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+ CARO 2.0 & FUNCARO David Osumi-Sutherland + Review of CARO (v1) Many definitions are complicated and opaque: No explicit disjointness declarations ‘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.” despite assertion of pairwise disjointness in paper. Rigid single inheritance Lack of necessary and sufficient definitions means no way to manage multiple classification + Problems with existing implementations Assuming pairwise disjointness in CARO(v1): Classified as both material and immaterial entities: Classified as both cell and ‘portion of tissue’ pyloric chamber; scale adult sensory neuron disjointness violations hidden by enforced single inheritance? The following are classified under ‘organism subdivision’ 'unicellular gland’; scale; vent + 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 fomalised so that auto-classification by reasoners can be used in place of hand classification. Disjoint declarations must be present for error checking + 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. + Fundamental, disjoint classes + material vs immaterial Examples potential importance includes lumen of stomach (space) vs wall of stomach (structure) vs the outside surface of the stomach (boundary with the body cavity; a 2D structure) 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 + amorphous vs has shape Example Importance includes blood vs tibia 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’ + cellularization state • Disjoint classes: • acellular (e.g.- cuticle) • cell (e.g. guard cell) • multicellular (e.g. upper epidermis) • multi-cell component (fanshaped 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) + cellularization state • formalization: • cell – import class from CL • acellular anatomical structure • EquivalentTo ‘anatomical structure’ and (has_part only not (cell or ‘cell part’)) • multicellular anatomical structure • EquivalentTo: ‘anatomical structure’ and has_component min 2 cell • multi-cell part structure • EquivalentTo: ‘anatomical structure’ and has_component min 2 ‘cell part’ and has_part only not cell Fan shaped body (synaptic neuropil) + connected vs not anatomical group: anatomical structure ‘anatomical structure’ DisjointWith ‘anatomical group’ PATO quality – connected ? Examples “A material anatomical entity consisting of a single connected whole.” Formalisation “A material anatomical entity consisting of multiple parts that are not physically connected to each other.” 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 mereological reasoning + 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” + From the organism down: organisms and their subdivisions. + organism organism def: “An individual member of a species.” How to classify? Make agnostic about unicellular vs multicellular. 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!) + Anatomical system Examples: nervous system; immune system; musculo-skeletal system attempt at formalization: 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 + connected system An anatomical system that is connected Examples: vertebrate circulatory system nervous system + Organism subdivision Examples: insect head; insect abdominal segment; insect leg Some necessary conditions has a contiguous integumental boundary has parts of multiple organ systems + types of multicellular structure + 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? + 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) + 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 + 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. + Relations for defining function capable_of expands to: bearer_of some (realised_by only ?P) domain: ‘continuant’ range: ‘process’ capable_of_part_of expands_to: bearer_of some (realized_by only (part_of some ?P) domain: ‘continuant’ range: ‘process’ property chain: bearer_of o part_of -> bearer_of_part_of If X bearer_of Y and Y part_of Z then X bearer_of_part_of Z + Terms for classifying by sensory function Gene Ontology classification of sensory processes: + Some necessary and sufficient definitions * *Strictly speaking, ‘some’ is a fudge. Better to use expanded forms in OWL? + Autoclassification capable_of + Functional systems – autopopulating partonomies functional system respiratory system EquivalentTo: ‘functional system’ that capable_of some ‘respiratory gaseous exchange’ respiratory system component 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. EquivalentTo: ‘anatomical structure’ that capable_of some ‘respiratory gaseous exchange’ SubClassOf: part_of some ‘respiratory system’ ‘tracheolar cell’ SubClassOf capable_of some ‘respiratory gaseous exchange’ + Auto-populating respiratory system partonomy + 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 + 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_of some ‘sensory perception of smell’) SubClassOf (part_of some ‘olfactory system’) + + 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 vs multicellular organismal 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.” + Please download, try and comment http://code.google.com/p/caro2/ use the issue tracker to comment + Acknowledgments Michael Ashburner Chris Mungall Melissa Haendal Matt Yoder Andy Deans