Phenotype And Trait Ontology (PATO)

An ontology of phenotypic qualities (properties, attributes or characteristics).

Open in the Ontology Lookup Service (OLS)


2-D shape [PATO_0002006]

A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.

3-D shape [PATO_0002266]

[3-D shape]

abnormal [PATO_0000460]

A quality inhering in a bearer by virtue of the bearer’s deviation from normal or average.

absent [PATO_0000462]

A quality denoting the lack of an entity. See documentation here: http://code.google.com/p/phenotype-ontologies/wiki/ModelingOfAbsence

acidophilic [PATO_0002418]

An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions.

acinar [PATO_0002422]

Pertaining to the individual parts making up an aggregate fruit like a many-lobed “berry,” such as a raspberry. Acinus is Latin for berry.

altered number of [PATO_0002083]

Having extra or fewer parts.

amount [PATO_0000070]

The number of entities of this type that are part of the whole organism. This term was originally named “presence”. It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.

anatomical histological quality [PATO_0070045]

A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes.

anatomical structure quality [PATO_0070044]

A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.

anucleate [PATO_0001405]

A nucleate quality inhering in a bearer by virtue of the bearer’s having no nucleus.

aplastic/hypoplastic [PATO_0002290]

[aplastic/hypoplastic; physical object quality]

atrophied [PATO_0001623]

A size quality inhering in a bearer by virtue of a part or parts of the bearer’s being decreased in size due to reduction in tissue mass through wasting.

auxotrophic [PATO_0000422]

A nutritional quality inhering in a bearer by virtue of the bearer’s inability to synthesize a particular organic compound required for its growth.

basophilic [PATO_0002094]

An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions.

biconcave [PATO_0002039]

A concave quality inhering in a bearer by virtue of the bearer’s curving inward on both sides or surfaces.

bilateral [PATO_0000618]

A positional quality inhering in a bearer by virtue of the bearer’s having two sides; two-sided.

binucleate [PATO_0001406]

A nucleate quality inhering in a bearer by virtue of the bearer’s having two nuclei.

branched [PATO_0000402]

[branchiness; branched]

branchiness [PATO_0002009]

[branchiness; shape]

cellular potency [PATO_0001397]

A cellular quality that arises by virtue of whether the bearer’s disposition to differentiate into one or more mature cell types.

cellular quality [PATO_0001396]

A monadic quality of continuant that exists at the cellular level of organisation.

cellularity [PATO_0001992]

An organismal quality inhering in a bearer by virtue of the bearer’s consisting cells.

ciliatedness [PATO_0001408]

A cellular quality inhering in a bearer by virtue of the bearer’s having thin, tail-like projections extending outwards from the cell body.

circular [PATO_0000411]

A shape quality inhering in a bearer by virtue of the bearer’s being such that every part of the surface or the circumference is equidistant from the center.

collagenous [PATO_0002462]

A composition quality inhering in an bearer by virtue of the bearer’s consisting of collagen.

color [PATO_0000014]

A composite chromatic quality composed of hue, saturation and intensity parts.

composition [PATO_0000025]

A single physical entity inhering in an bearer by virtue of the bearer’s quantities or relative ratios of subparts. For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).

concave [PATO_0001857]

A shape quality in a bearer by virtue of the bearer’s curving inward.

concavity [PATO_0002005]

Surface shape that refers to the inward or outward curvature of the surface.

contractile [PATO_0001690]

A contractility quality inhering in a bearer by virtue of the bearer’s ability of contracting or being contracted. This refers to the disposition of the bearer.

contractility [PATO_0001579]

A physical quality that is the ability to contract or shrink.

convex 3-D shape [PATO_0002007]

A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Use this term or an is_a child of this term when the entire shape of the object is known.

curvature [PATO_0001591]

A surface shape quality inhering in a bearer by virtue of the bearer’s exhibiting a degree of bending.

cylindrical [PATO_0001873]

A convex 3-D shape quality inhering in a bearer by virtue of the bearer’s exhibiting a consistently-sized round cross section.

decreased amount [PATO_0001997]

An amount which is relatively low.

decreased efficacy [PATO_0015003]

A decrease in the ability of a process to produce its output.

decreased fecundity [PATO_0001696]

A fecundity which is relatively low.

decreased female fertility [PATO_0001830]

A female fertility which is relatively low.

decreased fertility [PATO_0001834]

A fertility which is relatively low.

decreased male fertility [PATO_0001833]

A male fertility which is relatively low.

decreased mass [PATO_0001562]

A mass which is lower than normal or average.

decreased object quality [PATO_0002303]

A quality of an object that has a value that is decreased compared to normal or average.

decreased occurrence [PATO_0002052]

An occurrence which is relatively low.

decreased position [PATO_0001476]

A positional which is relatively low.

decreased process quality [PATO_0002302]

A quality of a process that has a value that is decreased compared to normal or average.

decreased quality [PATO_0002301]

A quality that has a value that is decreased compared to normal or average.

decreased rate [PATO_0000911]

A rate which is relatively low.

decreased resistance to [PATO_0001651]

A resistance to a stimulus which is relatively low.

decreased size [PATO_0000587]

A size quality which is relatively low.

defasciculated [PATO_0001959]

[defasciculated]

degree of pigmentation [PATO_0002247]

A quality inhering in a bearer by virtue of the bearer’s having or lacking of substances produced by living organisms that have a color resulting from selective color absorption.

dendritic [PATO_0002045]

A branched quality inhering in a bearer by virtue of the bearer’s having smaller branches arising from larger branches. Resembling a tree in branching structure.

deviation (from_normal) [PATO_0000069]

A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.

disconnected [PATO_0010001]

[structure; disconnected]

elastic [PATO_0001171]

An elasticity quality inhering in a bearer by virtue of the bearer’s ability to recover its size and shape after deformation in any way.

elasticity [PATO_0001031]

A physical quality inhering in a bearer by virtue of the bearer’s disposition to recover its size and shape after deformation in any way.

electromagnetic (EM) radiation quality [PATO_0001291]

A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.

elliptic [PATO_0000947]

A spheroid quality inhering in a bearer by virtue of the bearer’s being oval with two axes of symmetry, as produced by a conical section.

euploid [PATO_0001393]

A ploidy quality inhering in a bearer by virtue of the bearer’s containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.

extra or missing processual parts [PATO_0001564]

A quality of a process inhering in a bearer by virtue of the bearer’s processual parts.

fasciculated [PATO_0001861]

A structural quality inhering in a bearer by virtue of the bearer’s forming a bundle of aligned anatomical fibers, as of muscle or nerve.

fasciculation [PATO_0002013]

A structural quality inhering in a bearer by virtue of whether the bearer forms a bundle of anatomical fibers, as of muscle or nerve.

fecundity [PATO_0000273]

A reproductive quality inhering in an organism or population by virtue of the bearer’s potential reproductive capacity ad measured by the number of gametes.

female [PATO_0000383]

[female; phenotypic sex]

female fertile [PATO_0000888]

A female fertility quality inhering in a female by virtue of the bearer’s disposition to initiate, sustain, or support reproduction.

female fertility [PATO_0000277]

A fertility quality inhering in a female by virtue of the bearer’s disposition to initiate, sustain, or support reproduction.

female semi-fertile [PATO_0001760]

[female semi-fertile]

female semi-sterile [PATO_0001763]

[female fertility; female semi-sterile]

female sterile [PATO_0000892]

A female fertility quality inhering in a female by virtue of the bearer’s being incapable of initiating, sustaining, or supporting reproduction.

female-specific [PATO_0060003]

A quality inhering in a bearer by virtue of the bearer’s being present in females and absent from males in members of the same species.

fertile [PATO_0000955]

A fertility quality inhering in a bearer by virtue of the bearer’s being capable of initiating, sustaining, or supporting reproduction.

fertility [PATO_0000274]

A reproductive quality inhering in a bearer by virtue of the bearer’s initiating, sustaining, or supporting reproduction.

fiber shaped [PATO_0002309]

A convex 3-D shape quality inhering in a bearer by virtue of the bearer’s exhibiting a by virtue of the bearer’s exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope).

flat [PATO_0000407]

A quality inhering in a bearer by virtue of the bearer’s having a horizontal surface without a slope, tilt, or curvature.

flattened [PATO_0002254]

A quality inhering in a bearer by virtue of the bearer’s surface becoming more extended in a plane. Becoming flat but not necessarily completely flat.

grooved [PATO_0002255]

Texture quality inhering in a bearer by virtue of the bearer’s being marked with one or more channels.

has extra parts of type [PATO_0002002]

The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. In polydactyly, the bearer of the quality is the hand, and the entity type being counted is ‘finger’. In EQ syntax, E=hand, Q= E2=finger.

has fewer parts of type [PATO_0002001]

The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type.

has number of [PATO_0001555]

The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.

hollow [PATO_0002078]

A quality inhering in a bearer by virtue of the bearer’s having an empty space or cavity within.

hyperplastic [PATO_0000644]

A increased size quality inhering in an organ or tissue by virtue of the bearer’s exhibiting increased number of cells.

hypoplastic [PATO_0000645]

A decreased size quality inhering in a bearer by virtue of the bearer’s exhibiting reduced number of cells within an organ or tissue.

increased amount [PATO_0000470]

An amount which is relatively high.

increased contractility [PATO_0001580]

A contractility which is relatively high.

increased efficacy [PATO_0015004]

A increase in the ability of a process to produce its output.

increased elasticity [PATO_0002287]

An elasticity which is relatively high.

increased fecundity [PATO_0001695]

A fecundity which is relatively high.

increased female fertility [PATO_0001831]

A female fertility which is relatively high.

increased fertility [PATO_0001835]

A fertility which is relatively high.

increased male fertility [PATO_0001832]

A male fertility which is relatively high.

increased mass [PATO_0001563]

A mass which is higher than normal or average.

increased object quality [PATO_0002305]

A quality of an object that has a value that is increased compared to normal or average.

increased occurrence [PATO_0002051]

An occurrence which is relatively high.

increased position [PATO_0001475]

A position which is relatively high.

increased process quality [PATO_0002304]

A quality of a process that has a value that is increased compared to normal or average.

increased quality [PATO_0002300]

A quality that has a value that is increased compared to normal or average.

increased rate [PATO_0000912]

A rate which is relatively high.

increased resistance to [PATO_0001650]

A resistance to a stimulus which is relatively high.

increased size [PATO_0000586]

A size quality which is relatively high.

invaginated [PATO_0001748]

A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave.

lack of fertility in offspring [PATO_0001862]

A fertility quality inhering in a bearer by virtue of the bearer’s disposition to make its offspring sterile.

lacking processual parts [PATO_0001558]

A quality of a process inhering in a bearer by virtue of the bearer’s lacking a processual part as specified by the additional entity.

lacks all parts of type [PATO_0002000]

A quality of physical entities inhering in a bearer by virtue of the bearer’s lacking a physical part as specified by the additional entity. Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2.

lacks parts or has fewer parts of type [PATO_0001999]

The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type.

laminar [PATO_0002124]

[laminar; structure]

lethal (sensu genetics) [PATO_0000718]

A viability quality inhering in a population by virtue of the bearer’s long term survival inability.

linear [PATO_0001199]

[shape; linear]

male [PATO_0000384]

[male; phenotypic sex]

male fertile [PATO_0000891]

A male fertility quality inhering in a male by virtue of the bearer’s being capable of initiating, sustaining, or supporting reproduction.

male fertility [PATO_0000279]

A fertility quality of inhering in a male by virtue of the bearer’s disposition to initiate, sustain, or support reproduction.

male semi-fertile [PATO_0001761]

[male semi-fertile]

male semi-sterile [PATO_0001762]

[male fertility; male semi-sterile]

male sterile [PATO_0000890]

A male fertility quality inhering in a male by virtue of the bearer’s being incapable of initiating, sustaining, or supporting reproduction.

male-specific [PATO_0060002]

A quality inhering in a bearer by virtue of the bearer’s being present in males and absent from females in members of the same species.

mass [PATO_0000125]

A physical quality that inheres in a bearer by virtue of the proportion of the bearer’s amount of matter. For any biological use of PATO, the concept that should be used is ‘mass’ and not ‘weight’. For example, increased weight of an organism.

maximally connected [PATO_0010000]

[maximally connected; structure]

mononucleate [PATO_0001407]

A nucleate quality inhering in a bearer by virtue of the bearer’s having one nucleus.

morphology [PATO_0000051]

A quality of a single physical entity inhering in the bearer by virtue of the bearer’s size or shape or structure.

multicellular [PATO_0001993]

A cellularity quality inhering in a bearer by virtue of the bearer’s consisting of more than one cell.

multinucleate [PATO_0001908]

A nucleate quality inhering in a bearer by virtue of the bearer’s having more than one nucleus.

multipotent [PATO_0001402]

A cellular potency that is the capacity to form multiple differentiated cell types.

neoplastic [PATO_0002011]

A structural quality which is held by a bearer when the latter’s disposition the presence of abnormally proliferating masses of cells.

normal [PATO_0000461]

A quality inhering in a bearer by virtue of the bearer’s exhibiting no deviation from normal or average.

nucleate quality [PATO_0001404]

A cellular quality inhering in a bearer by virtue of bearer’s number of nuclei.

nucleated [PATO_0002505]

A nucleate quality inhering in a bearer by virtue of the bearer’s having one or more nucleus.

occurrence [PATO_0000057]

A quality of a single process inhering in a bearer by virtue of the bearer’s occurrence.

oligopotent [PATO_0001401]

A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. Less potent than multipotent, often thought of as precursor or progenitor cell status.

opacity [PATO_0000957]

An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.

opaque [PATO_0000963]

A optical quality inhering in a bearer by virtue of the bearer’s not being clear; not transmitting or reflecting light or radiant energy.

optical quality [PATO_0001300]

An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.

organismal quality [PATO_0001995]

A quality that inheres in an entire organism or part of an organism.

phenotypic sex [PATO_0001894]

[quality; phenotypic sex]

physical object quality [PATO_0001241]

A quality which inheres in a continuant. Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

physical quality [PATO_0001018]

A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.

physical quality of a process [PATO_0002062]

[physical quality of a process; process quality]

ploidy [PATO_0001374]

A cellular quality inhering in a bearer by virtue of the bearer’s number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.

polychromatophilic [PATO_0070047]

An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions.

polymeric [PATO_0015006]

A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array. A complete coverage of this domain would subclasses homopolymeric, copolymeric, crystalline.

position [PATO_0000140]

A spatial quality inhering in a bearer by virtue of the bearer’s spatial location relative to other objects in the vicinity.

positional polarity [PATO_0001769]

A positional quality inhering in a bearer by virtue of the bearer’s location of features or characteristics along an axis.

present [PATO_0000467]

A quality inhering in a bearer by virtue of the bearer’s existence.

process efficacy [PATO_0015002]

The ability of a process to produce its output.

process quality [PATO_0001236]

A quality which inheres in an process. See comments of relational quality of a physical entity.

qualitative [PATO_0000068]

TODO: define this or obsolete it and move children somewhere else. [quality; qualitative]

quality [PATO_0000001]

A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.

quality of a gas [PATO_0001547]

A physical quality inhering in a bearer by virtue of the bearer’s exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.

quality of a liquid [PATO_0001548]

A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.

quality of a solid [PATO_0001546]

A physical quality inhering in a bearer by virtue of the bearer’s exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.

quality of a substance [PATO_0002198]

A quality inhering in a bearer by virtue of its constitution.

radiation quality [PATO_0001739]

A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.

rate [PATO_0000161]

A quality of a single process inhering in a bearer by virtue of the bearer’s occurrence per unit time.

reproductive quality [PATO_0001434]

An organismal quality inhering in a bearer by virtue of the bearer’s ability to produce new life or offspring.

resistance to [PATO_0001046]

A quality inhering in a bearer by virtue of the bearer’s disposition to resist to a stimulus.

resistant to [PATO_0001178]

A resistance quality inhering in a bearer by virtue of the bearer’s resistance to a stimulus.

semi-fertile [PATO_0001767]

[semi-fertile; fertility]

sex-specific [PATO_0060001]

A quality inhering in a bearer by virtue of the bearer’s being present in one sex and absent from the other in members of the same species.

sexually dimorphic [PATO_0002451]

A quality inhering in a bearer by virtue of the bearer’s exhibiting a phenotypic difference between males and females of the same species.

shape [PATO_0000052]

A morphological quality inhering in a bearer by virtue of the bearer’s ratios of distances between its features (points, edges, surfaces and also holes etc). Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.

size [PATO_0000117]

A morphology quality inhering in a bearer by virtue of the bearer’s physical magnitude.

solid configuration [PATO_0001736]

A physical quality inhering in a bearer by virtue of the bearer’s parts having the arrangement which exhibits characteristics of solids.

spatial pattern [PATO_0000060]

A spatial quality inhering in a bearer by virtue of the bearer’s exhibiting repetition of placement of its parts.

sterile [PATO_0000956]

A fertility quality inhering in a bearer by virtue of the bearer’s being incapable of initiating, sustaining, or supporting reproduction.

striated [PATO_0001410]

A shape quality inhering in a bearer by virtue of the bearer’s being marked by narrow lines or grooves, usually parallel.

structure [PATO_0000141]

A morphology quality inhering in a bearer by virtue of the bearer’s relative position, shape, arrangements and connectivity of an organism’s various parts; the pattern underlying its form.

structure, cavities [PATO_0002014]

A structural quality that inheres in a bearer by virtue of the bearer’s containing hollow areas.

subcylindrical [PATO_0002226]

A cylindrical shape quality inhering in a bearer by virtue of the bearer’s being imperfectly cylindrical or approximately cylindrical.

superelliptic [PATO_0002318]

A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt

temporal distribution quality [PATO_0002323]

A temporal distribution pattern of process occurrences within a regulation/reference process.

texture [PATO_0000150]

A morphologic quality inhering in a bearer by virtue of the bearer’s relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.

transparent [PATO_0000964]

A optical quality inhering in a bearer by virtue of the bearer’s lacking opacity.

transversely striated [PATO_0002478]

A shape quality inhering in a bearer by virtue of the bearer’s being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer.

trophic quality [PATO_0000056]

An organismal quality inhering in a bearer by virtue of the bearer’s disposition to synthesize a particular organic compound required for its growth.

tubular [PATO_0002299]

A cylindrical shape that is hollow.

unilateral [PATO_0000634]

A spatial pattern inhering in a bearer by virtue of the bearer’s involvement of only one part or side.

unipotent [PATO_0001400]

A cellular potency that is the capacity to produce only one differentiated cell type. Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells.

viability [PATO_0000169]

An organismal quality inhering in a bearer or a population by virtue of the bearer’s disposition to survive and develop normally or the number of surviving individuals in a given population.

viable [PATO_0000719]

A viability quality inhering in a bearer or a population by virtue of the bearer’s ability to survive or the long term survival ability of a given population.


Last modified January 5, 2022: adding pato (e47de7b)