Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
[1st arch mandibular component; ventral mandibular arch; anatomical entity; embryonic structure; is part of; pharyngeal arch 1]
Mesenchyme that is part of a 1st arch mandibular component.
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
Mesenchyme that is part of a pharyngeal arch 1.
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
Mesenchyme that is part of a pharyngeal arch 6.
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
A blood vessel that is part of an abdomen [Automatically generated definition].
A portion of connective tissue that is part of an abdomen [Automatically generated definition].
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
Set of all muscles in abdomen.
A nerve that is part of an abdomen [Automatically generated definition].
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].
An artery that originates from the abdominal aorta.
The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).
A ganglion that is part of a abdominal segment of trunk.
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
A bone that is part of an abdominal segment of trunk [Automatically generated definition].
A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition].
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition].
The abdominal segment of the torso.
A skin of body that is part of an abdominal segment of trunk [Automatically generated definition].
A viscus that is part of a abdomen.
The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles.
The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity.
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
An acellular anatomical structure that is the bounding layer of a anatomical structure.
An acinus that is part of a exocrine gland.
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
An adventitia that is part of a esophagus.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
The part of the digestive system that excludes the hepatobiliary system.
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
Anatomical group that has its parts adjacent to one another.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
Any tube, opening or passage that connects two distinct anatomical spaces.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
An anatomical structure that connects two structures.
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism’s own genome.
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism’s environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n Old definition: ‘Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.’ Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
Material anatomical entity that forms the outermost boundary of an anatomical structure.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
An epithelium that is part of a anterior chamber of eyeball.
The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.
[ALPM; anterior lateral plate mesoderm; mesoderm-derived structure; embryonic tissue; is part of; material anatomical entity]
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
[anterior neural tube; develops from; anatomical entity; is part of; embryonic structure; pre-chordal neural plate]
[anterior_to; posterior region of body; only in taxon; organism subdivision; Bilateria; anterior region of body]
Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).
The anterior segment of the lamellated connective tissue layer of the cornea.
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
[heart left ventricle; is part of; anterior wall of left ventricle; in_anterior_side_of]
Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle.
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity.
The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall.
The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall.
The nonstriated, involuntary muscle tissue located in the wall of the aorta.
The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers.
The innermost layer of the aorta, containing the endothelium and an inner elastic membrane.
The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers.
An anatomical wall that is part of an aorta, enclosing the luminal space.
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates.
The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions.
Major subdivision of an organism that protrudes from the body[DOS, CARO].
A blood vessel that is part of a limb/fin.
Any collection of muscles that is part of an appendage.
A vasculature that is part of a limb/fin.
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
A blood that is part of a artery.
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. only in MA - supertype of artery, arteriole, aorta.
The part of the cardiovascular system consisting of all arteries.
An endothelium that is part of an arterial system [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
[labial artery; supplies; artery of lip]
The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
An anatomical wall that is part of an artery [Automatically generated definition].
Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt].
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
Anatomical system that consists of all the joints of the body.
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles.
An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart.
The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve.
Epithelium that consists of epithelial cells not arranged in one ore more layers.
Is the sensory system for the sense of hearing.
Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa.
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
One of the skeletal muscles of the head and neck, spine, and ribs.
Musculature of the head and neck, spine, and ribs.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
A blood vessel that is part of a back [Automatically generated definition].
A portion of connective tissue that is part of a back [Automatically generated definition].
A nerve that is part of a back [Automatically generated definition].
[basal plate metencephalon; metencephalon basal plate; neural tube basal plate]
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
Organism at the blastula 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.
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.
A fluid that is composed of blood plasma and erythrocytes.
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
The liquid component of blood, in which erythrocytes are suspended.
A vascular network consisting of blood vessels.
A vessel through which blood circulates in the body.
Elastic tissue layer that lines a blood vessel layer.
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart.
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
Smooth muscle found within, and composing the majority of the wall of blood vessels.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
Any substance in the body or expelled from the body that is in a gaseous state.
Dermal, epidermal, glandular and pigment structures of the body integument.
The region of the organism associated with the visceral organs.
An anatomical boundary that corresponds to some physical discontinuity. One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity.
Skeletal element that is composed of bone tissue.
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
The soft tissue that fills the cavities of bones.
A bone that is part of a craniocervical region.
A bone that is part of the dorsal region of an animal.
A bone element that is part of a jaw region.
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular.
A bone that is part of a reproductive organ.
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
A blood vessel that is part of a brain [Automatically generated definition].
Vascular endothelium found in blood vessels of the blood-brain-barrier.
A gray matter that is part of a brain [Automatically generated definition].
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. ‘brainstem’ is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
A nucleus of brain that is part of a brainstem.
[branch of external carotid artery; external carotid arterial subdivision; branching part of; systemic artery; structure with developmental contribution from neural crest]
A systemic artery that supplies the lung with with oxygenated blood. Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches.
A myocardium that is part of a bulbus cordis [Automatically generated definition].
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
Any of the smallest blood vessels connecting arterioles with venules.
A blood that is part of a capillary.
The elastic, clear, membrane-like structure, that is outer most layer of the lens.
Cardiac chamber in which blood enters the heart.
A cardiac chamber surrounds an enclosed cavity within the heart. generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures.
A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
[cardiac muscle tissue of ventricle; cardiac ventricle; cardiac muscle tissue of myocardium; ventricular muscle; is part of; myocardium of ventricle]
Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle.
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.
Vein of heart that drains the myocardium.
Cardiac chamber through which blood leaves the heart.
The first recognizable structure derived from the heart field.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
Anatomical system that has as its parts the heart and blood vessels.
An elastic tissue that is part of a circulatory system [Automatically generated definition].
An endothelium that is part of the cardiovascular system.
[carotid artery endothelium; is part of; carotid artery segment; carotid endothelium; endothelium of artery; carotid epithelium]
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
A cartilage element of chondrocranium. Example: neurocranial trabecula.
A cartilage element that is part of a respiratory system [Automatically generated definition].
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. Previous: “A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten].” See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA].
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood. In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life. Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
Compound organ that contains one or more macroscopic anatomical spaces.
[cavity of cardiac chamber; luminal space of; surrounded by; anatomical entity; anatomical cavity; endocardium; immaterial entity; cardiac chamber cavity]
Luminal space of the left atrium of the heart.
Luminal space of the left ventricle of the heart.
An anatomical space that is enclosed by a pharynx.
Luminal space of the right atrium of the heart.
Luminal space of the right ventricle of the heart.
A cluster of cells, largely surrounded by a morphological boundary.
A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. Examples include arthropod sensilla.
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
A multi cell part structure that is part of a central nervous system.
A layer of of the central nervous system that is part of gray matter.
The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers.
An artery of the neck.
[only in taxon; subdivision of organism along main body axis; Sarcopterygii; neck subdivision; cervical region; is part of; neck]
A spinal cord segment that adjacent_to a cervical region.
A gray matter of spinal cord that is part of a cervical spinal cord.
A ventral horn of spinal cord that is part of a cervical spinal cord.
A segment of the eyeball that is filled with refractive media.
[chemosensory sensory organ; chemosensory organ; capable of; sensory perception of chemical stimulus; nervous system; is part of; material anatomical entity; chemosensory system; sense organ]
[sensory perception of chemical stimulus; chemosensory system; capable of]
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
The portion of neural plate posterior to the mid-hindbrain junction.
The central region of trunk mesoderm. This tissue forms the notochord.
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. Consider generalizing to deuterostome pharynx
The part of the eye that consists of both the retina and the optic choroid.
A blood vessel that is part of a choroid [Automatically generated definition]. cannot find singular in FMA, using Set class
The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes.
A double layer covering the ciliary body that produces aqueous humor.
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye’s accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm’s canal. [WP,unvetted].
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA].
Epithelium bearing vibratile cilia on the free surface.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
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.
Organism at the cleavage stage.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
A bodily fluid that is located in the coelom.
[collection of collagen fibrils; collagen trimer; composed_primarily_of; acellular anatomical structure; banded collagen fibril]
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].
[common atrial chamber; cardiac atrium; anatomical entity; embryonic structure; is part of]
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
An artery that connects two larger arteries. Grouping for anterior and posterior
A light sensing organ composed of ommatidia.
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO].
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure.
A blood vessel that is part of a cornea [Automatically generated definition].
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
The smooth stratified squamous epithelium that covers the outer surface of the cornea.
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity.
The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm. This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
A capillary that is part of the coronary system.
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation.
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
A blood vasculature that is part of a head.
A bone that is part of a cranium.
A cartilage element that is part of the cranial skeleton.
Anatomical cavity that is the lumen of the skull and contains the brain.
The groups of nerve cell bodies associated with the twelve cranial nerves.
Any skeletal muscle that is part of the head region. defined generically so could in theory encompass FBbt:00003260 ‘skeletal muscle of head’, or the muscle of a starfish Aristotle’s lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves.
Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
Any muscle organ that is part of either the head or the neck.
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
Musculature system of the pharyngeal and head regions.
A vein that is part of a craniocervical region.
Upper portion of the skull that excludes the mandible (when present in the organism).
The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium.
An epithelium consisting of cuboidal epithelial cells.
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity.
End of the life of an organism.
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Mesenchyme with little extracellular matrix.
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Dermis-derived entity that is made of skeletal tissue.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
An adipose tissue that is part of a dermis [Automatically generated definition].
A portion of connective tissue that is part of a dermis [Automatically generated definition].
The bilaminar epithelium formed from the myotome and dermatome.
A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. 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].
[developing anatomical structure; material anatomical entity; developmental structure; developing structure]
A delimited region of dense mesenchyme within looser mesenchyme.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
An embryonic or larval epithelium that is committed to form part of the nervous system.
A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
A duct that is part of a digestive system [Automatically generated definition].
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Any gland that is part of the digestive system.
A tube extending from the mouth to the anus.
An epithelium that lines the lumen of the digestive tract.
An anatomical junction between two parts of the digestive tract.
The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax.
The part of the trunk that is in the dorsum[cjm].
Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
A tubular structure that transports secreted or excreted substances.
. relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to ‘early PA endoderm’
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
Primary germ layer that is the outer of the embryo’s three germ layers and gives rise to epidermis and neural tissue.
An ectoderm that is part of a buccopharyngeal membrane.
An anatomical structure that develops (entirely or partially) from the ectoderm.
A portion of the gut that is derived from ectoderm.
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO].
Connective tissue composed of elastic fibers.
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
A cardiovascular system that is part of a conceptus.
One of five swellings formed during the development of the face.
A head that is part of a embryo.
[external ectoderm; basal cell layer of skin; embryonic skin basal layer; develops from; unilaminar epithelium; integument; ecto-epithelium; is part of]
Anatomical structure that is part of an embryo.
A portion of tissue that is part of an embryo.
The connection between the embryo proper and extraembryonic tissues.
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA].
The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form
The endothelial lining of the endocardium.
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
Endocardium that is part of the atrium.
Any endocardium that is part of the left ventricle of the heart.
Any endocardium that is part of the right ventricle of the heart.
Endocardium that is part of the cardiac ventricle.
Replacement bone that forms within cartilage.
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
An endoderm that is part of a buccopharyngeal membrane.
An endoderm that is part of a foregut [Automatically generated definition].
An anatomical structure that develops (entirely or partially) from the endoderm.
A portions of the gut that is derived from endoderm.
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. The term ‘endothelium’ has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
An endothelium that is part of an arteriole [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of a vein [Automatically generated definition].
An endothelium that is part of a venule [Automatically generated definition].
Sum total of mesenchyme in the embryo.
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
[pharyngeal arch system; embryonic tissue; digestive tract epithelium; is part of; entire pharyngeal arch endoderm; foregut epithelium; endo-epithelium]
Sum of all sensory systems in an organism.
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
Outermost layer of cells surrounding the embryo.
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]
Cranial ganglion which develops from an epibranchial placode. Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.
Visceral intrapericardial fat contiguous with the myocardial surface.
A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
An epicardial layer that lines a cardiac ventricle.
A gland that is part of a epidermis.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
A bud is a protrusion that forms from an epithelial sheet by localized folding.
An epithelial sheet bent on a linear axis.
[ductal epithelium; duct epithelium; epithelial tube; epithelial layer of duct; is part of]
An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
An epithelial tube open at both ends that allows fluid flow.
A closed epithelium with a lumen.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
The epithelial layer that lines the luminal space of the esophagus.
An epithelium surrounding an ovary.
An epithelium surrounding a gonad.
An epithelium that is part of a left lung [Automatically generated definition].
A layer of epithelial cells that is part of the eye.
An epithelium that is part of a lower jaw [Automatically generated definition].
A layer of epithelial cells on the surface of the mucosa. lies on top of lamina propria
An epithelium that is part of a right lung [Automatically generated definition].
The epithelial layer of the stomach .
Any of several arteries that arise from the aorta and supply blood to the esophagus.
A hole in the diaphragm through which the esophagus passes.
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
A mucosa that is part of a esophagus [Automatically generated definition].
Any muscle organ that is part of a esophagus [Automatically generated definition].
A secretion that is part of a esophagus [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal
A squamous epithelium that is part of a esophagus.
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas.
An exocrine gland that is part of a integumental system.
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
An external genitalia that is part of a female reproductive system [Automatically generated definition]. TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals. TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
[entire extraembryonic component; extraembryonic cavity; extraembryonic cavities; anatomical entity; is part of; anatomical space]
An epithelium that is part of a extraembryonic structure.
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. see also conceptus extraembryonic component in EHDAA2.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
An organ that detects light.
An epithelium that is part of a camera-type eye.
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
Mesenchyme that is part of a developing camera-type eye.
A muscle that is part of the eye region.
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
A skin gland that is part of a camera-type eye [Automatically generated definition].
The core globe-shaped component of the camera-type eye.
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
A bone that is part of a facial skeleton [Automatically generated definition].
Mesenchyme that is part of a developing face.
Subdivision of skull that consists of the facial bones.
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
A part of the body present only in females.
Gonochoristic organism that can produce female gametes.
A sex gland that is part of a female reproductive system.
A portion of organism substance that is secreted by a female reproductive gland.
A female organ involved in reproduction.
The organs and associated structures associated with bearing offspring in a female animal.
Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse.
[fibrous connective tissue; has quality; fibrocollagenous connective tissue]
[fibrous connective tissue; elastic tissue; elastic fiber; fibroelastic connective tissue; composed_primarily_of]
[fibrous connective tissue; dense irregular connective tissue]
[fibrous membrane of synovial tendon sheath; fibrous connective tissue; organ component layer; bounding layer of; composed_primarily_of]
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA].
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
An organ of the digestive tract that is capable of retaining and storing food.
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Design pattern notes: check whether this fits the foramen design pattern
Anatomical space that is an opening in a bone of the skull.
Anterior subdivision of a digestive tract.
An epithelium that is part of a foregut.
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
The embryonic precursor of the brain.
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
Primordium that develops into the central nervous system
A tendon that has the potential to develop into a central tendon.
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
Mesenchyme that has the potential to develop into a dermis.
A structure that will develop into a diaphragm.
[mandibular prominence; lower jaw future lip; develops from; unilaminar epithelium; future lower lip; epithelium of lower jaw]
A developing anatomical structure that has the potential to develop into a metencephalon.
The primordial mouth region of the developing head.
A developing anatomical structure that has the potential to develop into a myelencephalon.
Primordium that develops into the nervous system
[presumptive spinal cord neural keel; presumptive structure; central nervous system; is part of; neural tube; future spinal cord; has potential to develop into]
A gray matter that has the potential to develop into a superior salivatory nucleus.
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 – consider merging into trigeminal ganglion, as this complicates the model [trigeminal placode complex; develops from; trigeminal neural crest; transformation of; trigeminal preganglion; presumptive ganglion; future trigeminal ganglion; has potential to develop into]
A biological tissue mass, most commonly a mass of nerve cell bodies.
A ganglion that is part of a central nervous system [Automatically generated definition].
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
Any portion of gas located in a part of the respiratory system.
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
An epithelium that is part of a digestive system [Automatically generated definition].
A lamina propria that is part of a gastrointestinal system.
A mucosa that is part of a gastrointestinal system. The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
A serous membrane that is part of a digestive system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition].
Organism at the gastrula 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.
One of the laterally paired arteries that supply the gonads.
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
[epiblast (generic); germ layer / neural crest; embryonic tissue; embryonic structure; develops from; anatomical entity]
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.
An organ that functions as a secretory or excretory organ.
[luminal space of; gland lumen; immaterial entity; anatomical space; lumen of gland]
A gland that is part of a digestive tract [Automatically generated definition].
A gland that is part of a foregut [Automatically generated definition].
A gland that is part of a integumental system [Automatically generated definition].
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA].
[glandular epithelial cell; glandular epithelium; glandular cuboidal epithelium; simple cuboidal epithelium; composed_primarily_of]
An epithelium that is composed primarily of secretory cells.
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Mesenchyme that is part of a developing gonad [Automatically generated definition].
Portion of tissue that gives rise to the immature gonad.
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
[brain gray matter; gray matter of hindbrain; gray matter of the hindbrain; is part of]
[brain gray matter; is part of; gray matter of midbrain]
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. Groupings may vary - typically pulmonary vessels and aorta and vena cavae
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
The head is the anterior-most division of the body [GO].
A blood vessel that is part of a head [Automatically generated definition].
A bone that is part of a head [Automatically generated definition]. Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A portion of connective tissue that is part of a head [Automatically generated definition].
Dermal, epidermal, glandular and pigment structures of the external head integument.
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
A head mesenchyme that develops_from a mesoderm.
A zone of skin that is part of a craniocervical region.
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
[is part of; head sensillum; arthropod sensillum]
Somite located in the head region, caudal to the otic vesicle.
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Taxon notes:" the ascidian tube-like heart lacks chambers….The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium…. The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates… all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
A blood vessel that is part of a heart [Automatically generated definition].
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
An endothelium that is part of a heart [Automatically generated definition].
The laminar structure of the heart.
A cardiac ventricle that is in the left side of the heart.
[heart/pericardium; heart plus pericardium; cardiovascular system; is part of; thoracic cavity element]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
A cardiac ventricle that is in the right side of the heart.
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
An epithelial tube that will give rise to the mature heart.
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
Anatomical system that is involved in the production of hematopoietic cells.
Blood-forming tissue, consisting of reticular fibers and cells.
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
A gland that is part of a hemolymphoid system [Automatically generated definition].
Organ that is part of the hematopoietic system.
[portion of heterogeneous tissue; heterogeneous tissue]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
[MZH; neural tube marginal layer; central nervous system cell part cluster; is part of; hindbrain marginal layer]
A neural plate that develops_from a presumptive hindbrain.
Nucleus located within the hindbrain.
A venous system that is part of a hindbrain.
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
Any skeletal muscle organ in the hypodermis / superficial fascia.
Anatomical entity that has no mass.
Developing anatomical structure that develops into the eyeball and associated structures.
An organ that is part of a immune system [Automatically generated definition].
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
[embryo; indifferent external genitalia; is part of]
A gonad prior to differentiating into a definitive testis or ovary. typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage
The dermis, epidermis and hypodermis.
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
An organ component layer that is part of a integumental system.
A cardiac septum that divides the left and right atria of the heart.
The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted].
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Cardiac septum which separates the right ventricle from the left ventricle.[FMA].
An endocardium that is part of a interventricular septum [Automatically generated definition].
The muscular portion of the wall between the two lower chambers of the heart.
[intrinsic ocular muscle; mesoderm-derived structure; intrinsic muscle of eyeball; intra-ocular muscle; is part of; smooth muscle of eye; eye muscle]
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye.
A blood vessel that is part of a iris [Automatically generated definition].
An epithelium that is part of a iris [Automatically generated definition].
Any nerve that innervates the iris.
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
[jaw epithelium; is part of; digestive tract epithelium; jaw region]
Mesenchyme that is part of a developing jaw [Automatically generated definition].
[mastication; cranial muscle; capable_of_part_of; mandibular muscles; jaw muscle]
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
Subdivision of skeleton which includes upper and lower jaw skeletons.
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
Any thin layer or plate.
[rexed lamina; nervous system cell part layer; central nervous system cell part cluster; is part of; lamina of gray matter of spinal cord]
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
A lamina propria that is part of a esophagus [Automatically generated definition].
A lamina propria that is part of a respiratory airway.
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Any structure that is placed on one side of the left-right axis of a bilaterian.
Any organ component layer that consists of muscle tissue.
Any of the layers that make up the retina[MP].
Any organ component layer that consists of smooth muscle tissue.
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
Endocardium that is part of the left atrium.
A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve.
Any chamber of the left side of the heart.
[left dorsal aorta; is part of; trunk blood vessel]
An eye that is part of a left side of organism [Automatically generated definition].
Lung which consists of the left upper lobe and left lower lobe.[FMA].
Mesenchyme that is part of a developing left lung.
An endothelium that is part of a left lung.
An ovary that is part of a left side of organism [Automatically generated definition].
The pulmonary artery that supplies the left lung.
Vein that drains left lung and returns blood to the heart.
Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane.
A myocardium that is part of a left ventricle of a heart.
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Tissue that surrounds the lens nucleus.
The core of the crystalline lens, surrounded by the cortex.
Transparent part of camera-type eye that helps to refract light to be focused on the retina. The lens is avascular and nourished by diffusion from the aqueous and vitreous
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Portion of tissue that gives rise to the lens.
An anatomical cavity that is part of a lens vesicle.
An epithelium that is part of a lens vesicle.
An entire span of an organism’s life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
One of the two fleshy folds which surround the opening of the mouth.
An epithelium that is part of a lip.
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An anatomical space that is part of a bone of lower jaw.
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. See notes for jaw w.r.t skeletal element vs subdivision of head
Lip that covers the lower portion of the mouth.[TAO].
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
A cartilage that is part of a lower respiratory tract [Automatically generated definition].
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
An anatomical cavity that surrounded_by a blood vessel.
An anatomical space that surrounded_by a digestive tract.
An anatomical cavity that is part of a esophagus.
[cavity of gastrointestinal tract; lumen of gastrointestinal system; digestive system; anatomical cavity; is part of; cavity of digestive tract; gastrointestinal tract lumen]
Respiration organ that develops as an outpocketing of the esophagus. Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
A blood vessel that is part of a lung [Automatically generated definition].
Structure derived from foregut that becomes a lung[GO].
The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin.
Elastic tissue that is part of a lung [Automatically generated definition].
A blood vessel endothelium that is part of a lung [Automatically generated definition].
The epithelial layer of the lung.
A specific region of the foregut into the area in which the lung will develop.
The mass of tissue made up of mesenchymal cells in the lung.
A parenchyma that is part of a lung.
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
[heterogeneous tissue; lymphomyeloid tissue]
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
Cranial neural crest that migrates into the mandibular arch.
Mesenchyme that is part of a mandibular prominence.
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip.
Anatomical entity that has mass.
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
[sensory perception of mechanical stimulus; mechanosensory system; capable of]
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
A sulcus limitans of neural tube that is part of a future medulla oblongata.
Bone element that arises as a result of intramembranous ossification.
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA].
An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged.
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
Mesenchyme that develops_from a cranial neural crest.
Mesenchyme that develops_from the neural crest[Automatically generated definition].
Mesenchyme that develops_from a trunk neural crest.
Mesenchyme that develops_from a rhombencephalon neural crest.
Mesenchyme that develops_from a splanchnopleure.
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
Mesenchyme that is part of a developing ovary [Automatically generated definition].
Epithelium that derives from the mesoderm. [Automatically generated definition].
The middle germ layer of the embryo, between the endoderm and ectoderm.
A blood island that is part of a mesoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A mesothelium that is part of a diaphragm [Automatically generated definition].
A mesothelium that is part of a pericardium [Automatically generated definition].
A mesothelium that is part of a pleural cavity [Automatically generated definition].
A mesothelium that is part of a serous pericardium.
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
A sulcus limitans of neural tube that is part of a future metencephalon.
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
[microvascular endothelium; cardiovascular system endothelium]
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
[MHB neural plate; presumptive structure; is part of; presumptive midbrain hindbrain boundary; immediate transformation of; midbrain hindbrain boundary neural plate]
[midbrain lateral wall mantle layer; midbrain mantle layer; mantle layer lateral wall mesencephalon; is part of; presumptive midbrain; neural tube mantle layer]
A neural plate that develops_from a presumptive midbrain.
Portion of neural tube that gives rise to the midbrain.
A neuromere that is part of the presumptive midbrain.
Nucleus located in the midbrain.
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. ‘tegmentum’ is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label ‘midbrain tegmentum’ to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
Mesenchymal cells that are migrating.
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
An anatomical structure that develops from the endoderm and the mesoderm.
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
A mucous membrane that lines the mouth.
An anatomical junctions that overlaps the mouth and foregut.
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP].
A mucosa that is part of a lip region [Automatically generated definition].
A mucosa that is part of a lower lip [Automatically generated definition].
A mucosa that is part of a oral opening [Automatically generated definition].
The mucosal layer that lines the stomach.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
An multicellular anatomical structure that has subparts of multiple organs as a part.
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
An eye consisting of multiple light-sensing organs.
An anatomical structure that has more than one cell as a part.
Anatomical structure that is an individual member of a species and consists of more than one cell.
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].
Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.
Any muscle organ that is part of a back [Automatically generated definition].
Any muscle that is part of the cervical (neck) region.
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
A subdivision of the muscular system corresponding to a subdisivision of an organism.
Any collection of muscles that is part of a back [Automatically generated definition].
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
Any collection of muscles that is part of a face.
Any collection of muscles that is part of a neck [Automatically generated definition].
Any collection of muscles that is part of a thorax [Automatically generated definition].
Any collection of muscles that is part of a trunk [Automatically generated definition].
Anatomical system that consists of the muscular and skeletal systems.
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
A sulcus limitans of neural tube that is part of a future myelencephalon.
The middle layer of the heart, comprised mainly of striated cardiac muscle fibers.
[is part of; myocardium of anterior wall of left ventricle; left ventricle myocardium]
[myocardium of anterior wall of right ventricle; is part of; right ventricle myocardium]
The atrial part of middle layer of the heart, comprised of involuntary muscle.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
The cavity within a myotome.
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
A blood vessel that is part of a neck [Automatically generated definition].
A bone that is part of a neck [Automatically generated definition].
A cartilage that is part of a neck [Automatically generated definition].
A portion of connective tissue that is part of a neck [Automatically generated definition].
A nerve that is part of a neck [Automatically generated definition].
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A nerve that is part of an abdominal segment of trunk [Automatically generated definition].
The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP]
A nerve that is part of a head.
A nerve that is part of a thorax [Automatically generated definition].
A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk).
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
An anatomical structure that develops from the neural crest.
One of the two elevated edges of the neural groove[GO,MP].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO).
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
In the developing vertebrate, the neural tube is the embryo’s precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons.
A brain that develops_from a neural tube.
Portion of tissue on the side of the lumen of the neural tube.
An anatomical space that surrounded_by a neural tube.
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.
Embryonic ectoderm that gives rise to nervous tissue.
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
A bone that is part of a neurocranium [Automatically generated definition].
Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli.
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila. for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
An embryo at the neurula 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.
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). [epidermal ectoderm; non-neural ectoderm; tissue; ectoderm-derived structure; material anatomical entity]
Ectodermal placode that does not develop into a component of the nervous system.
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
Fluid contained within the notochordal canal. Distinct feature of coelocanths
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Gray matter of the central nervous system which is a collection of clustered nuclei.
A neural nucleus that is part of the brain.
A neural nucleus that is part of a medulla oblongata.
A nucleus of brain that spans a midbrain tegmentum.
A neural nucleus that is part of the spinal cord.
Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.
The bone at the lower, posterior part of the skull.
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
A sensory system that is capable of olfaction (the sensory perception of smell).
The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells.
Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
The embryonic structure that gives rise to the corneal ectoderm.
An ectoderm that is part of a optic eminence [Automatically generated definition].
Mesenchyme that is part of a optic eminence.
An external ectoderm that is part of a optic eminence [Automatically generated definition].
[migrating mesenchyme population; optic neural crest; is part of; mesenchyme derived from head neural crest]
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 “Developmental Biology”]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present).
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues.
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
A lamina propria that is part of a mucosa of oral region.
The orifice that connects the mouth to the exterior of the body.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present.
Anatomical structure that performs a specific function or group of functions [WP].
A part of a wall of an organ that forms a layer.
A multicellular structure that is a part of an organ.
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
A subdivision of an anatomical system.
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
[is part of; skull orifice; orifice of skull]
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
An outflow tract of atrium that is part of a left atrium.
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA].
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk.
The outflow tract is the portion of the heart through which blood flows into the arteries.
An outflow tract that is part of a aorta.
An endothelium that is part of a outflow tract [Automatically generated definition].
A myocardium that is part of a outflow tract [Automatically generated definition].
An outflow tract that is part of a cardiac atrium.
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
A pericardium that is part of a outflow tract [Automatically generated definition].
[outflow tract pulmonary component]
The outflow tract septum is a partition in the outflow tract.
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
An artery that supplies an ovary.
A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
The gonad of a female organism which contains germ cells.
Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO].
The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis.
The pair of anatomical structures comprised of a left lung and right lung.
[panarthropod head; is part of; Panarthropoda]
Fat deposits in the mediastinum outside the parietal pericardium .
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].
Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
The functional tissue of the central nervous system consisting of neurons and glial cells.
The outer layer of peritoneum that is attached to the abdominal and pelvic walls.
The outer serous membrane of the pulmonary pleural. the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax
Serous membrane layer that lines to a body cavity.
Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac.
A potential space between the visceral and parietal layers of the pericardium.
The sum of epicardial and paracardial fat deposits.
Transudate contained in the pericardial cavity.[FMA].
A double-walled sac containing the heart and the roots of the great vessels.
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Bone element that is adjacent to the notochord.
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Anatomical cavity bounded by visceral and parietal peritoneum.
A mesothelium that is part of a peritoneal cavity.
Transudate contained in the peritoneal cavity.
A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity.
A serous membrane that lines the peritoneal cavity[VHOG,modified].
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries.
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles.
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP].
The vessels formed within the first pair of branchial arches in embryogenesis.
The vessels formed within the sixth pair of branchial arches in embryogenesis.
A cartilage element that is part of a splanchnocranium.
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
An epithelium that is part of a pharynx [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
A mucosa that is part of a pharynx [Automatically generated definition].
[pharyngeal region of foregut; is part of; developing anatomical structure; anatomical entity]
A vasculature that is part of a chordate pharynx.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
An array of photoreceptors and any supporting cells found in an eye.
An artery that supplies the diaphragm.
A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium.
The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins.
Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
The fluid-filled cavity that lies between the visceral and parietal pleurae.
Transudate contained in the pleural cavity.
A serous sac that has the pleura and the pleural cavity as parts.
Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity.
An anatomical space that is enclosed by a pleuroperitoneal canal.
A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities.
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).
A notochord that has persisted beyond the embryonic stage.
A multicellular organism that existence_starts_with a post-embryonic stage.
stage succeeding embryo, including mature structure
Cartilage which is part of the axial skeleton.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. previous some AOs had used the term ‘axial skeleton’ to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
[chordal neural plate; develops from; anatomical entity; embryonic structure; is part of; posterior neural tube]
[Bilateria; posterior region of body; only in taxon; organism subdivision]
Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive).
The posterior segment of the lamellated connective tissue layer of the cornea.
[anatomical surface region; posterior surface of head; in_posterior_side_of; is part of]
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
The portion of neural plate anterior to the mid-hindbrain junction.
[pre muscle mass; muscle structure; muscle precursor cell; pre-muscle condensation; has part; developing mesenchymal condensation; premuscle mass; composed_primarily_of; has potential to develop into]
The area of axial mesoderm that develops into the prechordal plate.
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann’s organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue.
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
[presumptive blood; future blood; has potential to develop into; presumptive structure]
Presumptive structure of the blastula that will develop into ectoderm.
A presumptive structure that has the potential to develop into a endocardium.
Presumptive structure of the blastula that will develop into endoderm.
A presumptive structure that has the potential to develop into a ganglion.
[primordial gut; future digestive tube; existence starts during; has developmental contribution from; endoderm; future digestive tract; primordial digestive tube; mesoderm; presumptive structure; embryonic digestive tube; presumptive gut; digestive tract; primitive gut; future gut; gastrula stage; has potential to develop into]
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, ‘rhombencephalosynapsis’ is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
Presumptive structure of the blastula that will develop into mesoderm.
A presumptive structure that has the potential to develop into a midbrain.
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a neural plate.
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
The part of the blastula that has the potential to develop into a paraxial mesoderm.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
Portion of tissue that is part of the heart tube and will become the sinus venosus.
Portion of embryonic tissue determined by fate mapping to become a structure.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. Gene notes: Bmp, Nkx, Gata
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
[primary subdivision of cranial skeletal system; is part of; subdivision of skeletal system]
The skull can be divided into two: the neurocranium and the facial skeleton.
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A portion of tissue that will develop into vasculature.
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A roughly circular bulge in a surface.
An section of a respiratory tract.
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
A capillary that is part of a lung.
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity.
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles.
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is ‘set of raphe nuclei’
The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream.
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
A multi-tissue structure that is part of a spinal cord.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
Bone that forms as a replacement of another structural tissue.
Skeletal element that forms as a replacement or substitution of another element or tissue.
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
A portion of organism substance that is secreted by a reproductive gland.
An organ involved in reproduction.
Any anatomical structure that is part of the reproductive system.
Anatomical system that has as its parts the organs concerned with reproduction.
[reproductive system mucosa; reproductive structure; is part of; genital mucosa]
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism’s cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
An airway through which respiratory air passes in organisms.
Muscle that is part of the respiratory system.
[anatomical entity; respiratory system; is part of; respiratory primordium; endoderm of foregut; has potential to develop into]
[develops from; splanchnopleure; is part of; respiratory primordium mesenchyme; material anatomical entity; respiratory primordium associated mesenchyme; mixed endoderm/mesoderm-derived structure]
Functional system which consists of structures involved in respiration.
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
[arterial system smooth muscle; respiratory system blood vessel smooth muscle; respiratory system arterial smooth muscle; respiratory system arterial blood vessel; is part of]
An arteriole that is part of a respiratory system [Automatically generated definition].
An artery that is part of a respiratory system [Automatically generated definition].
A basement membrane of epithelium that is part of a respiratory system.
A blood vessel that is part of a respiratory system [Automatically generated definition].