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CARO 2.0 & FUNCARO

CARO 2.0 & FUNCARO. David Osumi -Sutherland. Review of CARO (v1). Many definitions are complicated and opaque:

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CARO 2.0 & FUNCARO

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  1. CARO 2.0 & FUNCARO David Osumi-Sutherland

  2. Review of CARO (v1) • Many definitions are complicated and opaque: • ‘anatomical group: “[An] anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.” • No explicit disjointness declarations • despite assertion of pairwisedisjointness in paper. • Rigid single inheritance • Lack of necessary and sufficient definitions means no way to manage multiple classification

  3. Problems with existing implementations • Assuming pairwisedisjointness in CARO(v1): • Classified as both material and immaterial entities: • pyloric chamber; scale • Classified as both cell and ‘portion of tissue’ • adult sensory neuron • disjointness violations hidden by enforced single inheritance? • The following are classified under ‘organism subdivision’ • 'unicellular gland’; scale; vent

  4. Aims for CARO v2.0 • Clear definitions made for biologically defensible reasons or to ensure good modeling practice. • distinctions must be readily understandable by biologists and commonly distinguishable: • classification depending on criteria for which little data exists should be avoided. • Definitions should be fomalisedso that auto-classification by reasoners can be used in place of hand classification. • Disjoint declarations must be present for error checking

  5. Approach for CARO v2 • Master version • in OWL • imports relevant BFO and RO classes and relations (object properties) • Provide an OBO translation, although likely to have more limited semantics • Focus on defining differentia • potentially => safe multiple inheritance.

  6. Fundamental, disjoint classes

  7. material vs immaterial • Examples • lumen of stomach (space) vs wall of stomach (structure) vs the outside surface of the stomach (boundary with the body cavity; a 2D structure) • potential importance includes • error checking • immaterial structures can’t be • site of gene expression • site of functions/processes requiring cells • formalization: • material anatomical entity: has_quality some mass (PATO) • DisjointWith immaterial anatomical entity

  8. amorphous vs has shape • Example • blood vstibia • Importance includes • error checking, in case shape quality mistakenly asserted or implied for ‘anatomical substance’ • anatomical structure: • Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. • DisjointWith ‘organism substance’

  9. cellularization state • Disjoint classes: • acellular (e.g.- cuticle) • cell (e.g. guard cell) • multicellular (e.g. upper epidermis) • multi-cell component (fan-shaped body) • Importance • Error checking • Cells are a fundamental unit of structure in biology, CARO should reflect this. • Acellular structure: • Can’t be site of gene expression • Can’t be site of functions/processes requiring cells Fan shaped body (synaptic neuropil)

  10. cellularization state • formalization: • cell – import class from CL • acellular anatomical structure • EquivalentTo‘anatomical structure’ and(has_partonly not (cell or‘cell part’)) • multicellular anatomical structure • EquivalentTo: ‘anatomical structure’ and has_componentmin 2 cell • multi-cell part structure • EquivalentTo: ‘anatomical structure’ and has_componentmin 2 ‘cell part’ and has_partonly not cell Fan shaped body (synaptic neuropil)

  11. connected vs not • anatomical group: • “A material anatomical entity consisting of multiple parts that are not physically connected to each other.” • anatomical structure • “A material anatomical entity consisting of a single connected whole.” • Formalisation • ‘anatomical structure’ DisjointWith ‘anatomical group’ • PATO quality – connected ? • Examples • immune system vs vasculature • Importance • clarity about boundaries • Making good practice clear • use class reasoning where possible, avoid making anatomical groups that are mereological sums of other classes (e.g.- use finger not 'set of fingers') • Useful in some mereologicalreasoning

  12. Types of anatomical group • anatomical cluster • def: “anatomical group whose members are in close proximity to each other.” • aligned anatomical group • “anatomical group whose members are arranged in a line”

  13. From the organism down:organisms and their subdivisions.

  14. organism • organism • def: “An individual member of a species.” • How to classify? • Make agnostic about unicellular vsmulticellular. • This avoids confusion about fertilized egg stage of multicellular organisms. • anatomical structure? • rules out separated clones (e.g. cuttings in plants; which is probably OK) • difficult for Dicty (but then again, Dicty is difficult!)

  15. Anatomical system • Examples: • nervous system; immune system; musculo-skeletal system • attempt atformalization: • the (mereological) sum of all X in a single organism, • Where X can be: • a functionally defined class (see FUNCARO) • a set of high level anatomical classes • e.g.- vertebrate muscloskeletal system might be: • The mereological sum of all muscles, ligaments, bones, tendons, cartillage and joints

  16. connected system • An anatomical system that is connected • Examples: • vertebrate circulatory system • nervous system

  17. Organism subdivision • Examples: • insect head; insect abdominal segment; insect leg • Some necessary conditions • has a contiguous integumental boundary • has parts of multiple organ systems

  18. types of multicellular structure

  19. Tissue • tissue: • “Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.” • tissue types • by cell type • request PATO qualities? • lamina; mesenchymal, others?

  20. cell cluster organ • def: “A multicellular anatomical strucure consisting of a few cells of various types which forms a discrete structure with a largely bona fide boundary.” • Examples • ommatidium; neuromast (of lateral line)

  21. compound cell cluster organ • def: “An anatomical structure consisting of multiple cell cluster organs and that has a largely bona-fide boundary.” • Examples: • compound eye

  22. FUNCARO – a functional extension to CARO • Extends CARO with functional classed defined using relations to GO process terms • Aims • A set of logically defined upper level terms for classifying anatomical structures by function. • A reference set of design patterns for specifying the functions of anatomical structures using GO process terms.

  23. Relations for defining function • capable_of • expands to: bearer_ofsome (realised_byonly ?P) • domain: ‘continuant’ • range: ‘process’ • capable_of_part_of • expands_to: bearer_ofsome (realized_byonly (part_ofsome ?P) • domain: ‘continuant’ • range: ‘process’ • property chain: bearer_ofopart_of -> bearer_of_part_of • If X bearer_of Y and Y part_of Z then X bearer_of_part_of Z

  24. Terms for classifying by sensory function • Gene Ontology classification of sensory processes:

  25. Some necessary and sufficient definitions * *Strictly speaking, ‘some’ is a fudge. Better to use expanded forms in OWL?

  26. Autoclassification capable_of

  27. Functional systems – auto-populating partonomies • functional system • A material anatomical entity defined by the common function of its component parts. These parts may or may not be connected to form a single structure. • respiratory system • EquivalentTo: ‘functional system’ that capable_ofsome ‘respiratory gaseous exchange’ • respiratory system component • EquivalentTo: ‘anatomical structure’ that capable_ofsome‘respiratory gaseous exchange’ • SubClassOf:part_ofsome ‘respiratory system’ • ‘tracheolar cell’ • SubClassOfcapable_ofsome ‘respiratory gaseous exchange’

  28. Auto-populating respiratory system partonomy

  29. Inferring capable_of_part_of If X 'capable of' Y and Y part_of Z then X capable_of_part_of Z part_of capable_of_part_of capable_of

  30. A class for populating the partonomy of the olfactory system Note – in OWL this could be done without making this ugly class: (‘anatomical structure’ that capable_of_part_ofsome ‘sensory perception of smell’) SubClassOf(part_ofsome ‘olfactory system’)

  31. Challenges for FUNCARO - GO • Many potentially useful GO terms reference anatomical systems: • immune response: “Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.” • Granularity restrictions on GO terms may cause problems • cellular process vsmulticellularorganismal process • e.g.- detection of stimulus involved in sensory perception : • “The series of events involved in sensory perception in which a sensory stimulus is received by a cell and converted into a molecular signal.”

  32. Please download, try and comment • http://code.google.com/p/caro2/ • use the issue tracker to comment

  33. Acknowledgments • Michael Ashburner • Chris Mungall • Melissa Haendal • Matt Yoder • Andy Deans

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