Phenotype And Trait Ontology (PATO)

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

Open in the Ontology Lookup Service (OLS)


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

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.

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.

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]

[shape; branchiness]

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.

color [PATO_0000014]

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

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.

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]

electromagnetic (EM) radiation quality [PATO_0001291]

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

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]

[phenotypic sex; female]

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.

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.

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 efficacy [PATO_0015004]

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

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.

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 semi-sterile; male fertility]

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]

[structure; maximally connected]

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.

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.

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]

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.

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]

[fertility; semi-fertile]

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.

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.

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.

temporal distribution quality [PATO_0002323]

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

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.

unilateral [PATO_0000634]

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

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)