Outline. CUGS Core - Databases. Requirements. Work method. Databanks/Databases. Databank

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1 Outline CUGS Core - Databases Patrick Lambrix Linköpings universitet Introduction: storing and accessing data Semi-structured data Information integration Object-oriented and object-relational databases Work method For each topic: introductory presentation by topic responsible in smaller groups: reading papers, discussion guided by predefined questions, summary each smaller group presents their summary, final discussion moderated by topic Requirements Responsible for a topic (presentation + questions) (ca 60 hours) Participation in smaller discussion groups Take-home exam (ca 40 hours) responsible 3 4 s/databases One of many ways to store data in electronic form used in every-day life: bank, reservation of hotel or travel, library search, bar codes new applications : multimedia databases, geografic information systems, real-time databases DataBank Management System (DBMS): a collection of programs that allows a user to create and maintain a databank databank system = physical databank + DBMS 5 6

2 Real life information Management System s Model / updates Processing of queries and updates Access to stored data Answers Issues What information is stored? How is the information stored? (high and low level) How is the information accessed? (user level, system level) How is a databank recovered after a crash? Physical databank 7 8 Issues How to keep track of changes of the data over time? How can several users access and update information in a databank at the same time? How can a user access information in several databanks at the same time? 9 Persons databank administrator databank designer end user application programmer DBMS designer developer of tools operator, maintenance 0 DEFINITION Homo sapiens adrenergic, beta--, receptor SOURCE ORGANISM S, Collins, Daniel,,, Cloning of the cdna for the beta -adrenergic receptor S,,, Human beta - and beta -adrenergic receptors: structurally and functionally related receptors derived from distinct genes What information is stored? Model of reality - Entity-Relationship model (ER) - Unified Modeling Language (UML)

3 Entity-relationship Entity-Relationship protein-id PROTEIN source entities and attributes entity types key attributes relations cardinality constraints accession m Reference n definition title article-id ARTICLE 3 author 4 How is the information stored? (high level) How is the information accessed? (user level) Text (IR) Semi-structured data Data models (DB) Rules + Facts (KB) structure precision Text - Information Retrieval Search based on words conceptual models: boolean, vector, probabilistic, file models: flat files, inverted files, IR File model: inverted file inverted file postings file document file Vector model (simplified) WORD HITS LINK DOC# LINK DOCUMENTS adrenergic 3 cloning 53 receptor 5 5 Doc Doc 7 receptor cloning adrenergic Doc (,,0) Doc (0,,0) Q (,,) sim(d,q) = d. q d x q 8

4 Databases Relational databases: - model: tables + relational algebra - query language (SQL) Object-oriented databases: - model: persistent objects, messages, encapsulation, inheritance - query language (t.ex. OQL) 9 Relational databases PROTEIN PROTEIN-ID DEFINITION SOURCE Homo sapiens adrenergic, beta--, receptor ARTICLE ARTICLE-ID Collins Daniel PROTEIN-ID ARTICLE-ID Cloning of the cdna for the. Cloning of the cdna for the. Cloning of the cdna for the. Cloning of the cdna for the. Cloning of the cdna for the. Cloning of the cdna for the. Human beta - and beta -adrenergic receptors Human beta - and beta -adrenergic receptors Human beta - and beta -adrenergic receptors Human beta - and beta -adrenergic receptors 0 Relational databases PROTEIN PROTEIN-ID DEFINITION SOURCE Homo sapiens adrenergic, beta--, receptor ARTICLE- ARTICLE-ID ARTICLE- ARTICLE-ID PROTEIN-ID ARTICLE-ID SQL select source from protein where accession = ; Collins Daniel Cloning of the cdna for the beta -adrenergic receptor Human beta - and beta - adrenergic receptors: structurally and functionally related receptors derived from distinct genes PROTEIN PROTEIN-ID DEFINITION SOURCE Homo sapiens adrenergic, beta--, receptor SQL select title from protein, article-title, reference where protein.accession = and protein.protein-id = reference.protein-id and reference.article-id = article-title.article-id; PROTEIN PROTEIN-ID DEFINITION SOURCE Homo sapiens adrenergic, beta--, receptor PROTEIN-ID ARTICLE-ID ARTICLE- ARTICLE-ID Cloning of the Human beta - From relational to object model CASE CAD office automation multimedia applications 3 4

5 Object-Oriented Databases (OODB) World is modeled using objects. An object has a state (value) and a behavior (operations). Persistent objects - permanent storage (sometimes transient objects are allowed) Object An object has an object identifier (OID) that is not visible to the user. OID cannot be changed. object versus value (a value has no OID) object structure can be arbitrarily complex (atom, tuple, set, list, bag, array) 5 6 Example - object state o(id, tuple, <accession:, source :, definition: Homo sapiens adrenergic, reference: o>) o(id, set, {o3,o4}) Example - object state o3(id3, tuple, <title: `Cloning of, author: o5 >) o4(id4, tuple, <title: `Human beta-, author: o6 >) o5(id5, list, [, Collins, Daniel,,, ]) o6(id6, list, [,,, ]) Remark: These examples do not use a standard syntax 7 8 SOURCE Homo sapiens adrenergic, beta--, receptor Classes list Cloning of set Collins Daniel list DEFINITION Human beta- define class protein type tuple ( accession: string; source : string; definition: string; reference: set(article); ); operations create-protein(string,string,string,set(article)): protein; get-accession: string; get-source: string; get-definition: string; get-references: set(article); add-reference(article): void; end protein; 9 30

6 Classes define class article type tuple ( title: string; author: list(string); ); operations create-article(string, list(string)): article; get-title string; get-authors: list(string); print-article-info string; end article; 3 Example program program variables: article, article, protein; begin article := create-article( Cloning., list(, Collins, Daniel,,, )); protein := create-protein(,, Homo sapiens adrenergic, set(article)); article := create-article( Human beta-., list(,,, ]); protein.add-reference(article); end; 3 Operations encapsulation: operation = interface + body - interface: how is the operation called? What is the result of the operation? > visible to user, used in programs - body: how is the operation implemented? > invisible for user program is based on message passing Inheritance journal-article subtype-of article: journal-name journal-volume page-numbers journal-article inherits all attributes and operations from article and has in addition also journal-name, journalvolume and page-numbers as attributes -protein subtype-of protein (source = ) Operator overloading The same operator name can be used for different implementations example: print-article-info for article prints information on title and author. print-article-info for journal-article prints information on title, author and also on the journal s name, volume and page number.. Query language OQL select from where select distinct from where iterator variables path expressions struct 35 36

7 select o.source from o in protein where o.accession = ; SOURCE select struct (accession: o.accession, source: o.source) from o in protein where in (select a.author from a in o.reference); SOURCE set Query language OQL OQL also allows: views aggregation special operations for list and array (first, last, nth) order-by group-by Third-Generation DB Manifesto Objects and Rules - rich type system - inheritance - methods and encapsulation - unique identifiers - rules (triggers, constraints) Third-Generation DB Manifesto DBMS functionality - access through non-procedural high-level language - specify collections intensionally and extensionally - updatable views - no performance indicators in the model Third-Generation DB Manifesto Open systems - accessible via several high-level languages - persistency - SQL-like language - queries and answers are the lowest level of communication between client and server 4 4

8 OODBS Manifesto Thou shalt... complex objects object identity encapsulation types and classes inheritance overriding, overloading, late binding OODBS Manifesto computational completeness extensibility persistence secondary storage management concurrency recovery query facility OODBS Manifesto Optional multiple inheritance distribution long and nested transactions versions Semi-structured data data that is not just text, but that is not as well structured as data in databases often seen in web databanks and when integrating databanks Thou shalt question the golden rules Semi-structured data - properties irregular structure implicit structure partial structure data guide vs schema large data guides Semi-structured data - model Network of nodes object model (oid) query: path search in the network 47 48

9 Cloning of SOURCE Collins Daniel Homo sapiens adrenergic, beta--, receptor DEFINITION Human beta- select source where accession = ; SOURCE Knowledge bases select reference.title where accession = ; select #p.title where accession = ; Cloning of Human beta- Often based on a logic Query answering based on inference mechanism Knowledge bases often fit in main memory Useful for ontologies 5 5 Knowledge bases (F) source(, Human) (R) source(p?,human) => source(p?,mammal) (R) source(p?,mammal) => source(p?,vertebrate) Q:?- source(, Vertebrate) A: yes Q:?- source(x?, Mammal) A: x? = 53 How is the information stored? (low level) Real life information management system Model Processing of queries and updates Access to stored data Physical databank Answers 54

10 How is the information accessed? (system level) Real life information Model Answers management system Processing of queries and updates Access to stored data Physical databank How is a databank recovered after a crash? Recovery when system crash system error concurrency error disk error catastrophy How to keep track of changes of the data over time? Real life information Management System Model Processing of queries and updates Access to stored data Answers How to keep track of changes of the data over time? How can several users access and update information in a databank at the same time? data evolution (versioning) schema evolution Real life information management system Model Processing of queries and updates Access to stored data 59 Physical databank 60

11 Number-of-proteins = Number-of-proteins + 30 Transactions Administrator TIME Administrator Read(Number-of-proteins) Read(Number-of-proteins) Number-of-proteins = Number-of-proteins + 5 Write(Number-of-proteins) Authorization Authorization mechanisms (implicit/explicit, strong/weak, positive/negative) Extensions for the OO model (class, inheritance, composite objects, versions) Write(Number-of-proteins) 6 6 How can a user access information in several databanks at the same time? query 63 Access to multiple databanks - problems User needs to know where to find information and how to retrieve it (UI, QL). Terminology Different databanks may store different information about an entity. Same names in different databanks may refer to different entities. Query planning is difficult. 64 Integration methods Federations Data warehouses Mediators 65 Object-oriented and object-relational databases Data models and query languages Query processing and optimization Versioning and schema evolution Authorization Storage management and indexing (XML and databases) 66

Copyright 2016 Ramez Elmasri and Shamkant B. Navathe

Copyright 2016 Ramez Elmasri and Shamkant B. Navathe Chapter 12 Outline Overview of Object Database Concepts Object-Relational Features Object Database Extensions to SQL ODMG Object Model and the Object Definition Language ODL Object Database Conceptual