PATO update

PATO update Power of the Phenotype The meaningful cross species transla7on of phenotype is essen7al  phenotype-­‐driven gene func7on discovery and compara7ve pathobiology Goal -­‐ “A pla>orm for facilita7ng mutual understanding and interoperability of phenotype informa7on: •  across species •  domains of knowledge •  amongst people and machines” ….. 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 (‘hyperac7ve’) etc. •  in whatever dimension and granularity, however, there is a commonality so that phenotypic descrip7ons can be decomposed into two parts –  An en#ty that is affected. This en7ty may be an enzyme, an anatomical structure or a complex biological process. –  The quali#es of that en7ty. Basic Dis7nc7ons •  Quali7es of Objects –  Physical quali=es, such as mass, velocity and color; –  Cellular quali=es, such as ploidy (which inheres in a cell or cell nucleus by virtue of the number of chromosomes it has) and cellular poten7al (capability of differen7a7ng into other cell types); –  Organismal quali=es, such as behavioral quali7es •  Quali7es of Processes –  rates, onset, dura7on etc Some PATO stats •  1421 terms – 99% defined •  8 subset slim –  A\ribute Value slims  EAV –  Pathology Slim PATO-MPath
PATO-path
•  Slim version of PATO
•  Qualifiers for gross and microscopic anatomic pathology
•  Includes STP microscopical quality and INHAND qualifiers
Building up diagnostic components with anatomy, pathology
and qualifiers
MA
MPATH
PATO
INHAND
Mann, P.C. et al (2012). International harmonization of
toxicologic pathology nomenclature:
an overview and review of basic principles. Toxicol
Pathol, 40, 7S-13S.
Behavior Behavioral Phenotypes NBO process + PATO Increased drinking behavior  drinking behavior
(NBO:0000155) + increased (PATO:0002325) dipsosis vs hyperdipsia  phenotype of an organism that par7cipates-­‐in a regula7on of a Drinking behavior (NBO:
0000064) with Increased frequency (PATO 0000380). PATO temporal qualifiers, Chronic (PATO:0001863) and Temporally extended (PATO:0001333), to dis7nguish between the two observa7ons single process occurrences and mul7ple process occurrences characteris7cs of single drinking processes and characteris7cs of processes with some dura7on in which drinking processes occur. depending on the assay that is being used, only some of the quali7es can be measured, while some may be inferred. Increased drinking behavior •  the amount of substance that is consumed is increased over a fixed period of 7me (e.g., 24h) •  the amount of substance per drinking act is increased •  the amount of 7me that is being spent drinking within a fixed period of 7me is increased •  the amount of 7me spent per drinking act is increased •  the number of drinking acts per fixed period of 7me is increased •  the variety of substances that an organism drinks in a fixed period of 7me is increased •  the substance flow during a drinking act is increased •  etc Cellular Phenotype Ontology morphological and physiological phenotypic abnormali7es of cells, cell components and cellular processes GO + PATO Physiology of single occurrence of a cell component’s func7oning (e.g. dura7on of process or response) Physiology related to pa\ern of mul7ple occurrences of a cell component’s func7oning. (e.g frequency increased rate of cell division) PATO term requests a sensible approach check if the term exists – in many cases a synonym would be sufficient avoid blackish, whi7sh, redish, etc , many, narrower, narrowed, narrow in general, do not add adverbs (e.g., gently rounded) avoid plural – widths, wide, widened gray or white, white-or-brown-streaked, white-­‐tomentose-­‐floccose submit precomposed terms as necessary for use by the community) e.g., the burden of defini7on could be a limi7ng factor – avoid requests like tall and brown •  provide context through examples and counter examples of use, which go into the comments, if possible. • 
• 
• 
• 
• 
• 
•