TAXIS 3.5 (Meyke 2004) is an all-encompassing biodiversity information management system
2.4. UML static class diagrams and ER models
UML static class diagrams are used during many general and abstract discussions to illustrate issues of generalization, composition, and dependency. Classes are represented by rectangles and connected by associations and composition relationships (Fig.5). The role of the relationship is presented on the branch that attaches to the entity with which the role starts. Different modeling traditions exist for the role naming pattern at the end of association and composition relationships (UML does not define a standard here). Fowler & Scott (2001) recommend to use a noun phrase and to omit the role name when possible. In this discussion, however, the more conventional verb-phrases for roles (“is applicable to”, “controls”, etc.) have been used. The cardinality (or
“multiplicity”, Table 1) of association and composition relationships is given at each end next to the role name. Generalization relationships are indicated with a white triangle (Fig.5 left, iden-tical to those used in the use case diagrams, Fig.3ff).
UML class representations may have up to three sections separated by horizontal lines: class name, attribute list, and operations (or “methods”). In the thesis the operations section is almost universally suppressed; the attributes sections is suppressed where irrelevant to the discussion.
Business use case System
use case
actor business
actor
Figure 4. Some UML use case dialects may use different sym-bols for system and business actors. In the present work the first icon always signifies a gen-eral, undifferentiated use case.
SuperClass attribute
SubClass1 attribute1
SubClass2 attribute2
CompositeClass attribute
Part 1 attribute
Part 2 attribute 1
0..*
1 1 role 1
0..1
role 2 0..*
RequiredClass attribute
Generalization hierarchy Aggregation hierarchy Dependency
Figure 5. Relationships in UML static class diagrams. On the left side two subclasses are derived from a superclass. The triangle has the form of an arrow pointing from specialized to general class. Subclasses inherit attributes and methods of the superclass. – In the middle, a class is connected with two component classes (Part 1, Part 2). Composition associations are indicated by black diamonds. Part 1 must occur (1:1 relationship), whereas Part 2 may be missing, occur-ring once or multiple times (1:0..* relationship; compare Table 1). Component classes may not belong to other classes. – A class association with multiplicities and role names is shown be-tween SuperClass and CompositeClass in the center. Role names for association ends are used only in the database UML models. – On the right side an additional class is connected with a dashed arrow indicating a dependency relationship (i.e., Part 2 depends on RequiredClass).
Table 1. Common multiplicity indicators (i. e., ranges of allowable cardinalities) used in UML class associations.
Multiplicity code Description Association is:
0..1 Zero or one Optional
1 Exactly one Required
0..* (or “*” alone) Zero or more Optional 1..* At least one Required n (for example: 6) Specific number Required
The entity relationship model for DiversityDescriptions (p.322) is also presented using UML static class diagrams. In parallel to the general acceptance of UML for general software design, this has become common practice in database modeling (compare Connolly & Begg 2002 and Naiburg & Maksimchuk 2001). Entity types are represented by class diagrams (limited to persis-tent classes, showing only persispersis-tent attributes, and having the “operations section” of the UML class icon suppressed).
Both a logical model (using UML) and a physical model (using a tabular documentation) are presented. The ER diagrams for the logical model are generated with Microsoft Visio for Enter-prise Architects; the tabular documentation with DiversityModelDocumenter version 2.6 (Hage-dorn 2004a). Because of the extensive discussion above, which ends in requirements beyond those fulfilled by DiversityDescriptions, version 1.9, no conceptual model is presented.
In the logical model, no explicit assumptions on referential integrity are made. Implicitly, all associations and compositions are assumed to be protected by referential integrity. Cascading updates are implied where primary key values are natural keys that may change during edits (i.e., they are not system keys). Furthermore, composition (symbolized by a black diamond at the pa-rent class) indicates that instances of the component classes can only exist as part of instances of the parent class. For these relationships cascading deletes may be assumed.
In the logical model of DiversityDescriptions the data types for attributes are indicated using a small selection of generic data types (Naiburg & Maksimchuk 2001, Table 2).
Table 2. Generic data types used in ER-/UML-class diagrams.
Generic data type Description
Boolean Logical values “true” and “false”; may be Null if not defined as required.
Byte Positive integer numbers in the range 0-255 Date Date, time, or data-with-time values
Double Real (floating-point) numbers with 15-16 digits of precision
Integer Integer numbers with 32 bit precision (= “Long” in older programming languages which consider int/integer as 16 bit).
Single Real (floating-point) numbers with 7 digits of precision String An unlimited number of Unicode characters
2.5. Abbreviations
ABCD Access to Biological Collections Data (TDWG) AFLP Amplified Fragment Length Polymorphism
(a molecular identification technique) ANOVA Analysis of Variance
CBIT Centre for Biological Information Technology, Australia
Ch. Chapter
CDEFD Common Data structure for European Floristic Databases, a concluded European concerted action project
CSIRO Commonwealth Scientific and Industrial Research Organisation, Australia DBMS Database Management System DDBJ DNA Data Bank of Japan
DELTA Descriptive Language for Taxonomy (p.19) DNA Deoxyribonucleic Acid
EMBL European Molecular Biology Laboratory ER Entity-relationship (… model, … diagram, etc.) Fig. Figure
GBIF Global Biodiversity Information Facility;
www.gbif.org
GLOPP Global Plant Pathogen Index GUID Globally Unique Identifier
ICBN International Code of Botanical Nomenclature ICZN International Code of Zoological Nomenclature
/ International Commission on Zoological Nomenclature
ID Identifier, i. e. a number or code uniquely identifying an object
IPR Intellectual Property Rights IT Information Technology
IUBS International Union of Biological Sciences JET Joint Engine Technology, a database
technology developed by Microsoft
LIF Lucid Interchange format, used by CBIT Lucid programs (p.21)
NCBI National Center for Biotechnology Information, USA
NEXUS (not an abbreviation: phylogenetic data exchange standard, p.18)
NLP Natural Language Processing (machine reasoning from human-written text) OCR Optical character recognition OMG Object Management Group OOP Object-oriented programming PAUP Phylogenetic Analysis Using Parsimony, a
NEXUS-based software package.
PDF Portable Document Format (proprietary format by Adobe)
RAPD Random Amplified Polymorphic DNA (a molecular identification technique) RDF Resource Description Framework; a
w3c-standard for resource metadata suitable for ontological reasoners.
RFLP Restriction Fragment Length Polymorphism (a molecular identification technique)
SDD Structure of Descriptive Data (a TDWG interest group) and the resulting standard (Structured Descriptive Data, p.20)
SQL Structured Query Language, a language for defining, manipulating, and querying relational databases
STR Short Tandem Repeat (a molecular identification technique)
TDWG Taxonomic Databases Working Group (www.tdwg.org)
UML Unified Modeling Language, a modeling standard of the OMG
URI Universal Resource Identifier (including universal resource names, URNs)
URL Uniform Resource Locator (the most common type of URI, e.g., “http://x.net”)
W3C Worldwide Web Consortium (“www” = “w3”) WIKI (not an abbreviation: name of a class of internet
collaboration tools, Hawaiian for “simple”) XML Extensible Markup Language
XPS XML Paper Specification