Hybrid-Type Extensions for Actor-Oriented Modeling (a.k.a. Semantic Data-types for Kepler) Shawn Bowers & Bertram Ludäscher

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1 Hybrid-Type Extensions for Actor-Oriented Modeling (a.k.a. Semantic Data-types for Kepler) Shawn Bowers & Bertram Ludäscher University of alifornia, Davis Genome enter & S Dept. May, 2005 Outline 1. Hybrid Types 2. Hybrid Types and Scientific Workflow Design 3. Super Rapid Prototyping: The Sparrow Family of Languages 4. Next Steps: Adding a Hybrid-Type System to Kepler

2 Hybrid Types Hybrid Types: Superimposing Semantics Separation of oncerns: onventional Data Modeling (Structural Data Types) E.g., XML Schema / DTD, etc. onceptual Data Modeling (Semantic Types) Drawn from ontologies (expressed in Description Logic) apturing domain knowledge (e.g., biodiversity, ecology) Explicit (external) linkages (Semantic Annotations) Simple links (one concept per item) Links expressed as constraints (logical mappings)

3 Hybrid Types: Superimposing Semantics T1 := table meas Datatypes double a relational table of measurements T2 := list spp a list of s Hybrid Types: Superimposing Semantics SpeciesBiomass Measurement item.species prop.biomass loc.location Species biomass is a measure of the amount of biomass of a particular species within a location. Semtypes SpeciesommBiomass SpeciesBiomass loc.ommunity Species community biomass is a species biomass within a community. T1 := table meas SpeciesommBiomass table/x:meas => X:SpeciesommBiomass double each table/meas instance is a measurement

4 Hybrid Types: Superimposing Semantics SpeciesBiomass Measurement item.species prop.biomass loc.location Species biomass is a measure of the amount of biomass of a particular species within a location. Semtypes SpeciesommBiomass SpeciesBiomass loc.ommunity Species community biomass is a species biomass within a community. T1 := ommunity table meas SpeciesommBiomass table/x:meas, X/Y:site, X/Z:plot => X:SpeciesommBiomass, =f(y,z), (X,):loc, :ommunity, double Hybrid Types: Superimposing Semantics SpeciesBiomass Measurement item.species prop.biomass loc.location Species biomass is a measure of the amount of biomass of a particular species within a location. Semtypes SpeciesommBiomass SpeciesBiomass loc.ommunity Species community biomass is a species biomass within a community. SpeciesommBiomass T1 := table ommunity meas Species double table/x:meas, X/Y:site, X/Z:plot, X/U:spp => X:SpeciesommBiomass, =f(y,z), (X,):loc, :ommunity, (X,U):item, U:Species,

5 Hybrid Types: Superimposing Semantics SpeciesBiomass Measurement item.species prop.biomass loc.location Species biomass is a measure of the amount of biomass of a particular species within a location. Semtypes SpeciesommBiomass SpeciesBiomass loc.ommunity Species community biomass is a species biomass within a community. SpeciesommBiomass T1 := table ommunity meas Species Biomass double table/x:meas, X/Y:site, X/Z:plot, X/U:spp, X/B:bm => X:SpeciesommBiomass, =f(y,z), (X,):loc, :ommunity, (X,U):item, U:Species, (X,B):prop, B:Biomass. Hybrid Types: Superimposing Semantics Searching oncept-based, e.g., find all datasets containing biomass measurements Merging/Integrating ombining heterogeneous sources based on annotations oncatenate, Union (merge), Join, etc. Transforming onstruct mappings from schema S1 to S2 based on annotations Semantic Propagation Pushing semantic annotations through transformations/queries

6 Semantic Annotation Propagation apture I/O constraints Similar to unit type constraints an enable automated metadata creation (annotation propagation ) an help refine ontologies and existing annotations Semantic Annotation Propagation T1 := table meas double Port 1 Annotation table/x:meas, X/Y:site, X/Z:plot, X/U:spp, X/B:bm => X:SpeciesommBiomass, =f(y,z), (X,):loc, :ommunity, (X,U):item, U:Species, (X,B):prop, B:Biomass. p1::t1 p2::t2 seasonal species p3::t3 Actor I/O constraint (approx.) p3.obs(site, plot, spp, bm) :- p1.meas(site, plot, spp, bm), p2.spp(spp). T3 := table Port 2 hased Annotation table/x:obs, X/Y:site, X/Z:plot, obs X/U:spp, X/B:bm => X:SpeciesommBiomass, =f(y,z), (X,):loc, :ommunity, (X,U):item, U:Species, (X,B):prop, B:Biomass. double

7 Hybrid Types and Scientific Workflow Design Workflow Design Primitives End-to-End Workflow Design and Implementation Viewed as a series of primitive transformations Each takes a WF and produces a new WF an be combined to form design strategies Workflow Design W 0 W 1 W 2 W m W n t t t Workflow Implementation Top-Down Task Driven Data Driven Bottom-Up Structure Driven Output Driven Semantic Driven Input Driven

8 Workflow Design Primitives Semantic types and Actor Oriented Modeling: Actors and Workflows: can have semantic types conceptually describing their function Ports: can have semantic types conceptually describing what they consume and produce I/O onstraints: a general form of constraint between input and output (e.g., like unit constraints) approximating the function of an actor Basic Design Primitives Inherited from Ptolemy Basic Transformations Starting Workflow Resulting Workflow Resulting Workflow t 1 : Entity Introduction (actor or data connection) t 2 : Port Introduction t 3 : Datatype Refinement (s s, t t) s t s t s t t 4 : Hierarchical Abstraction t 5 : Hierarchical Refinement t 6 : Data onnection t 7 : Director Introduction

9 Additional (Planned) Design Primitives for Semantic Types Extended Transformations Starting Workflow Resulting Workflow t 9 : Actor Semantic Type Refinement (T T) T T t 10 : Port Semantic Type Refinement (, D D) t 11 : Annotation onstraint Refinement (α α) t 12 : I/O onstraint Strengthening (ψ ϕ ) t 13 : Data onnection Refinement α 1 s ϕ ψ Resulting Workflow D D D D α2 α 1 t s D α2 t α 1 s D α 2 t t 14 : Adapter Insertion t 15 : Actor Replacement f f t 16 : Workflow ombination (Map) f 1 f 2 f 1 f 2 Adapters for Semantic and Structural Incompatibility D D D Adapters may: be abstract (no impl.) 1 2 D 1 1 D D 2 D be concrete bridge a semantic gap fix a structural mismatch f 1 f [S] 2 f 1 S T [S][S ] map f 2 [T] f 1 f [[S]] 2 f 1 S T [[S]][[S ]] map map f 2 [[T]] be generated automatically (e.g., Taverna s list mismatch ) be reused components (based on signatures)

10 Applying the Replacement Primitive f D f D D D f general replacement unsafe replacement context-sensitive replacement ( wiggle room ) f D f D f D D D D, overlap (e.g., ) D,D overlap (e.g., D D ) (e.g., ) D D (e.g., D D ) General replacement doesn t consider surrounding connections ontext-sensitive replacement gives more wiggle room by tuning the actors semtypes based on connections Workflow Elaboration Adapter insertion, replacement, and search provide a powerful mechanism for workflow elaboration : 1. Given an initial, user specified set of connected abstract actors 2. Repeatedly search for replacement concrete actors (atomic and composite) 3. At each step, insert adapters when necessary 4. Allow user to select returned workflows to be combined

11 Super Rapid Prototyping: The Sparrow Family of Languages The Sparrow Family of Language Basic Idea: Have both Machine and Human readable syntax Sparrow-DL Description logic Sparrow-DTD Datatypes, variant of XML DTDs Sparrow-Annotate onfiguring concepts; linking datatypes and ontologies Sparrow-SWF KSW-Based MoML Metadata Sparrow-Rule Fancy stuff, like type constraints (a la unit types), function approximation, and misc. other constraints

12 The Sparrow Family of Languages Sparrow-DTD Sparrow-SWF Sparrow-DL Sparrow-Toolkit Operations w1 Author Author ISBN ASIN AMSQuote a1 a3 a4 p1:: [] p1:: p2:: int p1:: P2:: {price=, cond=, seller={ }} Sparrow-Toolkit (example) Operations Is w1 semantically and/or structurally well typed? What can be semantically connected to a3? Insert abstract adapter between a3 and a4 What can replace (e.g., implement) the adapter?

13 Future Steps: Adding a Hybrid-Type System to Kepler urrent and Future Implementation oncept-based Actor Search Implemented as proof-ofconcept About to undergo major revision Additional operations slated for next Kepler Release (data search, actor-based port search, etc.) Biggest hallenges Building/searching a repository Making changes to MoML (see KSW) GUI changes Ontology management Workflow omponents (MoML) urn ids Semantic Annotations instance expressions Ontologies (OWL) Default + Other