
# everything as type AnatomicalStructure
-dbpedia_all.pro: dbpedia_all_AnatomicalStructure.pro
+dbpedia_all.pro: dbpedia_subjects.pro
blip-findall -debug sparql -i $< -u sparql_util "row(A),dbpedia_query_links(A,row(S,P,O),1000,[])" -select "rdf(S,P,O)" -write_prolog > $@
dbpedia_all-after-%.pro: dbpedia_all_AnatomicalStructure.pro
blip-findall -debug sparql -i $< -u sparql_util "row(A),A@>'http://dbpedia.org/resource/$*',dbpedia_query_links(A,row(S,P,O),1000,[])" -select "rdf(S,P,O)" -write_prolog > $@
View
154 dbpedia_ontol.obo
@@ -26909,6 +26909,160 @@ name: zygomaticus minor muscle
def: "The zygomaticus minor is a muscle of facial expression. It originates from malar bone and continues with orbicularis oculi on the lateral face of the Levator labii superioris and then inserts into the outer part of the upper lip. Do not confuse this with the Zygomaticus major, which insets into the angle of the mouth. It draws the upper lip backward, upward, and outward (used in making sad facial expressions). &lt;/gallery&gt; Like all muscles of facial expression, it is innervated by the facial nerve (CN VII)." [Wikipedia:Zygomaticus_minor_muscle]
synonym: "zygomaticus minor" RELATED [Wikipedia:Zygomaticus_minor_muscle]
+
+[Term]
+id: Wikipedia:Ambulacral
+name: ambulacral
+def: "Ambulacral is a term typically used in the context of anatomical parts of the phylum Echinodermata or class Asteroidea and Edrioasteroidea. Echinoderms can have ambulacral parts that include ossicles, plates, spines, and suckers. For example, sea stars or \"star fish\" have an ambulacral groove on their oral side (underside). This ambulacral groove extends from the mouth to the end of each ray or arm. Each groove of each arm in turn has four rows of hollow tube feet that can be extended or withdrawn. Opposite the ambulacral groove is an ambulacral ridge on the aboral side of each ray." [Wikipedia:Ambulacral]
+
+[Term]
+id: Wikipedia:Arthropod_exoskeleton
+name: arthropod exoskeleton
+def: "Arthropods are covered with a tough or resistant exoskeleton, which may be mineralised or constructed of a tough polymer such as chitin. This external skeleton is moulted as the organism grows." [Wikipedia:Arthropod_exoskeleton]
+
+[Term]
+id: Wikipedia:Branchiostegal_lung
+name: branchiostegal lung
+def: "A branchiostegal lung is a respiration organ used by some air-breathing arthropods. It is one of the most significant adaptations of some crabs and hermit crabs such as coconut crabs to their terrestrial habitats. The branchiostegal (gill) tissue is supported by folds or other mechanisms to increase surface area and are of a similar tissue to that normally found in gills. In this case, the lung is more suited to the absorption of oxygen from air, rather than water. Instead of branchiostegal lungs, some terrestrial hermit crabs (Coenobita and Birgus) possess multiple gills and small lungs, with other varieties of gas diffusion methods supporting the transition from aquatic to terrestrial dwelling. The developmental shift from water diffusion \"gills\" to air perfusion \"lungs\" may have been related to the need for reduce rates of water loss in air." [Wikipedia:Branchiostegal_lung]
+
+[Term]
+id: Wikipedia:Cnidocyte
+name: cnidocyte
+def: "A cnidocyte, cnidoblast, or nematocyte is a type of venomous cell unique to the phylum Cnidaria. The cnidocyte cell provides a means for them to catch prey and defend themselves from predators. Despite being morphologically simple, lacking a skeleton and usually being sessile, cnidarians prey on fish and crustaceans. A cnidocyte fires a structure that contains the toxin, from a characteristic sub-cellular organelle called a cnidocyst (also known as a cnida or nematocyst). This is responsible for the stings delivered by jellyfish." [Wikipedia:Cnidocyte]
+
+[Term]
+id: Wikipedia:Convoluted_tubule
+name: convoluted tubule
+def: "Convoluted tubule is the compound of a metanephridium which is wrapped with capillaries. The process of reabsorption occurs in this part of the metanephridium." [Wikipedia:Convoluted_tubule]
+
+[Term]
+id: Wikipedia:Crocodilian_armor
+name: crocodilian armor
+def: "The crocodile exoskeleton consists of the protective dermal and epidermal components of the integumentary system in animals of the order Crocodilia. It is a form of armour." [Wikipedia:Crocodilian_armor]
+
+[Term]
+id: Wikipedia:Deaf_animals
+name: deaf animals
+def: "Some strains of animals, such as white cats, have a tendency to congenital deafness. It is also not an uncommon problem for purebred dogs. Some known chemicals and elements can also affect deafness in animals. Deafness can occur in almost any breed of cat or dog. This includes both pure-breed and mixed-breed animals although there may be more prevalence in some specific breeds. \"The association between patterns of pigmentation and deafness in the dog has a long-documented history, with reports dating back over one hundred years. Long suspected of having a genetic basis, the search for loci with a pronounced influence in the expression of hearing loss in the dog has yet to be successful. \" Deafness in animals can occur as either unilateral (one ear effected) or bilateral (both ears effected). This occurrence of either type of deafness seems to be relatively the same in both mixed-breed animals and pure-breed animals. Research as tired a significant association between deafness in dogs and the pigment genes piebald and merle. Although merle dogs seem to have higher occurrences of both deafnesses than some other breeds, this research also showed that they had lower occurrences than others. So still there is more to be known about the causes of deafness in animals such as dogs. Common misconceptions may lead potential owners to believe that deaf dogs may be more likely to have an unpleasant disposition, or that the condition implies other brain abnormalities. Many people have successfully raised and trained deaf animals. Teaching a deaf dog may present unusual challenges, but inventiveness can overcome many of them. For example, deaf dogs, when out on a walk, a laser pointer could be used to attract the animals attention." [Wikipedia:Deaf_animals]
+
+[Term]
+id: Wikipedia:Dorsal_nerve_cord
+name: dorsal nerve cord
+def: "The dorsal nerve cord is one of the embryonic features unique to chordates, along with a notochord, a post-anal tail and pharyngeal slits. The dorsal nerve cord is a hollow cord dorsal to the notochord. It is formed from a part of the ectoderm that rolls, forming the hollow tube, compared to other animal phyla, which have solid, ventral tubes. The dorsal nerve cord is later modified into the brain and spinal cord. Dorsal nerve cord is mainly found in phylum Vertebrata. Dorsal means the \"back\" side, as opposed to the belly side (ventral)." [Wikipedia:Dorsal_nerve_cord]
+
+[Term]
+id: Wikipedia:Egg_tooth
+name: egg tooth
+def: "s, the egg tooth is a small, sharp, cranial protuberance used by offspring to break or tear through the egg's surface during hatching. It is present in most birds and reptiles, and similar structures exist in monotremes, Eleutherodactyl frogs, and spiders. Some lizards and snakes develop a true tooth that is shed after use; other reptiles and birds generally develop an analogous epidermal horn that is reabsorbed or falls off." [Wikipedia:Egg_tooth]
+
+[Term]
+id: Wikipedia:Endostyle
+name: endostyle
+def: "An endostyle is a longitudinal ciliated groove on the ventral wall of the pharynx which produces mucus to gather food particles. It is found in urochordates and cephalochordates, and in the larvae of lampreys. It aids in transporting food to the esophagus. It is also called the hypopharyngeal groove. The endostyle in larval lampreys (ammocetes) metamorphoses into the thyroid gland in adults, and is regarded as being homologous to the thyroid gland in vertebrates. However, Dumont, et al. question whether the endostyle in ammocetes is homologous with that of the urochordates and cephalochordates. Since the endostyle is found in the three branches of chordates, it is presumed to have arisen in the common ancestor of these taxa, along with a shift to internal feeding for extracting suspended food from the water." [Wikipedia:Endostyle]
+
+[Term]
+id: Wikipedia:Flame_cell
+name: flame cell
+def: "A flame cell is a specialized excretory cell found in the simplest freshwater invertebrates, including flatworms (except the turbellarian order Acoela), rotifers and nemerteans; these are the simplest animals to have a dedicated excretory system. Flame cells function like a kidney, removing waste materials. Bundles of flame cells are called protonephridia. The flame cell has a nucleated cell body, with a \"cup-shaped\" projection, with cilia covering the inner surface of the cup. The beating of these cilia resemble a flame, giving the cell its name. The cup is attached to a tube cell, whose inner surface is also coated in cilia, which help to move liquid through the tube cell. The tube opens externally through a nephropore, or, in the trematoda, into an excretory bladder. The function of these cells is to regulate the osmotic pressure of the worm, and maintain its ionic balance. Microvilli in the tube cell may be used to reabsorb some ions." [Wikipedia:Flame_cell]
+
+[Term]
+id: Wikipedia:Flank_gland
+name: flank gland
+def: "The flank gland is an organ in certain animals the generates scents used to attract mates or deter attack. Animals having flank glands include some voles and shrews. Numerous scientific studies have been carried out on the properties of these structures." [Wikipedia:Flank_gland]
+
+[Term]
+id: Wikipedia:Gular_scute
+name: gular scute
+def: "The gular scute or gular projection on a tortoise is the most anterior part of the plastron, the underside of the tortoise's shell. Some tortoises have paired gular scutes, while others have a single undivided gular scute. The gular scutes may be referred to as a gular projection if they stick out like a trowel." [Wikipedia:Gular_scute]
+
+[Term]
+id: Wikipedia:Humeral_spine
+name: humeral spine
+def: "spines are ventrolateral extensions of the humeral crista ventralis. This structures are present in the humerus of some frogs. The majority of anuran species that present humeral spines are glassfrogs but humeral spines have been reported in various other species of different families of frogs, including Ceratophryidae and Hylidae. In all cases, humeral spines are present in males but not in females." [Wikipedia:Humeral_spine]
+
+[Term]
+id: Wikipedia:Icelandic_Phallological_Museum
+name: icelandic phallological museum
+def: "The Icelandic Phallological Museum in Húsavík, Iceland is a museum devoted to phallology. As of September 2009, the museum houses 272 specimens from 92 species of animals displayed, like hunting trophies, embalmed in formaldehyde, or dried in display cases. The museum attempts to collect penis specimens from every mammal in Iceland, including several species that are endangered or currently extinct in Icelandic waters. Sigurður Hjartarson, a former teacher of history at an institute in Reykjavík, is the founder and current director of the museum, which also exhibits a few specimens from mammals not living in Iceland, as well as folkloric specimens and penis-themed art. Although the museum does not yet have a Homo sapiens specimen, in the interest of advancing phallological knowledge, a patron (Páll Arason, born in 1915 and currently 94 years old) has donated, presumably posthumously, an affidavit for his penis." [Wikipedia:Icelandic_Phallological_Museum]
+
+[Term]
+id: Wikipedia:Interstitial_fluid
+name: interstitial fluid
+def: "Interstitial fluid (or tissue fluid) is a solution that bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. The interstitial fluid is found in the interstitial spaces, also known as the tissue spaces. On average, a person has about 11 litres (2.4 imperial gallons) of interstitial fluid, providing the cells of the body with nutrients and a means of waste removal." [Wikipedia:Interstitial_fluid]
+
+[Term]
+id: Wikipedia:Largest_body_part
+name: largest body part
+def: "The largest body part is either the largest given body part across all animals or the largest example of a body part within a species. The largest animals on the planet are not the only ones to have large body parts, with some smaller animals actually having one particularly enlarged area of the body. The largest organ of a mammal is its skin." [Wikipedia:Largest_body_part]
+
+[Term]
+id: Wikipedia:Lateral_line
+name: lateral line
+def: "The lateral line is a sense organ in aquatic organisms, used to detect movement and vibration in the surrounding water. Lateral lines are usually visible as faint lines running lengthwise down each side, from the vicinity of the gill covers to the base of the tail. Sometimes parts of the lateral organ are modified into electroreceptors, which are organs used to detect electrical impulses. It is possible that vertebrates such as sharks use the lateral organs to detect magnetic fields as well. Most amphibian larvae and some adult amphibians also have a lateral organ. Some crustaceans and cephalopods have similar organs." [Wikipedia:Lateral_line]
+
+[Term]
+id: Wikipedia:Madreporite
+name: madreporite
+def: "The madreporite is an opening used to filter water into the water vascular system of echinoderms. It is visible as a small red or yellow button-like structure, looking like a small wart, on the aboral surface of the central disk of a sea star. Close up, it is visibly structured, resembling a \"madrepore\" colony. From this, it derives its name. The water vascular system of the sea star consists of a series of seawater-filled ducts that function in locomotion and feeding and respiration. Its main parts are the madreporite, the stone canal, the ring canal, the radial canals, the lateral canals, and the tube feet. The sieve-like madreporite allows entry of seawater into the stone canal, which connects to the ring canal around the mouth. Five or more radial canals extend from the ring canal, one in each arm above the ambulacral groove. From the radial canals extend many lateral canals, each of which leads to a tube foot. Each tube foot is a closed cylinder with muscular walls, having a sucker at the outer end and a bulb-like ampulla at its inner end within the body cavity." [Wikipedia:Madreporite]
+
+[Term]
+id: Wikipedia:Mesohyl
+name: mesohyl
+def: "The mesohyl, formerly known as mesenchyme, is the gelatinous matrix within a sponge. It fills the space between the external pinacoderm and the internal choanoderm. The mesohyl resembles a type of connective tissue and contains several amoeboid cells such as amebocytes, as well as fibrils and skeletal elements. For hundreds of years, it has been largely accepted that sponges lack true tissue, but it is currently debated as to whether mesohyl and pinacoderm layers are in fact tissues. The mesohyl is composed of the following main elements: collagen, fibronectin-like molecules, galectin, and a minor component, dermatopontin. These polypeptides form the extracellular matrix which provides the platform for specific cell adhesion as well as for signal transduction and cellular growth." [Wikipedia:Mesohyl]
+
+[Term]
+id: Wikipedia:Nephridiopore
+name: nephridiopore
+def: "Nephridiopore is part of the nephridia, an excretory organ found in many organisms, such as flatworms or annelids. Nephridia are analogous to nephrons or uriniferous tubules found in the kidney of humans. The nephridia consists of an opening called nephrostome, a long convoluted tubule and another opening called the nephridiopore. Body fluids are filtered in through the nephrostome and passed through the convoluted tubule system. Essential substances are reabsorbed through active mechanisms and waste products are secreted back into the lumen of the tube. The resulting excretory fluid or urine is passed out through the nephridiopore." [Wikipedia:Nephridiopore]
+
+[Term]
+id: Wikipedia:Nephridium
+name: nephridium
+def: "Nephridia are invertebrate organs which occur in pairs and function similar to kidneys. They remove metabolic wastes from an animal's body. They are present in many different invertebrate lines. There are two basic types, metanephridia and protonephridia, but there are other types." [Wikipedia:Nephridium]
+
+[Term]
+id: Wikipedia:Nephrostome
+name: nephrostome
+def: "Nephrostome is the funnel-like component of a metanephridium. It is always oriented towards the coelom. The nephrostome is covered from the inside with cilia, which push the water, metabolic wastes, unnecessary hormones and other substances into the metanephridium." [Wikipedia:Nephrostome]
+
+[Term]
+id: Wikipedia:Odontode
+name: odontode
+def: "Odontodes, or dermal teeth, are hard structures found on the external surfaces of animals or near internal openings. They comprise a soft pulp surrounded by dentine and covered by a mineralized substance such as enamel, a structure similar to that of teeth. They generally do not have the same function as teeth, and are not replaced the same way teeth are in most fish. In some animals (notably catfish) the presence or size of odontodes can be used in determining the sex. The name comes from the Greek \"odon\" meaning tooth; a similarly named subject are the Class of animals known as Conodonts (\"cone teeth\"), which were first known from their fossilised primitive teeth. http://www. em-consulte. com/article/189295/auto See also Dermal denticle" [Wikipedia:Odontode]
+
+[Term]
+id: Wikipedia:Oral_arm
+name: oral arm
+def: "Oral arms are a anatomical structures of \"true\" sea jellies (or Scyphozoans), which belong to the class Scyphozoa. Oral arms characterize Semaeostomeae, an order of large jellyfish. The oral arms (of which there are usually four) are located around the mouth and hold the stinging cells, or cnidocysts, which are used to inject potential prey (or potential predators) with venom." [Wikipedia:Oral_arm]
+
+[Term]
+id: Wikipedia:Papula
+name: papula
+def: "Papulae (sing. papula), also known as dermal branchiae or skin gills, are projections of the coelom of Asteroidea that serve in respiration and waste removal. Papulae are soft, covered externally with the epidermis, and lined internally with peritoneum. They extend through the mesodermal ossicles and are protected from microscopic larvae by pedicellariae." [Wikipedia:Papula]
+
+[Term]
+id: Wikipedia:Parietal_eye
+name: parietal eye
+def: "A parietal eye, also known as a parietal organ or third-eye, is a part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation." [Wikipedia:Parietal_eye]
+
+[Term]
+id: Wikipedia:Parotoid_gland
+name: parotoid gland
+def: "The parotoid gland (alternatively, paratoid gland) is an external skin gland on the back, neck, and shoulder of toads and some frogs and salamanders. It secretes a milky alkaloid substance to deter predators. The substance produced acts as a neurotoxin. Parotoid glands are sometimes said to be wart-like in appearance, though warts are abnormal growths caused by viral infections while parotoid glands are normal, healthy parts of the animals that bear them. The vague similarity in appearance, however, is the reason behind the mistaken belief that touching a toad causes warts." [Wikipedia:Parotoid_gland]
+
+[Term]
+id: Wikipedia:Pedicellaria
+name: pedicellaria
+def: "A pedicellaria (plural. pedicellariae) is a small wrench or claw-shaped structure commonly found on Echinoderms, particularly in sea stars and sea urchins (class Echinoidea). Pedicellariae are poorly understood but in some taxa, they are thought to keep the body surface clear of algae, encrusting organisms, and other debris in conjunction with the ciliated epidermis present in all echinoderms. Pedicellariae in some taxa, such as the deep-sea Brisingida, and the Antarctic Labidiaster are known to function in food capture. In forcipulate sea stars, each pedicellaria is typically composed three forceps-like valves. Other asteroids can have pedicellariae composed of only two components. In some asteriid sea stars pedicellariae are present around the base of a spine or on the surface of the animal's body. In other sea stars, they are present in pits on the abactinal, marginal, or actinal surface; oftentimes on the adambulacral plate adjacent to the tube foot furrow." [Wikipedia:Pedicellaria]
+
+[Term]
+id: Wikipedia:Phalanx_bones
+name: phalanx bones
+def: "In anatomy, phalanx bones (plural phalanges) are those that form the fingers and toes. In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three. Phalanges are classified as long bone" [Wikipedia:Phalanx_bones]
+
+[Typedef]
+id: has_origin
+
[Typedef]
id: develops_from
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1,853 uberon-simple.obo
1,606 additions, 247 deletions not shown
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4,457 uberon-with-isa.obo
4,186 additions, 271 deletions not shown
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1,885 uberon.obo
1,635 additions, 250 deletions not shown
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87,658 uberon.owl
46,306 additions, 41,352 deletions not shown
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1,879 uberon_edit-implied.obo
1,629 additions, 250 deletions not shown
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420 uberon_edit.obo
@@ -14,6 +14,7 @@ subsetdef: metazoa_core "core classes typically found across metazoa. one purpos
subsetdef: major_organ "somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads"
subsetdef: upper_ontology_conflict "Terms in this subset group together terms from different anatomy ontologies that have conflicting upper ontology/CARO assignments. For example, in FMA the naris is immaterial and in ZFA it is an organism subdivision."
subsetdef: disjointness_axiom_removed "A class which has a weakened disjointness axiom, to avoid inconsistency. These are kept separately in the uberon_disjoint_from_strict ontology."
+subsetdef: early_development "A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes."
synonymtypedef: PLURAL "plural term"
synonymtypedef: DUBIOUS "dubious or contested synonym"
synonymtypedef: SENSU "taxonomic disambiguation"
@@ -1367,7 +1368,6 @@ synonym: "sinew" RELATED [Wikipedia:Tendon]
xref: BTO:0001356
xref: FMA:9721 ! Tendon
xref: GAID:276 ! tendon
-xref: HAO:0000996 ! tendon
xref: OG:0001286 ! tendon
xref: MA:0000115 ! tendon
xref: OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA
@@ -2427,6 +2427,7 @@ xref: EMAPA:16041 ! inner cell mass
is_a: UBERON:0002050 ! embryonic structure
relationship: surrounded_by UBERON:0000088 ! trophoblast
relationship: develops_from UBERON:0000358 {source="Wikipedia"} ! blastocyst
+subset: early_development
[Term]
id: UBERON:0000088
@@ -2441,16 +2442,16 @@ xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Blastocyst_Englis
xref: MESH:A.11.936 ! trophoblast
xref: EV:0100120 ! trophoblast
is_a: UBERON:0002050 ! embryonic structure
+subset: early_development
[Term]
id: UBERON:0000089
name: hypoblast
-def: "The inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>" [Wikipedia:Hypodermis, ZFIN:curator]
-comment: This class was created automatically from a combination of ontologies
+def: "The inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm" [Wikipedia:Hypoblast, ZFIN:curator]
+comment: this term groups together disparate structures with different relationships. TODO - condier relationship to UBERON:0000091 ! bilaminar disc
subset: uberon_slim
subset: vertebrate_core
-synonym: "hypoblast" EXACT []
-synonym: "mesendoderm" RELATED []
+synonym: "mesendoderm" EXACT [ZFIN:ZDB-PUB-961014-576]
xref: AAO:0000229 ! hypoblast
xref: OG:0001222 ! hypoblast
xref: MAT:0000418 ! hypoblast
@@ -2460,13 +2461,46 @@ xref: XAO:0003044 ! endomesoderm
xref: ZFA:0000117 ! hypoblast
xref: ncithesaurus:Hypoblast ! Hypoblast
xref: EFO:0001930 ! hypoblast
-xref: EHDAA2:0000796 ! hypoblast
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png
xref: BTO:0003953 ! endomesoderm
is_a: UBERON:0002050 ! embryonic structure
-relationship: develops_from UBERON:0000087 ! inner cell mass
+relationship: part_of UBERON:0004750 ! blastoderm
+subset: early_development
+
+[Term]
+id: UBERON:0008776
+name: inner cell mass derived hypoblast
+def: "The hypoblast is a tissue type that forms from the inner cell mass. It lies beneath the epiblast and consists of small cuboidal cells. Extraembryonic endoderm is derived from hypoblast." [Wikipedia:Hypoblast]
+is_a: UBERON:0000089 ! hypoblast
relationship: adjacent_to UBERON:0002532 ! epiblast
-relationship: part_of UBERON:0000091 ! bilaminar disc
+relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass
+xref: EHDAA2:0000796 ! hypoblast
+subset: early_development
+
+[Term]
+id: UBERON:0000417
+name: primitive endoderm
+alt_id: UBERON:0003226
+alt_id: UBERON:BTO_0002123-FMA_85520
+xref: BTO:0002123
+xref: FMA:85520 ! Primitive endoderm
+xref: EHDAA:44 ! primitive endoderm
+xref: EHDAA:79 ! primitive endoderm
+xref: EMAPA:16051 ! primitive endoderm of embryo
+xref: EMAPA:16063 ! primitive endoderm of endoderm of embryo
+is_a: UBERON:0000925 ! endoderm
+subset: early_development
+
+[Term]
+id: UBERON:0003225
+name: primitive endoderm of inner cell mass
+def: "A primitive endoderm that is part of a inner cell mass [Obol]." [OBOL:automatic]
+comment: TODO - check
+synonym: "inner cell mass primitive endoderm" EXACT [OBOL:automatic]
+xref: EHDAA:44 ! primitive endoderm
+intersection_of: UBERON:0000417 ! primitive endoderm
+intersection_of: part_of UBERON:0000087 ! inner cell mass
+subset: early_development
[Term]
id: UBERON:0000090 ! blastocele
@@ -2486,6 +2520,7 @@ xref: EHDAA:50 ! blastocoelic cavity
is_a: UBERON:0002553 ! anatomical cavity
relationship: surrounded_by UBERON:0002532 ! epiblast
relationship: dubious_for_taxon NCBITaxon:7955 {source="http://zfin.org/zf_info/zfbook/stages/gast.html"} ! Danio rerio
+subset: early_development
[Term]
id: UBERON:0000091
@@ -2494,6 +2529,7 @@ def: "the epiblast and the hypoblast, evolved from the embryoblast" [Wikipedia:B
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e3/Gray21.png/200px-Gray21.png
is_a: UBERON:0002050 ! embryonic structure
relationship: develops_from UBERON:0000087 ! inner cell mass
+subset: early_development
[Term]
id: UBERON:0000092
@@ -3956,7 +3992,6 @@ subset: inconsistent_with_fma
synonym: "blastosphere" RELATED [Wikipedia:Blastula]
synonym: "blastula embryo" EXACT [BILA:0000059]
xref: BTO:0000128
-xref: FMA:83041 ! Blastocyst
xref: OGEM:000006 ! blastula
xref: GAID:1294 ! blastula
xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg ! blastula
@@ -4575,7 +4610,7 @@ id: UBERON:0000358
name: blastocyst
alt_id: UBERON:BTO_0001099-FMA_83041
def: "The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]." [GO:0001824, Wikipedia:Blastocyst]
-synonym: "Blastula" EXACT [FMA:83041]
+synonym: "blastula" RELATED [FMA:83041]
xref: BTO:0001099
xref: EFO:0000295
xref: FMA:83041 ! Blastocyst
@@ -7829,6 +7864,8 @@ xref: MESH:A.07.231.114.056 ! aorta
xref: EMAPA:18601 ! aorta
xref: EV:0100027 ! aorta
is_a: UBERON:0001637 ! artery
+is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel
+relationship: overlaps UBERON:0002224 {source="MA-modified"} ! thoracic cavity
[Term]
id: UBERON:0005805 ! dorsal aorta
@@ -7852,12 +7889,13 @@ is_a: UBERON:0000947 ! aorta
relationship: develops_from UBERON:0003064 ! intermediate mesoderm
relationship: develops_from UBERON:0001917 ! endothelium of artery
relationship: part_of UBERON:0002201 ! vasculature of trunk
+relationship: homologous_to UBERON:0001514 {source="Wikipedia"} ! descending aorta
[Term]
id: UBERON:0003085
name: ventral aorta
alt_id: UBERON:XAO_0000338-ZFA_0000604
-def: "Outflow artery from the heart to the aortic arches. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>" [ZFIN:curator]
+def: "The artery in vertebrate embryos that carries blood from the ventricle of the heart to the aortic arches. In adult fish it branches into afferent branchial arteries supplying the gills. In adult tetrapods it is represented by the ascending part of the aorta." [BTO:0004674]
comment: This class was created automatically from a combination of ontologies
subset: uberon_slim
xref: OG:0000121 ! ventral aorta
@@ -7866,6 +7904,7 @@ xref: XAO:0000338 ! ventral aorta
xref: ZFA:0000604 ! ventral aorta
xref: BTO:0004674 ! ventral aorta
is_a: UBERON:0000947 ! aorta
+relationship: homologous_to UBERON:0001496 {source="Wikipedia", source="PMID:2297080"} ! ascending aorta
[Term]
id: UBERON:0000949
@@ -11178,6 +11217,7 @@ is_a: UBERON:0002050 ! embryonic structure
relationship: part_of UBERON:0004735 ! archenteron
relationship: homologous_to FBbt:00000123 {source="vOG:0001202"} ! amnioproctodeal invagination
relationship: dubious_for_taxon NCBITaxon:7955 {source="http://zfin.org/zf_info/zfbook/stages/gast.html"} ! Danio rerio
+subset: early_development
[Term]
id: UBERON:0004879
@@ -11189,6 +11229,7 @@ xref: XAO:0000068 ! marginal zone
xref: ZFA:0000038 ! margin
is_a: UBERON:0002050 ! embryonic structure
xref: ncithesaurus:Marginal_Zone-Marginal Zone
+subset: early_development
[Term]
id: UBERON:0002541
@@ -11205,6 +11246,7 @@ xref: EFO:0003427 ! germ ring
is_a: UBERON:0002050 ! embryonic structure
relationship: part_of UBERON:0004734 ! gastrula
relationship: dubious_for_taxon NCBITaxon:40674 ! Mammalia
+subset: early_development
[Term]
id: UBERON:0003062 ! primitive knot
@@ -11244,6 +11286,7 @@ is_a: UBERON:0002050 ! embryonic structure
relationship: part_of UBERON:0002541 {source="ZFA"} ! germ ring
relationship: part_of UBERON:0004341 {source="EHDAA"} ! primitive streak
relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata
+subset: early_development
[Term]
id: UBERON:0004341 ! primitive streak
@@ -11259,35 +11302,54 @@ xref: OG:0001202 ! primitive streak - blastopore - amnioproctodeal invagination
is_a: UBERON:0002050 ! embryonic structure
relationship: part_of UBERON:0002532 ! epiblast
relationship: dubious_for_taxon NCBITaxon:32443 ! Teleostei
+subset: early_development
[Term]
id: UBERON:0002532
name: epiblast
alt_id: UBERON:MIAA_0000067-ZFA_0000018
-def: "In embryology, the epiblast is a tissue type derived from the inner cell mass. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]" [Wikipedia:Epiblast, ZFIN:curator]
-comment: MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. TODO - mammalian/vertebrate. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS).
+def: "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]" [Wikipedia:Epiblast, ZFIN:curator]
+comment: MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
subset: uberon_slim
+subset: grouping_class
subset: vertebrate_core
synonym: "blastocyst" RELATED []
-synonym: "embryonic epiblast" RELATED [MP:0003886]
synonym: "primitive ectoderm" RELATED [OG:0000243]
-xref: EHDAA:42 ! epiblast
-xref: EHDAA:75 ! epiblast
xref: OG:0000243 ! epiblast
xref: MAT:0000067 ! epiblast
xref: MIAA:0000067 ! epiblast
-xref: TAO:0000018 ! epiblast
-xref: ZFA:0000018 ! epiblast
-xref: ncithesaurus:Epiblast ! Epiblast
-xref: EHDAA2:0000444 ! epiblast
xref: BTO:0004593 ! epiblast
-xref: EMAPA:16050 ! epiblast
is_a: UBERON:0002050 ! embryonic structure
+relationship: has_part CL:0000352 ! epiblast cell
+subset: early_development
+
+[Term]
+id: UBERON:0008780
+name: inner cell mass derived epiblast
+synonym: "embryonic epiblast" RELATED [MP:0003886]
+intersection_of: UBERON:0002532 ! epiblast
+intersection_of: develops_from UBERON:0000087 ! inner cell mass
relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass
relationship: part_of UBERON:0000091 ! bilaminar disc
-relationship: part_of UBERON:0004749 {source="BTO"} ! blastodisc
+xref: EMAPA:16050 ! epiblast
+xref: EHDAA2:0000444 ! epiblast
+xref: EHDAA:42 ! epiblast
+xref: EHDAA:75 ! epiblast
+xref: ncithesaurus:Epiblast ! Epiblast
+subset: early_development
+
+[Term]
+id: UBERON:0008781
+name: blastodisc derived epiblast
+comment: part of blastodisc in BTO; indirect development in ZFA: df DEL df deep blastomere isa blastomere po blastodisc
+intersection_of: UBERON:0002532 ! epiblast
+intersection_of: develops_from UBERON:0004749 ! blastodisc
+relationship: develops_from UBERON:0004749 {source="Wikipedia"} ! blastodisc
relationship: part_of UBERON:0002541 {source="ZFA"} ! germ ring
-relationship: has_part CL:0000352 ! epiblast cell
+xref: TAO:0000018 ! epiblast
+xref: ZFA:0000018 ! epiblast
+relationship: dubious_for_taxon NCBITaxon:40674 ! Mammalia
+subset: early_development
[Term]
id: UBERON:0007026 ! primitive gut
@@ -11483,7 +11545,7 @@ relationship: part_of UBERON:0000165 ! mouth
id: UBERON:0001047
name: neural glomerulus
alt_id: UBERON:FBbt_00005386
-def: "Roundish subunit structure of synaptic neuropil, often ensheathed by glial lamellae and reflecting the terminal arborization domain(s) of one or more neurons[FBbt]. Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets[NIF]." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, Wikipedia:Glomerulus, http://ccdb.ucsd.edu/SAO/images/glomerulus_sw_512x512.jpg]
+def: "Roundish subunit structure of synaptic neuropil, often ensheathed by glial lamellae and reflecting the terminal arborization domain(s) of one or more neurons[FBbt]. Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets[NIF]." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, http://ccdb.ucsd.edu/SAO/images/glomerulus_sw_512x512.jpg]
comment: isa or partof neuropil? TODO. Add to GO?
subset: uberon_slim
synonym: "glomerulus" BROAD []
@@ -11491,7 +11553,7 @@ xref: FBbt:00005386 ! glomerulus
xref: NIF_Subcellular:sao587858733 ! Glomerulus
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Gray1130.svg/200px-Gray1130.svg.png
is_a: UBERON:0002606 ! neuropil
-relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme
+disjoint_from: UBERON:0000074 ! renal glomerulus
xref: ncithesaurus:Glomerulus-Glomerulus
[Term]
@@ -18835,30 +18897,6 @@ relationship: part_of UBERON:0000362 ! renal medulla
synonym: "zona interna (medullaris renalis)" EXACT [FMA:TA, FMA:17734]
[Term]
-id: UBERON:0002450
-name: decidua
-alt_id: UBERON:MA_0001722-MIAA_0000290
-def: "Uterine lining (endometrium) during a pregnancy, which forms the maternal part of the placenta. It is formed under the influence of progesterone and forms highly-characteristic cells." [Wikipedia:Decidua]
-comment: This class was created automatically from a combination of ontologies
-subset: uberon_slim
-synonym: "decidua basalis" RELATED []
-synonym: "endometrium" RELATED []
-synonym: "decidous membrane" EXACT [FMA:85538]
-synonym: "uterine decidua" RELATED [BTO:0001360]
-xref: BTO:0001360
-xref: GAID:378 ! decidua
-xref: MA:0001722 ! decidua
-xref: MAT:0000290 ! decidua
-xref: MIAA:0000290 ! decidua
-xref: FMA:85538 ! Decidua
-xref: ncithesaurus:Decidua ! Decidua
-xref: http://upload.wikimedia.org/wikipedia/commons/thumb/f/fa/Gray33.png/200px-Gray33.png
-xref: EMAPA:29917 ! endometrium
-xref: MESH:A.05.360.319.679.490.373 ! decidua
-is_a: UBERON:0000478 ! extraembryonic structure
-relationship: part_of UBERON:0001987 ! placenta
-
-[Term]
id: UBERON:0004547
name: decidua capsularis
xref: FMA:86478 ! Decidua capsularis
@@ -20481,7 +20519,7 @@ xref: OpenCyc:Mx4rvVjdMZwpEbGdrcN5Y29ycA ! gluteus maximus
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/70/Posterior_Hip_Muscles_3.PNG/200px-Posterior_Hip_Muscles_3.PNG
xref: EMAPA:18527 ! gluteus maximus
is_a: UBERON:0002000 ! gluteal muscle
-elationship: part_of UBERON:0004470 {source="FMA"} ! musculature of pelvic girdle
+relationship: part_of UBERON:0004470 {source="FMA"} ! musculature of pelvic girdle
[Term]
id: UBERON:0001371
@@ -20499,7 +20537,7 @@ xref: ncithesaurus:Gluteus_Medius ! Gluteus Medius
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/70/Posterior_Hip_Muscles_3.PNG/200px-Posterior_Hip_Muscles_3.PNG
xref: EMAPA:19163 ! gluteus medius
is_a: UBERON:0002000 ! gluteal muscle
-relationship: attaches_to UBERON:0002503 {source="FMA"} ! greater trochanter
+relationship: attached_to UBERON:0002503 {source="FMA"} ! greater trochanter
relationship: part_of UBERON:0004470 {source="FMA"} ! musculature of pelvic girdle
[Term]
@@ -20511,7 +20549,7 @@ synonym: "glutaeus minimus" RELATED [Wikipedia:Gluteus_minimus_muscle]
synonym: "gluteus minimus" RELATED [Wikipedia:Gluteus_minimus_muscle]
synonym: "gluteus minimus muscle" EXACT []
is_a: UBERON:0002000 {source="FMA"} ! gluteal muscle
-relationship: attaches_to UBERON:0002503 {source="FMA"} ! greater trochanter
+relationship: attached_to UBERON:0002503 {source="FMA"} ! greater trochanter
relationship: part_of UBERON:0004470 {source="FMA"} ! musculature of pelvic girdle
xref: FMA:22317 ! gluteus minimus
@@ -20765,7 +20803,8 @@ def: "In humans, the gastrocnemius muscle is a very powerful superficial muscle
comment: This class was created automatically from a combination of ontologies
subset: uberon_slim
synonym: "m.gastrocnemius" EXACT []
-synonym: "gastrocnemius muscle" RELATED [BTO:0000506]
+synonym: "gastrocnemius muscle" EXACT [BTO:0000506]
+synonym: "musculus gastrocnemius" RELATED [Wikipedia:Gastrocnemius_muscle]
xref: BTO:0000506
xref: EHDAA:8293 ! gastrocnemius
xref: FMA:22541 ! Gastrocnemius
@@ -20776,7 +20815,7 @@ xref: EFO:0001413 ! gastrocnemius
xref: EHDAA2:0000701 ! gastrocnemius
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/8/8e/Gastrocnemius.png/200px-Gastrocnemius.png
is_a: UBERON:0001383 ! muscle of leg
-relationship: part_of UBERON:0001665 ! triceps surae
+relationship: part_of UBERON:0001665 {source="FMA"} ! triceps surae
relationship: part_of UBERON:0003823 ! lower leg
xref: ncithesaurus:Gastrocnemius_Muscle-Gastrocnemius Muscle
@@ -23104,7 +23143,7 @@ relationship: part_of UBERON:0001460 ! arm
relationship: part_of UBERON:0001814 ! brachial nerve plexus
[Term]
-id: UBERON:0001496
+id: UBERON:0001496 ! ascending aorta
name: ascending aorta
alt_id: UBERON:FMA_3736-MA_0002570
def: "a portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart’s axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]" [Wikipedia:Ascending_aorta]
@@ -23502,7 +23541,8 @@ alt_id: UBERON:FMA_3784-MA_0002571
def: "The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]." [Wikipedia:Descending_aorta]
comment: This class was created automatically from a combination of ontologies
subset: uberon_slim
-synonym: "pars descendens aortae" EXACT []
+synonym: "aorta descendens" RELATED [Wikipedia:Descending_aorta]
+synonym: "pars descendens aortae" EXACT [FMA:3784]
xref: FMA:3784 ! Descending aorta
xref: MA:0002571 ! descending aorta
xref: OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA
@@ -23510,9 +23550,9 @@ xref: ncithesaurus:Descending_Aorta ! Descending Aorta
xref: OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA ! descending aorta
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Gray506.svg/200px-Gray506.svg.png
xref: EMAPA:18605 ! descending
-is_a: UBERON:0005800 ! segment of aorta
+is_a: UBERON:0005800 {source="FMA"} ! segment of aorta
relationship: part_of UBERON:0001009 ! circulatory system
-relationship: part_of UBERON:0000947 ! aorta
+relationship: part_of UBERON:0000947 {source="FMA"} ! aorta
relationship: develops_from UBERON:0005805 {source="Wikipedia"} ! dorsal aorta
[Term]
@@ -23523,13 +23563,6 @@ def: "The thoracic aorta is contained in the posterior mediastinal cavity. It be
comment: This class was created automatically from a combination of ontologies
subset: uberon_slim
synonym: "thoracic part of aorta" EXACT []
-synonym: "adult aorta of thorax" EXACT [OBOL:automatic]
-synonym: "aorta of thorax" EXACT [OBOL:automatic]
-synonym: "thorax adult aorta" EXACT [OBOL:automatic]
-synonym: "thorax aorta" EXACT [OBOL:automatic]
-synonym: "thorax dorsal aorta" EXACT [OBOL:automatic]
-synonym: "thorax trunk of aortic tree" EXACT [OBOL:automatic]
-synonym: "trunk of aortic tree of thorax" EXACT [OBOL:automatic]
xref: FMA:3786 ! Thoracic aorta
xref: GAID:471 ! thoracic aorta
xref: MA:0002569 ! thoracic aorta
@@ -23550,21 +23583,15 @@ intersection_of: part_of UBERON:0000915 ! thorax
id: UBERON:0001516
name: abdominal aorta
alt_id: UBERON:FMA_3789-MA_0000474
-def: "The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]." [Wikipedia:Abdominal_aorta]
-comment: This class was created automatically from a combination of ontologies
-subset: uberon_slim
-synonym: "abdominal part of aorta" EXACT []
-synonym: "descending abdominal aorta" EXACT []
-synonym: "pars abdominalis aortae" EXACT []
-synonym: "abdomen adult aorta" EXACT [OBOL:automatic]
-synonym: "abdomen aorta" EXACT [OBOL:automatic]
-synonym: "abdomen dorsal aorta" EXACT [OBOL:automatic]
-synonym: "abdomen trunk of aortic tree" EXACT [OBOL:automatic]
-synonym: "adult aorta of abdomen" EXACT [OBOL:automatic]
-synonym: "aorta of abdomen" EXACT [OBOL:automatic]
-synonym: "dorsal aorta of abdomen" EXACT [OBOL:automatic]
-synonym: "trunk of aortic tree of abdomen" EXACT [OBOL:automatic]
-synonym: "aorta abdominalis" RELATED [BTO:0002976]
+def: "Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]." [Wikipedia:Abdominal_aorta, BTO:0002976]
+comment: This class was created automatically from a combination of ontologies
+subset: uberon_slim
+synonym: "abdominal part of aorta" EXACT [FMA:3789]
+synonym: "descending abdominal aorta" EXACT [FMA:3789]
+synonym: "pars abdominalis aortae" EXACT [FMA:3789]
+synonym: "abdominal part of aorta" RELATED [BTO:0002976]
+synonym: "aorta abdominalis" RELATED [BTO:0002976]
+synonym: "pars abdominalis aortae" RELATED [BTO:0002976]
xref: FMA:3789 ! Abdominal aorta
xref: GAID:470 ! abdominal aorta
xref: galen:AbdominalAorta
@@ -26004,12 +26031,11 @@ relationship: part_of UBERON:0001633 ! basilar artery
[Term]
id: UBERON:0003509 ! arterial blood vessel
name: arterial blood vessel
-def: "A blood vessel that carries blood from the heart to the body[tfd]." [http://www.thefreedictionary.com/arterial+blood+vessel]
+def: "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." [UBERON:cjm]
comment: only in MA - supertype of artery, arteriole, aorta.
xref: MA:0000061 ! arterial blood vessel
-xref: AEO:0000208 ! artery
-is_a: UBERON:0001981 ! blood vessel
-relationship: part_of UBERON:0004572 ! arterial system
+intersection_of: UBERON:0001981 ! blood vessel
+intersection_of: part_of UBERON:0004572 ! arterial system
[Term]
id: UBERON:0001637
@@ -26739,14 +26765,17 @@ id: UBERON:0001665
name: triceps surae
alt_id: UBERON:FMA_51062-MA_0002400
def: "The triceps surae is a pair of muscles located at the calf - the gastrocnemius and the soleus. These muscles both insert into the calcaneus, the bone of the heel of the human foot, and form the major part of the muscle of the back part of the lower leg, commonly known as the calf muscle. The triceps surae is connected to the foot through the Achilles tendon, and has 3 heads deriving from the 2 major masses of muscle. The superficial portion (the gastrocnemius) gives off 2 heads attaching to the base of the femur directly above the knee. The deep (profundis) mass of muscle (the soleus) forms the remaining head which attaches to the superior posterior area of the tibia. The triceps surae is innervated by the tibial nerve, specifically, nerve roots L5–S2. [WP,unvetted]." [Wikipedia:Triceps_surae]
-comment: This class was created automatically from a combination of ontologies
+comment: A set of muscles in FMA, a single organ in MA
subset: uberon_slim
+synonym: "calf muscle" RELATED [Wikipedia:Triceps_surae_muscle]
+synonym: "gastrosoleus" RELATED [Wikipedia:Triceps_surae_muscle]
+synonym: "gastrosoleus complex" RELATED [Wikipedia:Triceps_surae_muscle]
synonym: "sural triceps" RELATED []
xref: FMA:51062 ! Triceps surae
xref: MA:0002400 ! triceps surae
xref: ncithesaurus:Triceps_Surae ! Triceps Surae
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/57/Illu_lower_extremity_muscles.jpg/200px-Illu_lower_extremity_muscles.jpg
-is_a: UBERON:0001630 ! muscle organ
+is_a: UBERON:0001630 {source="MA"} ! muscle organ
relationship: part_of UBERON:0003823 ! lower leg
[Term]
@@ -35611,6 +35640,30 @@ intersection_of: UBERON:0001986 ! endothelium
intersection_of: part_of UBERON:0000964 ! cornea
[Term]
+id: UBERON:0002450
+name: decidua
+alt_id: UBERON:MA_0001722-MIAA_0000290
+def: "Uterine lining (endometrium) during a pregnancy, which forms the maternal part of the placenta. It is formed under the influence of progesterone and forms highly-characteristic cells." [Wikipedia:Decidua]
+comment: This class was created automatically from a combination of ontologies
+subset: uberon_slim
+synonym: "decidua basalis" RELATED []
+synonym: "endometrium" RELATED []
+synonym: "decidous membrane" EXACT [FMA:85538]
+synonym: "uterine decidua" RELATED [BTO:0001360]
+xref: BTO:0001360
+xref: GAID:378 ! decidua
+xref: MA:0001722 ! decidua
+xref: MAT:0000290 ! decidua
+xref: MIAA:0000290 ! decidua
+xref: FMA:85538 ! Decidua
+xref: ncithesaurus:Decidua ! Decidua
+xref: http://upload.wikimedia.org/wikipedia/commons/thumb/f/fa/Gray33.png/200px-Gray33.png
+xref: EMAPA:29917 ! endometrium
+xref: MESH:A.05.360.319.679.490.373 ! decidua
+is_a: UBERON:0000478 {source="FMA"} ! extraembryonic structure
+relationship: part_of UBERON:0001987 {source="MA"} ! placenta
+
+[Term]
id: UBERON:0001987
name: placenta
alt_id: UBERON:FMA_63934-MA_0000386-MIAA_0000279
@@ -35639,7 +35692,6 @@ relationship: develops_from UBERON:0004340 {source="ISBN10:0073040584"} ! allant
relationship: develops_from UBERON:0000995 {source="ISBN10:0073040584"} ! uterus
relationship: only_in_taxon NCBITaxon:9347 ! Eutheria
relationship: develops_from UBERON:0003124 {source="Wikipedia"} ! chorion
-relationship: develops_from UBERON:0002450 {source="Wikipedia"} ! decidua
[Term]
id: UBERON:0001988
@@ -37196,11 +37248,14 @@ relationship: part_of UBERON:0002165 ! endocardium
id: UBERON:0002063
name: sinus venosus
alt_id: UBERON:FMA_70303-ZFA_0000154
-def: "a large quadrangular cavity which precedes the atrium on the venous side of the chordate heart. In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis[Wikipedia]. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four heart chambers, the sinus venosus also acts as a pacemaker and is the first to contract. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>" [Wikipedia:Sinus_venosus, ZFIN:curator]
-comment: This class was created automatically from a combination of ontologies
+def: "The sinus venosus is a large quadrangular cavity which precedes the atrium on the venous side of the chordate heart. In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarum." [Wikipedia:Sinus_venosus]
subset: uberon_slim
subset: vertebrate_core
synonym: "inflow tract" EXACT [ZFA:0000154]
+synonym: "sinus venarum" RELATED [Wikipedia:Sinus_venosus]
+synonym: "venarum" RELATED [Wikipedia:Sinus_venosus]
+synonym: "venarum sinus" RELATED [Wikipedia:Sinus_venosus]
+synonym: "venosus" RELATED [Wikipedia:Sinus_venosus]
xref: EHDAA:480 ! sinus venosus
xref: FMA:70303 ! Sinus venosus
xref: OG:0000177 ! sinus venosus
@@ -37212,6 +37267,8 @@ xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c7/Gray465.png/200px
xref: EMAPA:16237 ! sinus venosus
is_a: UBERON:0004151 ! cardiac chamber
relationship: part_of UBERON:0000948 ! heart
+relationship: part_of UBERON:0002350 {source="OG"} ! conducting system of heart
+relationship: develops_from UBERON:0007278 {source="ZFA"} ! presumptive sinus venosus
[Term]
id: UBERON:0004344 ! cardinal vein
@@ -39059,7 +39116,6 @@ synonym: "nephromere" RELATED [Wikipedia:Nephrotome]
synonym: "intermediate cell mass" RELATED [BTO:0003673]
xref: BTO:0003673 ! nephrotome
is_obsolete: true
-relationship: develops_from UBERON:0000926 {source="Wikipedia"} ! mesoderm
[Term]
id: UBERON:0003918 ! kidney mesenchyme
@@ -39142,7 +39198,6 @@ relationship: part_of UBERON:0000922 ! embryo
relationship: develops_from UBERON:0005721 ! pronephric mesoderm
relationship: develops_from UBERON:0005754 ! rostral part of nephrogenic cord
relationship: part_of UBERON:0002323 ! body cavity
-relationship: develops_from UBERON:0005722 {source="Wikipedia"} ! nephrotome
[Term]
id: UBERON:0005794
@@ -44587,12 +44642,12 @@ relationship: attached_to UBERON:0002349 ! myocardium
id: UBERON:0002350
name: conducting system of heart
alt_id: UBERON:FMA_9476-ZFA_0005063
-def: "Conducting tissue of heart which consists of specialized cardiac myocyte in the myocardium.[FMA]" [, FMA:FMA]
-comment: This class was created automatically from a combination of ontologies
+def: "Conducting tissue of heart which consists of specialized cardiac myocyte in the myocardium.[FMA]" [FMA:9476]
subset: vertebrate_core
synonym: "cardiac conduction system" EXACT []
synonym: "cardionector" EXACT []
synonym: "central conduction system" RELATED []
+synonym: "impulse conducting system" EXACT [MA:0000094]
xref: FMA:9476 ! Conducting system of heart
xref: OG:0001271 ! cardiac conducting system
xref: TAO:0005063 ! cardiac conduction system
@@ -44600,6 +44655,7 @@ xref: ZFA:0005063 ! cardiac conduction system
xref: MESH:A.07.541.409 ! heart conduction system
xref: EV:0100025 ! cardiac conducting system
xref: EFO:0003909 ! heart conduction system
+xref: MA:0000094 ! impulse conducting system
is_a: UBERON:0001133 ! cardiac muscle tissue
relationship: has_part CL:0002068 {source="FMA"} ! Purkinje myocyte
relationship: has_part CL:0002073 {source="FMA"} ! transitional myocyte
@@ -44609,22 +44665,24 @@ relationship: has_part CL:1000410 {source="FMA"} ! myocyte of atrioventricular n
[Term]
id: UBERON:0002351
-name: sinuatrial node
+name: sinoatrial node
alt_id: UBERON:FMA_9477-MA_0000097-ZFA_0005069
def: "part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]." [Wikipedia:Sinoatrial_node, GO:0003163]
-comment: This class was created automatically from a combination of ontologies
-subset: uberon_slim
-subset: vertebrate_core
-synonym: "Koch's node" EXACT []
-synonym: "node of keith-flack" EXACT []
-synonym: "sa nodal muscle tissue" EXACT []
-synonym: "sa node" EXACT []
-synonym: "sinoatrial node" EXACT []
-synonym: "sinu-atrial node" EXACT []
-synonym: "sinuatrial nodal muscle tissue" EXACT []
-synonym: "sinus node" EXACT []
-synonym: "sinus node of keith and flack" EXACT []
-synonym: "cardiac pacemaker" EXACT [FMA:9477]
+comment: WP states: The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.
+subset: uberon_slim
+subset: vertebrate_core
+synonym: "cardiac pacemaker" EXACT [FMA:9477]
+synonym: "Koch's node" EXACT [FMA:9477]
+synonym: "node of Keith-Flack" EXACT [FMA:9477]
+synonym: "SA nodal muscle tissue" EXACT [FMA:9477]
+synonym: "SA node" EXACT [FMA:9477]
+synonym: "sinoatrial node" EXACT [FMA:9477]
+synonym: "sinu-atrial node" EXACT [FMA:9477]
+synonym: "sinuatrial nodal muscle tissue" EXACT [FMA:9477]
+synonym: "sinus node" EXACT [FMA:9477]
+synonym: "sinus node of Keith and Flack" EXACT [FMA:9477]
+synonym: "sinuatrial node" EXACT [FMA:9477]
+synonym: "nodus sinuatrialis" EXACT [FMA:TA, FMA:9477]
xref: FMA:9477 ! Sinuatrial node
xref: GAID:561 ! sinoatrial node
xref: MA:0000097 ! sinoatrial node
@@ -44637,8 +44695,8 @@ xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/Sinoatrial_node_l
xref: BTO:0004358 ! sinus node
xref: MESH:A.07.541.409.819 ! sinoatrial node
is_a: UBERON:0001133 ! cardiac muscle tissue
-relationship: part_of UBERON:0002350 ! conducting system of heart
-synonym: "nodus sinuatrialis" EXACT [FMA:TA, FMA:9477]
+relationship: part_of UBERON:0002350 {source="ZFA"} ! conducting system of heart
+relationship: has_function_in GO:0060048 ! cardiac muscle contraction
[Term]
id: UBERON:0002352
@@ -58100,10 +58158,10 @@ relationship: part_of UBERON:0003075 ! neural plate
id: UBERON:0003058
name: hypochord
alt_id: UBERON:XAO_0000056-ZFA_0000031
-def: "A transient rod-like structure which is endodermally derived and located immediately ventral to the notochord. The hypochord is thought to play a role in positioning the dorsal aorta[ZFA]." [ISBN:0815318960, PMID:10648245, ZFIN:curator]
+def: "The hypochord is a transient rod-like structure in the embryos of fish, lampreys and amphibians that is located immediately ventral to the notochord. The hypochord may play a role in positioning the dorsal aorta[GO]. near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle[AAO]" [ISBN:0815318960, PMID:10648245, GO:0055016, AAO:0000733]
comment: Unlike in frogs and axolotl, the hypochord does not appear to be endodermally derived[ZFA]
subset: dubious_grouping
-synonym: "subnotochordal rod" RELATED []
+synonym: "subnotochordal rod" EXACT [GO:0055016, PMID:10648245]
xref: AAO:0000733 ! hypochord
xref: OG:0000081 ! hypochord
xref: TAO:0000031 ! hypochord
@@ -58111,7 +58169,7 @@ xref: XAO:0000056 ! hypochord
xref: ZFA:0000031 ! hypochord
xref: EFO:0003475 ! hypochord
is_a: UBERON:0000479 ! portion of tissue
-relationship: part_of UBERON:0000925 ! endoderm
+relationship: part_of UBERON:0000925 {source="XAO"} ! endoderm
[Term]
id: UBERON:0005727
@@ -60917,29 +60975,6 @@ intersection_of: part_of UBERON:0003124 ! chorion
intersection_of: develops_from UBERON:0000371 {source="Obol"} ! syncytiotrophoblast
[Term]
-id: UBERON:0000417
-name: primitive endoderm
-alt_id: UBERON:0003226
-alt_id: UBERON:BTO_0002123-FMA_85520
-xref: BTO:0002123
-xref: FMA:85520 ! Primitive endoderm
-xref: EHDAA:44 ! primitive endoderm
-xref: EHDAA:79 ! primitive endoderm
-xref: EMAPA:16051 ! primitive endoderm of embryo
-xref: EMAPA:16063 ! primitive endoderm of endoderm of embryo
-is_a: UBERON:0000925 ! endoderm
-
-[Term]
-id: UBERON:0003225
-name: primitive endoderm of inner cell mass
-def: "A primitive endoderm that is part of a inner cell mass [Obol]." [OBOL:automatic]
-comment: TODO - check
-synonym: "inner cell mass primitive endoderm" EXACT [OBOL:automatic]
-xref: EHDAA:44 ! primitive endoderm
-intersection_of: UBERON:0000417 ! primitive endoderm
-intersection_of: part_of UBERON:0000087 ! inner cell mass
-
-[Term]
id: UBERON:0003229
name: epithelium of elbow
def: "An epithelium that is part of a elbow [Obol]." [OBOL:automatic]
@@ -71158,18 +71193,6 @@ relationship: develops_from UBERON:0000925 ! endoderm
xref: ncithesaurus:Primordium_of_the_Liver-Primordium of the Liver
[Term]
-id: UBERON:0003895
-name: hypaxial myotome region
-def: "trunk muscle that lie ventral to the horizontal septum of the vertebrae." [Wikipedia:Epaxial_and_Hypaxial_muscles]
-synonym: "hypaxial muscle" EXACT [ZFA:0001085]
-synonym: "body wall muscle" RELATED [XAO:0003228]
-xref: XAO:0003228 ! hypaxial muscle
-xref: ZFA:0001085 ! hypaxial myotome region
-xref: AAO:0000228 ! hypaxial muscles
-is_a: UBERON:0001134 ! skeletal muscle tissue
-relationship: part_of UBERON:0003082 ! myotome
-
-[Term]
id: UBERON:0003896
name: muscle of body wall
def: "A muscle organ that is part of a body wall [Obol]." [OBOL:automatic]
@@ -71228,27 +71251,57 @@ intersection_of: UBERON:0001134 ! skeletal muscle tissue
intersection_of: part_of UBERON:0000033 ! head
[Term]
-id: UBERON:0003900
-name: epaxial muscle
-def: "trunk muscle that lies dorsal to the septum." [Wikipedia:Epaxial_and_Hypaxial_muscles]
-synonym: "epaxialis" EXACT [ZFA:0000349]
+id: UBERON:0008777
+name: hypaxial musclulature
+def: "trunk muscles that lie ventral to the horizontal septum of the vertebrae." [Wikipedia:Epaxial_and_Hypaxial_muscles]
+synonym: "hypaxial muscle" RELATED [XAO:0003228]
+xref: XAO:0003228 ! hypaxial muscle
+xref: AAO:0000228 ! hypaxial muscles
+relationship: part_of UBERON:0001774 {source="XAO"} ! muscle of trunk
+intersection_of: UBERON:0001015 ! musculature
+intersection_of: develops_from UBERON:0003895 ! hypaxial muscle
+
+[Term]
+id: UBERON:0008778
+name: epaxial musclulature
+def: "trunk muscles that lies dorsal to the horizontal septum." [Wikipedia:Epaxial_and_Hypaxial_muscles]
+synonym: "epaxial muscle" EXACT [XAO:0003229]
xref: AAO:0000142 ! epaxial_muscles
xref: XAO:0003229 ! epaxial muscle
-xref: ZFA:0000349 ! epaxialis
-xref: TAO:0000349
-is_a: UBERON:0003898 ! skeletal muscle of trunk
-relationship: part_of UBERON:0001774 ! muscle of trunk
+relationship: part_of UBERON:0001774 {source="XAO"} ! muscle of trunk
+intersection_of: UBERON:0001015 ! musculature
+intersection_of: develops_from UBERON:0003900 ! epaxial muscle
+
+[Term]
+id: UBERON:0003895
+name: hypaxial myotome region
+def: "Portion of myotome that is ventral to the horizontal septum" [ISBN10:0073040584]
+synonym: "hypaxial myotome region" EXACT [ZFA:0001085]
+synonym: "body wall muscle" RELATED [XAO:0003228]
+xref: ZFA:0001085 ! hypaxial myotome region
+is_a: UBERON:0001134 ! skeletal muscle tissue
+relationship: part_of UBERON:0003082 ! myotome
+
+[Term]
+id: UBERON:0003900
+name: epaxial myotome region
+def: "Portion of myotome that is dorsal to the horizontal septum" [ISBN10:0073040584]
+synonym: "epaxial myotome regions" EXACT PLURAL [ZFA:0001084]
+is_a: UBERON:0001134 ! skeletal muscle tissue
+relationship: part_of UBERON:0003082 ! myotome
+xref: ZFA:0001084 ! epaxial myotome region
[Term]
id: UBERON:0003901
-name: horizontal myoseptum
-def: "A connective tissue partition developing at the apex of the chevron-shaped myotome and separating dorsal (epaxial) and ventral (hypaxial) body wall muscle masses." [ZFA:0000671]
-synonym: "horizontal septum" EXACT [ZFA:0000671]
+name: horizontal septum
+def: "A logitudinal sheet of continuous connective tissue partition developing at the apex of the chevron-shaped myotome and separating dorsal (epaxial) and ventral (hypaxial) body wall muscle masses; each is destined to become, respectively, the epaxial and hyopaxial musculature." [ZFA:0000671, ISBN10:0073040584]
+synonym: "horizontal myoseptum" EXACT [ZFA:0000671]
xref: ZFA:0000671 ! horizontal myoseptum
xref: EFO:0003555 ! horizontal myoseptum
is_a: UBERON:0003037 ! septum
-relationship: adjacent_to UBERON:0003900
-relationship: adjacent_to UBERON:0003895
+relationship: adjacent_to UBERON:0003900 ! epaxial muscle
+relationship: adjacent_to UBERON:0003895 ! hypaxial muscle
+relationship: only_in_taxon NCBITaxon:7776 {source="ISBN10:0073040584"} ! Gnathostomata
[Term]
id: UBERON:0003906
@@ -77168,6 +77221,7 @@ xref: EHDAA2:0002091 ! trophectoderm
xref: EHDAA:56 ! trophectoderm
is_a: UBERON:0000478 {source="EHDAA2"} ! extraembryonic structure
relationship: has_part CL:1000274 ! trophectodermal cell
+subset: early_development
[Term]
id: UBERON:0006280
@@ -77183,6 +77237,7 @@ relationship: develops_from UBERON:0004345 {source="EHDAA2"} ! trophectoderm
relationship: part_of UBERON:0004345 {source="EMAPA"} ! trophectoderm
relationship: part_of UBERON:0004345 ! trophectoderm
relationship: surrounds UBERON:0000087 ! inner cell mass
+subset: early_development
[Term]
id: UBERON:0006265
@@ -77197,6 +77252,7 @@ is_a: UBERON:0000478 ! extraembryonic structure
relationship: part_of UBERON:0004345 {source="EMAPA"} ! trophectoderm
relationship: part_of UBERON:0004345 ! trophectoderm
relationship: surrounds UBERON:0000090 ! blastocele
+subset: early_development
[Term]
id: UBERON:0004346
@@ -78445,12 +78501,11 @@ is_a: UBERON:0003662 {source="FMA"} ! forelimb muscle
id: UBERON:0001495
name: pectoral muscle
alt_id: UBERON:FMA_37349-MA_0002423
-def: "The pectoralis major is a thick, fan-shaped muscle, situated at the upper front of the chest wall. It makes up the bulk of the chest muscles in the male and lies under the breast in the female. Underneath the pectoralis major is the pectoralis minor, a thin, triangular muscle. [WP,unvetted]." [Wikipedia:Pectoral_muscle]
comment: Note: in FMA isa muscle of pectoral girdle; todo - resolve spatial disjointness inconsistencies and add
subset: uberon_slim
-synonym: "muscle of pectoral part of chest" EXACT []
-synonym: "muscle of pectoral region" EXACT []
-synonym: "pectoralis muscle" EXACT []
+synonym: "muscle of pectoral part of chest" EXACT [FMA:37349]
+synonym: "muscle of pectoral region" EXACT [FMA:37349]
+synonym: "pectoralis muscle" RELATED [BTO:0000023]
synonym: "breast muscle" RELATED [BTO:0000023]
xref: BTO:0000023
xref: FMA:37349 ! Pectoral muscle
@@ -78463,6 +78518,14 @@ is_a: UBERON:0001630 ! muscle organ
relationship: part_of UBERON:0004464 {source="BTO"} ! musculature of thorax
[Term]
+id: UBERON:0008779
+name: subclavius
+def: "The Subclavius is a small triangular muscle, placed between the clavicle and the first rib. Along with the pectoralis major and pectoralis minor muscles, the subclavius muscle makes up the anterior wall of the axilla." [Wikipedia:Subclavius_muscle]
+synonym: "subclavicular muscle" RELATED [Wikipedia:Subclavius_muscle]
+is_a: UBERON:0001495 {source="FMA"} ! pectoral muscle
+xref: FMA:13410 ! subclavius
+
+[Term]
id: UBERON:0004472
name: musculature of chest
def: "A musculature that is part of a chest [Obol]." [OBOL:automatic]
@@ -91053,7 +91116,7 @@ subset: emapa_ehdaa2
xref: EMAPA:17749 ! deltoid pre-muscle mass
xref: EHDAA2:0000340 ! deltoid pre-muscle mass
xref: EHDAA:6002 ! deltoid pre-muscle mass
-is_a: UBERON:0002050 ! embryonic structure
+is_a: UBERON:0008714 ! pre-muscle mass
[Term]
id: UBERON:0006220
@@ -91160,7 +91223,7 @@ subset: emapa_ehdaa2
xref: EMAPA:17845 ! extrinsic ocular pre-muscle mass
xref: EHDAA2:0000483 ! extrinsic ocular pre-muscle mass
xref: EHDAA:2925 ! extrinsic ocular pre-muscle mass
-is_a: UBERON:0002050 ! embryonic structure
+is_a: UBERON:0008714 ! pre-muscle mass
relationship: part_of UBERON:0003269 ! skeletal muscle of eye
[Term]
@@ -97110,7 +97173,7 @@ synonym: "musculus piriformis" RELATED [Wikipedia:Piriformis_muscle]
synonym: "piriform muscle" RELATED [Wikipedia:Piriformis_muscle]
synonym: "piriformis" RELATED [Wikipedia:Piriformis_muscle]
is_a: UBERON:0002000 {source="FMA"} ! gluteal muscle
-relationship: attaches_to UBERON:0002503 {source="FMA"} ! greater trochanter
+relationship: attached_to UBERON:0002503 {source="FMA"} ! greater trochanter
relationship: part_of UBERON:0004470 {source="FMA"} ! musculature of pelvic girdle
xref: FMA:19082 ! piriformis
@@ -97548,12 +97611,33 @@ xref: EHDAA2:0001422 ! pectoral girdle and thoracic body wall skeletal muscle
is_a: UBERON:0001134 ! skeletal muscle tissue
[Term]
-id: UBERON:0008714
+id: UBERON:0008714 ! pre-muscle mass
name: pre-muscle mass
synonym: "pre muscle mass" EXACT []
synonym: "premuscle mass" EXACT []
+is_a: UBERON:0002050 ! embryonic structure
is_a: UBERON:0002385 ! muscle tissue
+[Term]
+id: UBERON:0008772
+name: proximal epiphysis of tibia
+synonym: "head of tibia" EXACT [FMA:33113]
+synonym: "proximal end of tibia" EXACT [FMA:33113]
+synonym: "upper end of tibia" EXACT [FMA:33113]
+intersection_of: UBERON:0004380 ! proximal epiphysis
+intersection_of: part_of UBERON:0000979 ! tibia
+xref: FMA:33113 ! proximal epiphysis of tibia
+
+[Term]
+id: UBERON:0008775
+name: proximal epiphysis of fibula
+synonym: "head of fibula" EXACT [FMA:33729]
+synonym: "proximal end of fibula" EXACT [FMA:33729]
+synonym: "upper end of fibula" EXACT [FMA:33729]
+intersection_of: UBERON:0004380 ! proximal epiphysis
+intersection_of: part_of UBERON:0001446 ! fibula
+xref: FMA:33729 ! proximal epiphysis of fibula
+
[Typedef]
id: adjacent_to
name: adjacent_to
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