Transcript PATO5.08
PATO
An ontology for phenotypes.
The development of PATO is the work
of George Gkoutos, supported by the
NCBO, working in Cambridge.
Phenotype And Trait Ontology (PATO)
• Phenotypes may be described in many different dimensions, e.g.
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the biochemical ('alcohol dehydrogenase null')
the cellular ('cell division arrested at metaphase'),
the anatomical ('eye absent')
the behavioral (‘hyperactive’).
etc.
• In whatever dimension and granularity, however, there is a
commonality and the great majority of, if not all, phenotypic
descriptions can be decomposed into two parts
– An entity that is affected. This entity may be an enzyme, an
anatomical structure or a complex biological process.
– The qualities of that entity.
Features of Qualities
• Qualities are the basic properties that we can perceive and/or
measure:
– colors, sizes, masses, lengths etc.
• Qualities inhere to entities: every entity has certain qualities,
which exist as long as that entity exists.
• Qualities belong in a finite set of quality types (i.e. color, size
etc) and inhere in specific individuals. Each quality is
constantly dependent on the entity it inheres in.
PATO’s Top level divisions
PATO’s hierarchical organisation
• At lower levels PATO is organized by the nature of the
qualities:
– Physical qualities, such as mass, velocity and color;
– Cellular qualities, such as ploidy (which inhere in a cell or
cell nucleus by virtue of the number of chromosomes it
has) and cellular potential (capability of differentiating into
other cell types);
– Organismal qualities, such as behavioral qualities.
• The leaf nodes of PATO represent specific qualities,
such as “orange” (a kind of color), “concave” (a kind of
shape) and “increased length” (a kind of size).
Phenotypic Character
entity + quality
Phenotypic Character
(mouse anatomy: body + PATO: weight)
(mouse body weight)
(eye colour)
(glucose concentration)
(Drosophila anatomy: eye + PATO: color)
(ChEBI: glucose + PATO: concentration)
increased size [of a] hepatocellular carcinoma
hepatocellular carcinoma (MPATH:357) has_quality increased size (PATO:0000586)
Representation of
Phenotypic data
Assay (eg. Histopathology, blood chemistry) {constrained_by}
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(environmental &
genetic)- {of type} - conditions
{
Entity (eg. MA) - Quality (PATO)
Entity (eg.MPATH) - Quality (PATO)
Entity (eg. Cell) - Quality (PATO)
Measurements
• PATO – part of a representation of
qualitative phenotypic information
• More often than not it is important to
record quantitative information that results
from a specific measurement of a quality
The tail of my mouse is 2.1 cm
PATO & measurements
• Measurements involve units (Phenotypic
Character + Unit)
• UO – an ontology of units
– UO’s top-level division is between primary base units
of a particular measure and units that are derived
from base units
– mapping between the various scalar qualities (such as
weight, height, concentration etc.) and the
corresponding units used to measure those qualities
Mapping PATO to the UO
PATO Annotations
• Descriptions can be pre- or post- composed
• Post-coordinated
EQ methodology
PATO + Entity (quality bearer)
Entity = GO, AOs, Cell, etc.
–NCBO fly-fish-human disease gene annotations
–BIRN image annotation (neurodegenerative disease)
–NESCent / AToL - evolutionary character matrices
–…
• Pre-coordinated
–MGI Mouse genotype-phenotype annotation (Mammalian Phenotype)
–Gramene trait annotation (Plant Trait Ontology)
–Worm
–…
Reconciling pre and post composed
annotations
• Retrospective PATO definitions of pre-coordinated terms
in phenotype ontology
• Precomposed Ontologies
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Mammalian Phenotype
Plant trait
Worm phenotype
etc.
• OMIM
EQ definitions
Aristotelian definitions (genus-differentia)
A <Q> *which* inheres_in an <E>
[Term]
id: MP:0001262
name: decreased body weight
namespace: mammalian_phenotype_xp
Synonym: low body weight
Synonym: reduced body weight
def: " lower than normal average weight “[]
is_a: MP:0001259 ! abnormal body weight
intersection_of: PATO:0000583 ! decreased weight
intersection_of: MA:0002405 ! adult mouse
Some examples
Example 1
• MP:0000350 – abnormal cell proliferation
– MP:0000352 - decreased cell proliferation
– ..
• WBPhenotype0000171 – cell_proliferation_abnormal
– WBPhenotype0000171 – cell_proliferation_reduced
– ..
[Term]
id: WBPhenotype0000171 ! cell_proliferation_abnormal
Intersection_of: PATO:0000460 ! abnormal
Intersection_of: inheres_in GO:0008283 ! cell proliferation
[Term]
id: WBPhenotype0000171 ! cell_proliferation_reduced
Intersection_of: PATO:0000468 ! decreased
Intersection_of: inheres_in GO:0008283 ! cell proliferation
[Term]
id: MP:0000350 ! abnormal cell proliferation
Intersection_of: PATO:0000460 ! abnormal
Intersection_of: inheres_in GO:0008283 ! cell proliferation
[Term]
id: MP:0000350 ! decreased cell proliferation
Intersection_of: PATO:0000468 ! decreased
Intersection_of: inheres_in GO:0008283 ! cell proliferation
Example 2
MP, WBPhenotype, OMIM etc.
• MP:0001265 – decreased body size
– MP:0001255 – decreased body height
• WBPhenotype0000229 – small
• OMIM %210710 – short stature
[Term]
id: MP:0001265 ! decreased body size
intersection_of: PATO:0000587 ! decreased size
intersection_of: inheres_in MA:0002405 ! adult mouse
[Term]
id: MP:0001255 ! decreased body height
intersection_of: PATO:0000569 ! decreased height
intersection_of: inheres_in MA:0002405 ! adult mouse
[Term]
id: WBPhenotype0000229 ! small
intersection_of: PATO:0000587 ! decreased size
intersection_of: OBO_REL:inheres_in WBls:0000041 ! Adult
[Term]
id: OMIM:xxxxxxx ! short stature
intersection_of: PATO:0000587 ! decreased size
intersection_of: OBO_REL:inheres_in FMA!:20394 ! Body
[Term]
id: OMIM:xxxxxxx ! short stature
intersection_of: ATO:0000569 ! decreased height
intersection_of: OBO_REL:inheres_in FMA:20394 ! Body
Assay Controlled Vocabulary
• Abnormality
• Relative_to
• Ranges of values
• Allows the schema to be
dynamic
• Definition of qualities and their relations
• Explicit differences (between laboratories)
• Allows labs around the world to “plug-in” their
assays to the schema
Phenotypic
Character
Assay
Phenotypic
Character
Phenotypic
Character