pato an ontology for phenotypes. the development of pato is the work of george gkoutos, supported by...
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PATOAn ontology for phenotypes.
The development of PATO is the work of George Gkoutos, supported by the NCBO, working in Cambridge.
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Phenotype And Trait Ontology (PATO)
• Phenotypes may be described in many different dimensions, e.g.– 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.
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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.
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PATO’s Top level divisions
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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).
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Phenotypic Character
(mouse body weight) (mouse anatomy: body + PATO: weight)
(Drosophila anatomy: eye + PATO: color)
(ChEBI: glucose + PATO: concentration)
(eye colour)(glucose concentration)
Phenotypic Character entity + quality
increased size [of a] hepatocellular carcinoma
hepatocellular carcinoma (MPATH:357) has_quality increased size (PATO:0000586)
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Assay (eg. Histopathology, blood chemistry) {constrained_by}
| (environmental & genetic)- {of type} - conditions
Entity (eg. MA) - Quality (PATO)Entity (eg.MPATH) - Quality (PATO) Entity (eg. Cell) - Quality (PATO)
{
Representation of Phenotypic data
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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
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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
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Mapping PATO to the UO
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PATO Annotations
• Descriptions can be pre- or post- composed• Post-coordinated
EQ methodologyPATO + 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–…
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Reconciling pre and post composed annotations
• Retrospective PATO definitions of pre-coordinated terms in phenotype ontology
• Precomposed Ontologies– Mammalian Phenotype– Plant trait– Worm phenotype – etc.
• OMIM
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EQ definitions
Aristotelian definitions (genus-differentia)
A <Q> *which* inheres_in an <E>
[Term] id: MP:0001262 name: decreased body weightnamespace: mammalian_phenotype_xpSynonym: low body weightSynonym: reduced body weightdef: " lower than normal average weight “[] is_a: MP:0001259 ! abnormal body weightintersection_of: PATO:0000583 ! decreased weightintersection_of: MA:0002405 ! adult mouse
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Some examples
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Example 1
• MP:0000350 – abnormal cell proliferation– MP:0000352 - decreased cell proliferation – ..
• WBPhenotype0000171 – cell_proliferation_abnormal– WBPhenotype0000171 – cell_proliferation_reduced– ..
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[Term]id: WBPhenotype0000171 ! cell_proliferation_abnormalIntersection_of: PATO:0000460 ! abnormalIntersection_of: inheres_in GO:0008283 ! cell proliferation
[Term]id: WBPhenotype0000171 ! cell_proliferation_reducedIntersection_of: PATO:0000468 ! decreasedIntersection_of: inheres_in GO:0008283 ! cell proliferation
[Term]id: MP:0000350 ! abnormal cell proliferation Intersection_of: PATO:0000460 ! abnormalIntersection_of: inheres_in GO:0008283 ! cell proliferation
[Term]id: MP:0000350 ! decreased cell proliferation Intersection_of: PATO:0000468 ! decreasedIntersection_of: inheres_in GO:0008283 ! cell proliferation
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Example 2MP, WBPhenotype, OMIM etc.
• MP:0001265 – decreased body size– MP:0001255 – decreased body height
• WBPhenotype0000229 – small
• OMIM %210710 – short stature
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[Term]id: MP:0001265 ! decreased body sizeintersection_of: PATO:0000587 ! decreased sizeintersection_of: inheres_in MA:0002405 ! adult mouse
[Term]id: MP:0001255 ! decreased body heightintersection_of: PATO:0000569 ! decreased heightintersection_of: inheres_in MA:0002405 ! adult mouse
[Term]id: WBPhenotype0000229 ! smallintersection_of: PATO:0000587 ! decreased sizeintersection_of: OBO_REL:inheres_in WBls:0000041 ! Adult
[Term]id: OMIM:xxxxxxx ! short stature intersection_of: PATO:0000587 ! decreased sizeintersection_of: OBO_REL:inheres_in FMA!:20394 ! Body
[Term]id: OMIM:xxxxxxx ! short stature intersection_of: ATO:0000569 ! decreased heightintersection_of: OBO_REL:inheres_in FMA:20394 ! Body
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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” theirassays to the schema
Assay
Phenotypic Character
Phenotypic Character
Phenotypic Character