Uber-anatomy Ontology (UBERON)

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.

Open in the Ontology Lookup Service (OLS)


anatomical entity [UBERON_0001062]

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.

anatomical structure [UBERON_0000061]

Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism’s own genome.

anatomical surface [UBERON_0006984]

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.

anatomical system [UBERON_0000467]

Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.

blastula [UBERON_0000307]

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.

blastula stage [UBERON_0000108]

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.

bona-fide anatomical boundary [UBERON_0010199]

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)

central nervous system [UBERON_0001017]

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.

cleavage stage [UBERON_0000107]

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.

cleaving embryo [UBERON_0007010]

Organism at the cleavage stage.

death stage [UBERON_0000071]

End of the life of an organism.

developing anatomical structure [UBERON_0005423]

[developmental structure; material anatomical entity; developing structure; developing anatomical structure]

ectoderm [UBERON_0000924]

Primary germ layer that is the outer of the embryo’s three germ layers and gives rise to epidermis and neural tissue.

ectoderm-derived structure [UBERON_0004121]

An anatomical structure that develops (entirely or partially) from the ectoderm.

embryo [UBERON_0000922]

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.

embryo stage [UBERON_0000068]

A life cycle stage that starts with fertilization and ends with the fully formed embryo.

embryonic structure [UBERON_0002050]

Anatomical structure that is part of an embryo.

embryonic tissue [UBERON_0005291]

A portion of tissue that is part of an embryo.

entire sense organ system [UBERON_0004456]

Sum of all sensory systems in an organism.

epiblast (generic) [UBERON_0002532]

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]

fully formed stage [UBERON_0000066]

The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.

future central nervous system [UBERON_0016879]

Primordium that develops into the central nervous system

future nervous system [UBERON_0016880]

Primordium that develops into the nervous system

gastrula [UBERON_0004734]

Organism at the gastrula stage.

gastrula stage [UBERON_0000109]

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.

germ layer [UBERON_0000923]

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]

germ layer / neural crest [UBERON_0010316]

[embryonic tissue; epiblast (generic); anatomical entity; germ layer / neural crest; develops from; embryonic structure]

immaterial anatomical entity [UBERON_0000466]

Anatomical entity that has no mass.

life cycle [UBERON_0000104]

An entire span of an organism’s life, commencing with the zygote stage and ending in the death of the organism.

life cycle stage [UBERON_0000105]

A spatiotemporal region encompassing some part of the life cycle of an organism.

material anatomical entity [UBERON_0000465]

Anatomical entity that has mass.

multicellular anatomical structure [UBERON_0010000]

An anatomical structure that has more than one cell as a part.

multicellular organism [UBERON_0000468]

Anatomical structure that is an individual member of a species and consists of more than one cell.

nervous system [UBERON_0001016]

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].

neurula embryo [UBERON_0004455]

An embryo at the neurula stage.

neurula stage [UBERON_0000110]

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.

organ [UBERON_0000062]

Anatomical structure that performs a specific function or group of functions [WP].

organ system subdivision [UBERON_0011216]

A subdivision of an anatomical system.

organogenesis stage [UBERON_0000111]

A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.

peripheral nervous system [UBERON_0000010]

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.

post-embryonic organism [UBERON_0009953]

A multicellular organism that existence_starts_with a post-embryonic stage.

post-embryonic stage [UBERON_0000092]

stage succeeding embryo, including mature structure

presumptive ectoderm [UBERON_0006601]

Presumptive structure of the blastula that will develop into ectoderm.

presumptive structure [UBERON_0006598]

Portion of embryonic tissue determined by fate mapping to become a structure.

processual entity [UBERON_0000000]

An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.

sensory system [UBERON_0001032]

Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.

tissue [UBERON_0000479]

Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.

vestibulo-auditory system [UBERON_0002105]

Sensory system responsible for the perception of spatial orientation and auditory stimuli.

zygote stage [UBERON_0000106]

A stage at which the organism is a single cell produced by means of sexual reproduction.


Last modified January 5, 2022: adding UBERON (139f6ec)