Introducing Objects into Relational Databases Jörn Vorwald & Steffen Flemming Institute of Plant Genetics and Crop Plant Research Gatersleben Corrensstraße 3, D Gatersleben,

Introduction While modeling a new information system for the gene bank of the Institute of Plant Genetics and Crop Plant Research, Gatersleben (IPK), the idea of introducing object oriented concepts into the database model focussing the requirements of gene bank germplasm and data management came up. As a result, a sophisticated model of objects handled by the information system has been introduced into the model. Even if these concepts will not be introduced into the GBIS * database due to non-technical reasons, the approach seemed to be helpful for other databases or information systems to handle complexity and to avoid disadvantages of the relational paradigm. In the following presentation, the evolution of objects in GBIS will be described by example and in general. Huldén (2003) introduced a parallel development of a generic concept for multiple used entities into plant genetic resources community. Our approach has been developed since 2002 and became much more excessive. * GBIS = Gene Bank Information System Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Institutions, phase 1 Institution splitted_into merged_to (collecting) Expedition Project/ Experiment Person structures_in employs leads participates_in is_a structures_in Identifying forms of institutions or related objects Identifying self reflecting relationships of objects Identifying relationships between objects Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Replacing (multiple) relationships between objects by special „is A“ relationships Recreating former relationships between objects as self reflecting relationship of root object Institution splitted_into merged_to (collecting) Expedition Project/ Experiment Person structures_in employs leads participates_in is_a structures_in is_a employsleads participates_in Institutions, phase 2 Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Role Institution institutionId Role roleId role roleGerman roleRemark * validityStart validityEnd validityRemark to * * Abstracting all self reflecting relationships Generating database model Institution splitted_into merged_to structures_in employsleads participates_in Institutions, phase 3 Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Identifying all types of institutions or objects can be handled as institutions in the context of interest (here: managing plant genetic resources) Person User User group Project Experiment Collecting expedition Specimen collection (Germplasm) Core collection International crop database Institution sensu stricto Research institute IPK department Botanical garden Gene bank IPK curator group Breeder Governmental agency Non-governmental organisation Institutions, phase 4 Person User User group Project Experiment Collecting expedition Specimen collection (Germplasm) Core collection International crop database Institution sensu stricto Research institute IPK department Botanical garden Gene bank IPK curator group Breeder Governmental agency Non-governmental organisation Identifying a hierarchy Generating a database representation of the hierarchy Institution institutionId Role * to * * patternId pattern patternGerman patternRemark Pattern 1 isOf * * has 1 Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Identifying all types of relationships of interest between institutions Institutions, phase 5 ((person) v (institution s. str.)) leads (project) (person) heads (institution s. str.) (institution s. str.) subdivides into (person) (user group) subdivides into (user) (project) subdivides into ((person) v (institution s. str.)) (institution) devided into (institution) (institution) merged to (institution) ((institution s. str.) v (person)) carries out (experiment) (person) is responsible partner for ((collecting expedition) v (experiment)) ((institution s. str.) v (person)) maintains ((specimen collection) v (international crop database)) * syntax: (parent) role (child) | valid for all sub-patterns v represents logical ‚or‘ ^ represents logical ‚and‘ Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases *

Identifying other main patterns within the model Abstraction, phase 1 (Germplasm) accessions Samples (as materialisation of accessions) Specimens (as materialisation of accessions and non-accessions) Harvests Cultivations Sites (as geographical super-class) Publications Pictures Observation acts Descriptors Registers Transactions Object SampleAccession Specimen Site isAn 1 1 Institution Register PicturePublication CultivationHarvest ObservationAct Transaction isAn Descriptor isAn 1 1 Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Generating a database schema on objects Abstraction, phase 2 Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases Institution institutionId Role * to * * patternId pattern patternGerman patternRemark Pattern 1 isOf * * has 1 Object objectId Role * to * * patternId pattern patternGerman patternRemark Pattern 1 isOf * * has 1

Identifying other sub-patterns within the model I Abstraction, phase 3 Accessions Regular accession Potential accession Other accession Samples Seed sample In vitro sample Cryo sample Vegetative sample Root Bulbil Tuber Specimens Spike Wet preparation Seed/fruit specimen Herbarium specimen Complete Plant Publications Journal paper Monograph Book paper Edited book Informal paper Pictures Drawing Photo Colour Photo Colour Slide Digital Photo Scan Monochrome Slide Observation acts Descriptors Seedling I Seedling II Leaf Floret Cotyledon Stand of fruit Harvests Cultivations Sites Diversity area Continent Continental region Country Region Collecting site Federal state County > Township >> Cultivation site Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Abstraction, phase 3 Registers List Collecting list Sowing list Spring list Autumn list Safety duplicate sample box Scoring schema Document Formal document Phytosanitary certificate Material transfer agreement Informal document Worksheet Request Order request Delivery request (Management) Book Entry book Field book Group book Ancestry book Register card Cultivation register Main register Botanical register Cultivar register Transactions Order Delivery Material transaction Safety duplicate transaction Information transaction Specimen transaction Identifying other sub-patterns within the model II Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Identifying all types of relationships of interest between all objects I Abstraction, phase 4 (sample) bears (sample) (picture) illustrates ((accession) v (sample) v (specimen) v (institution) v (site)) (specimen) cirumstantiates (accession) (institution) publishes (publication) ((institution s. str.) v (person) v (collecting expedition)) collected at (collecting site) (institution s. str.) creates (formal document) ((institution s. str.) v (person) v (collecting expedition)) creates (collecting list) (accession) originally materialised in (sample) (accession) materialised in (sample) ((institution s. str.) v (person)) borrows (specimen) (publication) informs of ((project) v (accession) v (sample) v (specimen) v (collecting site)) (digital photo) copies ((picture) v (register)) (site) structures in (site) (list) lists ((accession) v (sample) v (institution) v (specimen) v (picture) v (list)) (publication) contains (picture) ((institution s. str.) v (person)) situated in (country) (experiment) observed at (cultivation site) (institutions s. str.) keeps (specimen) ((book) v (worksheet)) documents (sample) (worksheet) logs (experiment) * syntax: (parent) role (child) | valid for all sub-patterns v represents logical ‚or‘ ^ represents logical ‚and‘ * Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Identifying all types of relationships of interest between all objects II Abstraction, phase 4 (phytosanitary certificate) attests ((accession v (sample)) (site) is country of origin of ((accession) v (specimen)) (site) is collecting site of ((accession) v (specimen)) (site) is diversity area of (accession) (accession) splitted into (accession) (sample) splitted into (sample) (experiment) tests ((accession) v (sample)) (register card) registers ((accession) v (harvest) v (cultivation)) (gene bank) holds (accession) (specimen collection) extracted (specimen) ((institution s. str.) v (person) v (collecting expedition)) collected ((accession) v (specimen)) ((institution s. str.) v (person)) donated (accession) (accession) is duplicate of (accession) (institution) administers ((core collection) v (international crop database)) ((institution s. str.) v (person)) bred (accession) (IPK curator group) manages (accession) (user) creates (list) (experiment) implements (scoring schema) Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases

Results Summary generic solution for handling multiple relationships between database entities 13 main patterns of objects with 76 sub-patterns of several levels within the hierarchy identified as important for IPK‘s germplasm information system GBIS 46 types of relationships between the main or sub-patterns identified Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases central administration of all objects and their relationships, e. g. for barcode based identifications avoiding trigger based constructions in relational schemas, e. g. arcs extensibility of concept: easy introduction of new objects and relationships to other objects into database schema Advantages Disadvantages join of role table for correct identification of kind of relationship between objects rapid increase of object_to_object-table solution: indexing and partitioning additional join of pattern table solution: direct join of tables of inherited objects with object_to_object-table

Acknowledgement and Reference We thank all our colleagues for helpful discussions, namely Dr. Helmut Knüpffer and Stephan Weise from IPK, Dr. Theo van Hintum and Frank Menting from the Centre for Genetic Recources The Netherlands (CGN). Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases Huldén, M. (2003): Data abstraction models for PGR databases. Presentation on EPGRIS final conference: PGR documentation and information in Europe – towards a sustainable and user-oriented information infrastructure, September, Prague, Czech Republic. The project „Establishment of a central federal ex situ genebank for agricultural and horticultural crop plants: Fusion of genebanks of IPK and BAZ Braunschweig“ is kindly sponsored by the German Federal Ministry of Education and Research (BMBF).