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Tutorial #5: Scientific Data Integration and Mediation Bertram Ludäscher Ilkay Altintas Amarnath Gupta Kai Lin San Diego Supercomputer Center U.C. San Diego 1 • National Science Foundation (NSF) Acknowledgements – www.nsf.gov • GEOsciences Network (NSF) – www.geongrid.org • Biomedical Informatics Research Network (NIH) – www.nbirn.net • Science Environment for Ecological Knowledge (NSF) – seek.ecoinformatics.org • Scientific Data Management Center (DOE) – sdm.lbl.gov/sdmcenter/ Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 2 Outline • 8:30 – 10:30am: Tutorial: Data Integration & Mediation – Introduction to database mediation: • motivation and architecture • XML-based data integration – Database mediation theory primer: • logic view definitions, view unfolding, computing feasible plans – From XML-based to Knowledge-based mediation: • use of ontologies in data integration, ... • 10:30 – 10:45am: BREAK • 10:45 – 12:00: Applications and Demos – – – – 10:45 – 11:05 Mediator Demo 11:05 – 11:20 Queries w/ Ontology Support 11:20 – 11:40 Scientific Workflows 11:40 – 12:00 KNOW-ME Ontology Tool Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 3 Information Integration Challenges • System aspects: “Grid” Middleware – distributed data & computing – Web Services, WSDL/SOAP, … – sources = functions, files, databases, … Semantics Structure • Syntax & Structure: XML-Based Mediators Syntax – wrapping, restructuring – XML queries and views – sources = XML databases System aspects reconciling S4 heterogeneities “gluing” together multiple data sources bridging information and knowledge gaps computationally Scientific Data-Mediation AHM'03 • Semantics: Model-Based/Semantic Mediators – conceptual models and declarative views – SemanticWeb/KnowledgeGrid stuff: ontologies, description logics (RDF(S), DAML+OIL, OWL ...) – sources = knowledge bases (DB+CMs+ICs) National Partnership for Advanced Computational Infrastructure 4 Information Integration from a DB Perspective • Information Integration Problem – Given: data sources S1, ..., Sk (DBMS, web sites, ...) and user questions Q1,..., Qn that can be answered using the Si – Find: the answers to Q1, ..., Qn • The Database Perspective: source = “database” Si has a schema (relational, XML, OO, ...) Si can be queried define virtual (or materialized) integrated views V over S1 ,..., Sk using database query languages (SQL, XQuery,...) questions become queries Qi against V(S1,..., Sk) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 5 Standard (XML-Based) Mediator Architecture USER/Client Query Q ( G (S1,..., Sk) ) Integrated Global (XML) View G Integrated View Definition MEDIATOR G(..) S1(..)…Sk(..) XML Queries & Results Scientific Data-Mediation AHM'03 (XML) View (XML) View (XML) View Wrapper Wrapper Wrapper S1 S2 Sk wrappers implemented as web services National Partnership for Advanced Computational Infrastructure 6 Some BIRNing Data Integration Questions Biomedical Informatics Research Network http://nbirn.net • Data Integration Approaches: – – – – Let’s just share data, e.g., link everything from a web page! ... or better put everything into an relational or XML database ... and do remote access using the Grid ... or just use Web services! • Nice try. But: – “Find the files where the amygdala was segmented.” – “Which other structures were segmented in the same files?” – “Did the volume of any of those structures differ much from normal?” – “What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1? Any structure specificity? How about other rodents?” Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 7 An Online Shopper’s Information Integration Problem El Cheapo: “Where can I get the cheapest copy (including shipping cost) of Wittgenstein’s Tractatus Logicus-Philosophicus within a week?” addall.com ? Information Integration public library amazon.com barnes&noble.com “One-World” Mediation WWW half.com A1books.com A Home Buyer’s Information Integration Problem What houses for sale under $500k have at least 2 bathrooms, 2 bedrooms, a nearby school ranking in the upper third, in a neighborhood with below-average crime rate and diverse population? ? Information Integration Realtor Crime Stats School Rankings “Multiple-Worlds” Mediation Demographics A Geoscientist’s Information Integration Problem What is the distribution and U/ Pb zircon ages of A-type plutons in VA? How about their 3-D geometry ? How does it relate to host rock structures? ? Information Integration Geologic Map (Virginia) GeoChemical “Complex Multiple-Worlds” Mediation GeoPhysical GeoChronologic (gravity contours) (Concordia) Foliation Map (structure DB) A Neuroscientist’s Information Integration Problem Biomedical Informatics Research Network http://nbirn.net What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1? Any structure specificity? How about other rodents? ? Information Integration protein localization sequence info (NCMIR) (CaPROT) “Complex Multiple-Worlds” Mediation morphometry neurotransmission (SYNAPSE) (SENSELAB) Structural / XML-Based Mediation Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 12 Abstract XML-Based Mediator Architecture USER/Client Query Q o V (S_1,...,S_k) Integrated XML View V Integrated View Definition IVD(S1,...,Sn) MEDIATOR XML Queries & Results XML View XML View XML View Wrapper Wrapper Wrapper S_1 Scientific Data-Mediation AHM'03 S_2 S_k National Partnership for Advanced Computational Infrastructure 13 Extensible Markup Language (XML) ... in their wonderful book called SemWeb <title>SemWeb Tractat Tractat Tractat</title> </title> by <author>B. B.Lee, Schatz Schatz</author> T.B. Lee, by B. Schatz andby T.B. the and authors showthe how ... <book> authors and <author> show how T.B....Tractat</title> Lee</author>, the authors <title>SemWeb show how ... <author>B. Schatz</author> <author>T.B. Lee</author> </book> book title author author “SemWeb Tractat” “B. Schatz” “T.B. Lee” book: title: “SemWeb Tractat” author: “B. Schatz” author: “T.B. Lee” • (meta)language for marking up text & data with user-definable tags – (X)HTML, XSLT, XML Schema, ... – MathML, BioML, GeoML, NeuroML, ... – XML-RPC, SOAP, ... • semistructured tree data model – flexible: marked-up text, web-pages, databases, ... • container model: – “boxes within boxes” Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 14 Example: Relational Data => XML R A B C a1 b1 c1 a2 a3 b2 b3 c2 c3 R tuple tuple tuple A B C A B C A B C a1 b1 c1 a2 b2 c2 a3 b3 c3 Scientific Data-Mediation AHM'03 R tuple A a1 /A B b1 /B C c1 /C /tuple tuple A a2 /A B b2 /B C c2 /C /tuple … /R National Partnership for Advanced Computational Infrastructure 15 Tag Names & Nesting => XML DTDs (Grammars) Grammar Rules bibliography paper authors paper* authors fullPaper? title booktitle author+ XML DTD <!ELEMENT bibliography paper*> <!ELEMENT paper (authors,fullPaper?,title,booktitle)> <!ELEMENT authors author+> Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 16 XML DTDs vs. XML Schema • XML DTDs – set of allowed tag names – their nesting structure (via grammar rules) • XML Schema – – – – – tag names and nesting structure user-defined complex data types subtyping (no multiple inheritance): RESTRICT and EXTEND separate “namespace” for type names and tag (=element) names ... Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 17 XML Schema: User-Defined Type/Class Hierarchy Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 18 XML Schema Declarations (“home-style” syntax) Complex Type Declarations Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 19 XML Schema (“home-style”) Simple Type Declarations Complex Types Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 20 XML Schema: Substitution Groups Elements of a substitution group (hexagons) and associated complex types (boxes) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 21 XML Schema Declarations (W3C syntax) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 22 XML Query Languages • XPath: – root//books/book[cover_style=“paperback”][price<80] • XQuery – the W3C XML query language • XSLT – XML transformations (XML=>HTML, XML=>XML) • ... Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 23 Transforming and Rendering XML: XSLT Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 24 XMAS: XML Matching And Structuring language CONSTRUCT <books> <book> $a1 $t <pubs> $p { $p } </pubs> </book> { $a1, $t } </books> WHERE <books.book> $a1 : <author /> $t : <title /> </> IN "amazon.com" AND <authors.author> $a2 : <author /> <pubs> $p : <pub/> </> </> IN "www...DBLP… " AND value( $a1 ) = value( $a2 ) XMAS Scientific Data-Mediation AHM'03 Integrated View Definition: “Find books from amazon.com and DBLP, join on author, group by authors and title” XMAS Algebra National Partnership for Advanced Computational Infrastructure 25 Database Mediation Theory Primer 26 Mediator Query Processing Query Q Integrated View Definition V Translator parsed plan Composition (Q o V) composed plan Compile-time Run-time Rewriter/Optimizer optimized plan Plan Execution Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 27 Logic View Definitions (Global-as-View) or Querying and Reasoning with the Family ... • Warm up: Who says this? – “Your are my son, but I’m not your father!” • The mother! Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 28 Logic View Definitions (Global-as-View) • Globals-as-View (GAV) – Integrated view V is defined in terms of the sources Src_1, ... , Src_k • Given the following source databases: – Src_1 schema = { father(Father,Child), mother(Mother,Child) } – Src_2 schema = { spouse(Spouse, Spouse) } – Src_3 schema = { male(Person), female(Person) } • Can you define integrated views V for ... ? – parent(Parent,Child) • short: parent/2, i.e., table/relation name is ‘parent’, arity (#columns) is 2 – son/2, daughter/2 – brother/2, sister/2 – brother_in_law/2, sister_in_law/2 – aunt/2, uncle/2 – married/2, bachelor/2 Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 29 Logic View Definitions (Global-as-View) Source relations: father/2, mother/2, spouse/2, male/1, female/1 = “,” = conjunction (and) = “ ; ” = disjunction (or) • parent(C,P) father(C,P) ; mother(C,P) . • son(P,S) parent(S,P) , male(S) . • brother(X,B) parent(X,P), son(P,B), X B . • brother_in_law(X,B) sister(X, Z), spouse(Z, B) ; spouse(X, Z), brother(Z, B) . Scientific Data-Mediation AHM'03 = “not” = negation National Partnership for Advanced Computational Infrastructure 30 Logic View Definitions (Global-as-View) Source relations: father/2, mother/2, spouse/2, male/1, female/1 = “,” = conjunction (and) = “ ; ” = disjunction (or) = “not” = negation • uncle(X, U) parent(X, Z), brother(Z, U) ; parent(X, Z), brother_in_law(Z, U) . • aunt(X, A) parent(X, Z), sister(Z, A) ; parent(X, Z), sister_in_law(Z, A) . • married(X) spouse(X, _) . • bachelor(X) [person(X)] , not married(X) . Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 31 Query Rewriting and Query Evaluation • Query Rewriting: - Given a user query Q in terms of virtual views V... - Find an equivalent query Q’ in terms of the sources Src_1,...,Src_k • Query Evaluation: - Given a query Q’, evaluate Q’ over the source databases D := Src_1 ... Src_k • Examples: – Q_uncle/2 = { (X,Y) | uncle(X,Y) holds in D } – Q_tom’s_uncle/1 = { X | uncle(tom, X) holds in D } – Q_whose_uncle_is_tom/1 = { X | uncle(X, tom) holds in D } Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 32 Query Rewriting (for GAV) • Query rewriting: - Given a user query Q in terms of virtual views V... - Find an equivalent query Q’ in terms of the sources Src_1,...,Src_k • Query Q, views V, source schemas S • View unfolding: – starting with Q, repeatedly replace view predicates by the definition • Creating a feasible plan: – here: compute disjunctive normal form (DNF) – DNF = disjunction of conjunctions (= “union of joins”) – order goals within each conjunction according to sources’ query capabilities Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 33 Example • ?- plan(brother(X0,X1)) . brother(X0, X1) == LQP ==> (father(X0, X2) v mother(X0, X2)) & (father(X1, X2) v mother(X1, X2)) & male(X1) & neq(X0, X1) brother(X0, X1) ==NNF LQP==> (father(X0, X2) v mother(X0, X2)) & (father(X1, X2) v mother(X1, X2)) & male(X1) & neq(X0, X1) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 34 Example (Cont’d) • ?- plan(brother(X0,X1)) . brother(X0, X1) ==DNF LQP==> father(X0, X2)&father(X1, X2)&male(X1)&neq(X0, X1) v mother(X0, X2)&father(X1, X2)&male(X1)&neq(X0, X1) v father(X0, X2)&mother(X1, X2)&male(X1)&neq(X0, X1) v mother(X0, X2)&mother(X1, X2)&male(X1)&neq(X0, X1) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 35 Example (Cont’d) • ?- plan(brother(X0,X1)) . brother(X0, X1) ==Bp ordered LQP==> parentDb(father(X1, X2) & father(X0, X2)) & genderDb(male(X1)) & mediator(neq(X0, X1)) v parentDb(father(X1, X2) & mother(X0, X2)) & genderDb(male(X1)) & mediator(neq(X0, X1)) v parentDb(mother(X1, X2)&father(X0,X2)) & genderDb(male(X1)) & z_mediator(neq(X0, X1)) v parentDb(mother(X1, X2)&mother(X0, X2)) & genderDb(male(X1))&z_mediator(neq(X0, X1)) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 36 Computing Feasible Plans (Goal Ordering) • A conjunctive query Q is an expression of the form – q( X ) p1( X1 ) , ..., pn( Xn ) – order of subgoals p_i is irrelevant • An ordered plan P is an expression of the form – q( X ) [p1( X1 ) , ..., pn( Xn )] – order of subgoals p_i is important • Problem: – given Q, compute P which is feasible, i.e., observes the limited query capabilities of sources – Here: binding patterns, i.e., predicates’ arguments can be • “b” – bound • “f” – free • “_” – bound or free Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 37 A Simple Algorithm for Ordering Goals Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 38 Query Containment • A query Q1 is contained in Q2, denoted Q1 Q2 – if for all possible database instances, the set of answers to Q1 is contained in the set of answers to Q2. • Q1 and Q2 are called equivalent – if Q1 Q2 and Q2 Q1. • Query containment is undecidable for many languages, e.g., for the relational calculus (SQL). • For conjunctive queries, the problem is NPcomplete (and thus decidable) – Since query sizes tend to be “small” (in particular, when compared to database sizes), query containment is still of use in practice (indeed, it is one of the most fundamental tools for logic-based query optimization). Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 39 Query Containment • Q1(Xs,Ys) is contained in Q2(Xs,Zs) iff ALL Xs: (EXISTS Ys: Q1(Xs,Ys)) (EXISTS Zs: Q2(Xs,Zs)) • iff we can refute its negation • iff NOT ALL Xs: (EXISTS Ys: Q1(Xs,Ys)) (EXISTS Zs: Q2(Xs,Zs)) |= [] • iff EXISTS Xs: (EXISTS Ys: Q1(Xs,Ys)) AND NOT (EXISTS Zs: Q2(Xs,Zs)) |= [] • iff – canonical_db(Q1) AND Q2(Xs,Zs) |= [] • create database from Q1, then run Q2 as a query... Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 40 Query Containment Algorithm (in Prolog) • Applications: – query minimization (conjunctive query is minimal if not conjunct can be dropped) – semantic query optimization • Q denial • here: denial is an integrity constraint and states what must not hold • example: denial = false mother(X,M), father(Y,M) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 41 Example • 50% of the clauses of the executable plan are irrelevant ... Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 42 Mediator Demo • Computer Science Challenges: – Given a query Q over virtual integrated database V, how to come up with Q’ over the source schemas? (cf. Garlic, DiscoveryLink, ...) • query rewriting of Q(V) into Q’(SRCs) using unfolding and normalization • computation of feasible orders (NP-complete!?) while minimizing number of “chunks” sent to sources • semantic query optimization (reasoning over plans!); e.g. conjunctive query containment is NP-complete [Chandra-Merlin-77] • A Quick Demo of the current prototype: – Find 3D reconstructions of cells found in ‘cerebellar cortex’: • • • • • ?- ccdbData('cerebellar cortex'). Join everything reachable along ‘cerebellar-cortex’.(has-a)* in UMLS ....with concept markup in CCDB ... retrieve (links to) results ... also show on SmartAtlas tool Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 43 Mediator Demo Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 44 From XML-Based to Logic and ModelBased (“Semantic”) Mediation Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 45 What’s the Problem with XML & Complex Multiple-Worlds? • XML is Syntax – DTDs talk about element nesting – XML Schema schemas give you data types – need anything else? => write comments! • Domain Semantics is complex: – implicit assumptions, hidden semantics sources seem unrelated to the non-expert • Need Structure and Semantics beyond XML trees! employ richer OO models make domain semantics and “glue knowledge” explicit use ontologies to fix terminology and conceptualization avoid ambiguities by using formal semantics Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 46 From XML-Based to Model-Based Mediation • Data and Knowledge Sharing Potential: Database Mediation + Knowledge Representation ________________________ = Model-Based Mediation • Basic Ideas: – turn primary data sources into knowledge sources – employ secondary glue knowledge sources • generic: UMLS, ... • specific: community/laboratory ontologies Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 47 Information Integration Landscape conceptual complexity/depth high Model-Based Mediation GO EcoCyc Ontologies KR formalisms RiboWeb UMLS Bioinformatics Geoinformatics Tambis BLAST MIA Entrez Cyc WordNet DB mediation techniques low addall book-buyer one-world Scientific Data-Mediation AHM'03 home-buyer 24x7 consumer conceptual distance multiple-worlds National Partnership for Advanced Computational Infrastructure 48 Knowledge Representation: Relating Theory to the World via Formal Models John F. Sowa, Knowledge Representation: Logical, Philosophical, and Computational Foundations “All models are wrong, but some are useful!” Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 49 XML-Based vs. Model-Based Mediation CM ~ {Descr.Logic, ER, UML, RDF/XML(-Schema), …} Integrated-DTD := Glue Maps XML-QL(Src1-DTD,...) DMs, PMs CM-QL ~ {F-Logic, DAML+OIL, …} Integrated-CM := CM-QL(Src1-CM,...) No Domain Constraints IF THEN IF IFTHEN THEN Structural Constraints (DTDs), Parent, Child, Sibling, ... A = (B*|C),D B = ... C1 C2 .... XML Elements XML Models Raw Raw Data RawData Data C3 R .... . . .... .... Logical Domain Constraints Classes, Relations, is-a, has-a, ... (XML) Objects Conceptual Models What’s the Glue? What’s in a Link? Y X • Syntactic Joins – (X,Y) := X.SSN = Y.SSN – (X,Y) := X.UMLS-ID = Y.UID equality • “Speciality” Joins – (X,Y,Score) := BLAST(X,Y,Score) similarity • Semantic/Rule-Based Joins – (X,Y,C) := X isa C, Y isa C, BLAST(X,Y,S), S>0.8 homology, lub – (X,Y,[produces,B,increased_in]) := X produces B, B increased_in Y. rule-based e.g., X=-secretase, B=beta amyloid, Y=Alzheimer’s disease • Challenge: – compile semantic joins into efficient syntactic ones Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 51 Model-Based Mediation Methodology ... • Lift Sources to export CMs: CM(S) = OM(S) + KB(S) + CON(S) • Object Model OM(S): – complex objects (frames), class hierarchy, OO constraints • Knowledge Base KB(S): – explicit representation of (“hidden”) source semantics – logic rules over OM(S) • Contextualization CON(S): – situate OM(S) data using “glue maps” (GMs): domain maps DMs (ontology) = terminological knowledge: concepts + roles process maps PMs = “procedural knowledge”: states + transitions Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 52 ... Model-Based Mediation Methodology • Integrated View Definition (IVD) – declarative (logic) rules with object-oriented features – defined over CM(S), domain maps, process maps – needs “mediation engineers” = domain + KRDB experts • Knowledge-Based Querying and Browsing (runtime): – mediator composes the user query Q with the IVD ... rewrites (Q o IVD), sends subqueries to sources ... post-processes returned results (e.g., situate in context) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 53 Model-Based Mediator Architecture USER/Client “Glue” Maps GMs CM (Integrated View) DomainMaps Maps Domain Domain Maps DMs DMs DMs Mediator Engine Integrated View Definition IVD LP rule proc. XSB Engine DomainMaps Maps Domain Process Maps DMs DMs PMs semantic context CON(S) Graph proc. GCM GCM GCM First results & Demos: CM S1 CM S2 CM S3 KIND prototype, formal DM semantics, PMs [SSDBM00] [VLDB00] [ICDE01] [NIH-HB01] (w/ Gupta, Martone) CM Queries & Results (exchanged in XML) CM(S) = OM(S)+KB(S)+CON(S) CM-Wrapper CM-Wrapper CM-Wrapper (XML-Wrapper) (XML-Wrapper) (XML-Wrapper) S1 Scientific Data-Mediation AHM'03 FL rule proc. S2 S3 National Partnership for Advanced Computational Infrastructure 54 Domain Maps (Ontologies) as Glue Knowledge Sources • Domain Map = Ontology – representation of terminological knowledge • Use in Model-Based Mediation – (derived) concepts as “drop points”, “anchor points”, “context” for source classes – compile-time use: view definition, subsumption, classification,... – runtime use: querying/deduction, path queries, .... • Formalisms: – Semantic nets, Thesauri, Frame-logic, Description logics, ... Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 55 Ontologies • So what is an Ontology? – – – – – – definition of things that are relevant to your application representation of terminological knowledge (“TBox”) explicit specification of a conceptualization concept hierarchy (“is-a”) further semantic relationships between concepts abstractions of relational schemas, (E)ER, UML classes, XML Schemas • Examples: – – – – NCMIR ANATOM GO (Gene Ontology) UMLS (Unified Medical Language System CYC Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 56 Formalism for Ontologies: Description Logic • DL definition of “Happy Father” (Example from Ian Horrocks, U Manchester, UK) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 57 Description Logic Statements as Rules • In first-order logic (rule form): happyFather(X) man(X), child(X,C1), child(X,C2), blue(C1), green(C2), not ( child(X,C3), poorunhappyChild(C3) ). poorunhappyChild(C) not rich(C), not happy(C). Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 58 Description Logics • Terminological Knowledge (TBox) – Concept Definition (naming of concepts): – Axiom (constraining of concepts): => a mediators “glue knowledge source” • Assertional Knowledge (ABox) – the marked neuron in image 27 => the concrete instances/individuals of the concepts/classes that your sources export Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 59 Querying vs. Reasoning • Querying: – given a DB instance I (= logic interpretation), evaluate a query expression (e.g. SQL, FO formula, Prolog program, ...) – boolean query: check if I |= (i.e., if I is a model of ) – (ternary) query: { (X, Y, Z) | I |= (X,Y,Z) } => check happyFathers in a given database • Reasoning: – check if I |= implies I |= for all databases I, – i.e., if => – undecidable for FO, F-logic, etc. – Descriptions Logics are decidable fragments concept subsumption, concept hierarchy, classification semantic tableaux, resolution, specialized algorithms Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 60 What’s in an Answer? (What’s in a Link? revisited) Y X • Semantic/Rule-Based Joins – (X,Y,[produces,B,increased_in]) := X produces B, B increased_in Y. rule-based e.g., X=-secretase, B=beta amyloid, Y=Alzheimer’s disease • What is the Erdoes number of person P? – 3 • Really? Why? – authority based: <VIP> said so – faith based: don’t know but firmly believe – query statement Q = ... derived it from DB I – query Q = ... derived it from DB I and KB T using derivation D => logic-based systems often “come with explanations” (“computations as proofs”) Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 61 Formalizing Glue Knowledge: Domain Map for SYNAPSE and NCMIR Domain Map = labeled graph with concepts ("classes") and roles ("associations") • additional semantics: expressed as logic rules (F-logic) Purkinje cells and Pyramidal cells have dendrites that have higher-order branches that contain spines. Dendritic spines are ion (calcium) regulating components. Spines have ion binding proteins. Neurotransmission involves ionic activity (release). Ion-binding proteins control ion activity (propagation) in a cell. Ion-regulating components of cells affect ionic activity (release). Domain Expert Knowledge Domain Map (DM) Scientific Data-Mediation AHM'03 DM in Description Logic National Partnership for Advanced Computational Infrastructure 62 Source Contextualization & DM Refinement In addition to registering (“hanging off”) data relative to existing concepts, a source may also refine the mediator’s domain map... sources can register new concepts at the mediator ... Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 63 Example: ANATOM Domain Map Browsing Registered Data with Domain Maps Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 65 Process Maps with Abstractions and Elaborations: From Terminological to Procedural Glue • nodes ~ states • edges ~ processes, transitions • blue/red edges: • processes in Src1/Src2 • general form of edges: related formalisms Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 66 Summary: Mediation Scenarios & Techniques Federated Databases One-World Common Schema XML-Based Mediation Model-Based Mediation One-/Multiple-Worlds Complex Multiple-Worlds Mediated Schema Common Glue Maps SQL, rules XML query languages DOOD query languages Schema Transformations Syntax-Aware Mappings Syntactic Joins Syntactic Joins DB expert Scientific Data-Mediation AHM'03 DB expert Semantics-Aware Mappings “Semantic” Joins via Glue Maps KRDB + domain expert National Partnership for Advanced Computational Infrastructure 67 Semantic (Community) Webs “Within the next decade, computing technology will transform the Internet into the Interspace, an information infrastructure that supports semantics indexing and concept navigation across widely distributed community repositories.” Bruce Schatz, IEEE Computer, Jan. 2002 "The Semantic Web is an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation." Tim Berners-Lee et al., 2001 Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 68 Combine Everything: Die eierlegende Wollmilchsau: • Database Federation/Mediation – query rewriting under GAV/LAV – w/ binding pattern constraints – distributed query processing • Semantic Mediation – semantic integrity constraints, reasoning w/ plans, automated deduction – deductive database/logic programming technology, AI “stuff”... – Semantic Web technology • Scientific Workflow Management – more procedural than database mediation (often the scientist is the query planner) – deployment using web services Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 69 B R EAK ... followed by demos ... 70 Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 71 GEON SMART Metadata: Multihierarchical Rock Classification for “Thematic Queries” (GSC) Genesis Fabric Composition “smart discovery & querying” via multiple, independent concept hierarchies (controlled vocabularies) • data at different description levels can be found and processed Texture Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 72 GEON SMART Metadata:Multihierarchical Rock Classification for “Thematic Queries” http://klin-pc.sdsc.edu:8080/examples/jsp/geon/composition.jsp Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 73 GEON Ontology Demo • http://klin-pc.sdsc.edu:8080/examples/jsp/geon/old-rock.jsp • http://klin-pc.sdsc.edu:8080/examples/jsp/geon/rock.jsp Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 74 Architecture of Ontology Based Map Integration Global Web Map Server Ontology Mapping Web Map Server Web Map Server Web Map Server Database Database Database Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 75 DOE Scientific Datamanagement Center • Scientific Workflow Demo Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 76 Example: A Scientific Workflow Microarray analysis A Database search for promoter identification cDNA Cluster B C Promoter model Common promoter alignment Promoter sequences * * * * Database search Scientific Data-Mediation AHM'03 *- New candidate target genes * Adapted from Thomas Werner Biomolecular Engineering, 17: 87-94 (2001) National Partnership for Advanced Computational Infrastructure 77 Conceptual Workflow Compute clusters (min. distance) For each promoter Select gene-set (cluster-level) For each gene Retrieve matching cDNA Retrieve genomic Sequence Extract promoter Region(begin, end) Scientific Data-Mediation AHM'03 Retrieve Transcription factors Compute Subsequence labels Arrange Transcription factors With all Promoter Models Align promoters Create consensus sequence National Partnership for Advanced Computational Infrastructure Compute Joint Promoter Model 78 Mapping This Workflow To Web Sites Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 79 Customized CGI Application Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 80 Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 81 Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 82 ClustalW Transfac Output Query Results Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 83 SDM-SciDAC System Architecture User WF-Pilot Design Execution monitoring WF-Engine Scheduling and execution AWF EWF WF-Compiler AWF EWF Translation query rewriting web service matching semantic type checking data type conversion web service invocation web service invocation ET ET Genbank BLAST C AAV rules ET schemas Abstract Task Executable Task (AT) Repository (ET) Repository Scientific Data-Mediation AHM'03 C C Data & Parameter Ontologies conversion rules Datatype & Conversion Repository National Partnership for Advanced Computational Infrastructure 84 AWF to EWF Declarative specification For each gene Retrieve matching cDNA Retrieve genomic Sequence Extract promoter Region(begin, end) User supplied GetGenomicSequence (+{selectedGene}, -{{GenomicSequence}}) :GENBANK (+{selectedGene}, -{cDNASequence}), BLAST (+{cDNASequence}, +dbName, +format, {rankedGenomicSequenceList}). GetGenomicSequence (+{selectedGene}, -{{GenomicSequence}}) :GENBANK (+{selectedGene}, -{cDNASequence}), BLAT (+{cDNASequence}, +QueryType, +SortCriteria, +OutputType , {rankedGenomicSequenceList}). IdentifyPromoterElements (+{rankedGenomicSequenceList}, -{element}) :PromoterSequences (+{rankedGenomicSequenceList}, getBeginEnd(+Species, -Begin, -End), -{element}). Need extra domain knowledge Translation to EWF needs Same functionality, different creation of iterators operational constraints and Scientific Data-Mediation AHM'03availability National Partnership for Advanced Computational Infrastructure 85 Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 86 Abstract Task (AT) Registration Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 87 Abstract Task (AT) View and Delete Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 88 Abstract Task (AT) Update Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 89 AWF Design Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 90 EWF Planning and Compilation Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 91 EWF Execution Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 92 BIRN Tools Demo 93 Some References (starting points) • XML – General: http://xml.coverpages.org/xml.html – XQuery: http://www.w3.org/XML/Query – XSLT: http://xml.coverpages.org/xsl.html • Query Rewriting: – database research literature • Logic Programming – Learn Prolog Now! http://www.coli.uni-sb.de/~kris/learn-prolog-now/ – SWI-Prolog (nice free Prolog system): http://www.swi-prolog.org/ • Ontologies – Ontology Web language: http://www.w3.org/TR/owl-features/ – http://www-ksl.stanford.edu/kst/what-is-an-ontology.html – http://www.cs.utexas.edu/users/mfkb/related.html • Model-Based Mediation: – http://www.sdsc.edu/~ludaesch/Paper/icde01.html • Semantic Web: – http://www.w3.org/2001/sw/ Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 94 References: Project Web Sites • GEOsciences Network (NSF) – www.geongrid.org • Biomedical Informatics Research Network (NIH) – www.nbirn.net • Science Environment for Ecological Knowledge (NSF) – seek.ecoinformatics.org • Scientific Data Management Center (DOE) – sdm.lbl.gov/sdmcenter/ Scientific Data-Mediation AHM'03 National Partnership for Advanced Computational Infrastructure 95