SddIntroduction

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KevinThiele - Fri Sep 15 2006 - Version 1.19
Parent topic: SddContents

SDD Part 0: Introduction and Primer to the SDD Standard

Abstract

SDD Part 0 is a non-normative introduction to the Taxonomic Databases Working Group SDD (Structure of Descriptive Data) Standard. Its intention is to provide a background, introduction and primer to the SDD Standard, with examples. Since the SDD Standard is a work-in-progress, this document will be updated from time to time.

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1.0 Introduction

1.1 Background to the TDWG-SDD Subgroup

In September 1998 the Taxonomic Databases Working Group (TDWG) of the International Union of Biological Sciences (IUBS) established the Structure of Descriptive Data (SDD) subgroup. TDWG’s role is to facilitate and manage the development of international standards in the taxonomic domain. The SDD subgroup was established to develop an international XML-based standard for capturing and managing descriptive data for organisms.

Development of the SDD standard was initiated in response to recognition that the existing standard previously endorsed by TDWG – the DELTA data standard developed at CSIRO in Canberra from 1971 and adopted by TDWG as a descriptive data standard in 1991 – had become inadequate (FAQ: Why not continue to use DELTA?).

The SDD subgroup began discussing and scoping a standard through an email discussion group in November 1999 (see the SDD email list archives). Considerable progress has been made at face-to-face meetings amongst a small group of core contributors, in Nov. 2001 (Canberra), Oct. 2002 (Sao Paulo), Feb. 2003 (Paris), October 2003 (Lisbon), May 2004 (Berlin) and Oct. 2004 (Christchurch).

1.2 The nature of descriptive data in taxonomy

In taxonomy, descriptive data takes a number of very different forms.

Natural-language descriptions (Box 1.2.1) are semi-structured, semi-formalised descriptions of a taxon (or occasionally of an individual specimen). They may be simple, short and written in plain language (if used for a popular field guide), or long, highly formal and using specialised terminology when used in a taxonomic monograph or other treatment.

Box 1.2.1 - A typical natural language description

Red Knot (Calidris canutus)
Stout wader with bill same length as head, crown unstreaked, narrow white bar in wing, pale rump with grey barring, shortish olive legs. Non-breeding: grey above with narrow pale edging to feathers, pale eyebrow, smudged sides to neck with faint spotting. Juvenile: feathers of back edged white with dark subterminal bar, breast more heavily spotted pale buff and flanks barred, crown faintly streaked. Breeding: rufous underparts, feathers of back rufous patterned with black. Voice: 'knut-knut', `nyui , high-pitched `toowit-wit'.

from Slater, P., Slater, P. & Slater, R. (2001) The Slater Field Guide to Australian Birds  (Reed New Holland: Sydney)

Dichotomous keys (Box 1.2.2) are specialised identification tools comprising fragments of descriptive data arranged in couplets forming a branching tree. Each fragment (lead) comprises a small (occasionally verbose) natural-language description.

Box 1.2.2 - A simple dichotomous key

Key to Australian skinks in the genus Ctenotus
1 Dark upper lateral zone with one or more distinct series of pale spots or blotches along the body 2
1a Dark upper lateral zone obscurely mottled or uniform with at most a few pale spots anteriorly 3
2 Fewer than 25 lamellae under the fourth toe; supralabials 7-8 (usually 7); prefrontals separated C. arcanus
2a More than 25 lamellae under the fourth toe; supralabials 8-9 (usually 8); prefrontals usually in contact C. alleni
3 Pale mid-lateral stripe passes over the hindlimb to continue along the tail C. inornatus
3a Pale mid-lateral stripe extends to groin, then continues along the front edge of the hindlimb C. coggeri
Coded descriptions (Box 1.2.3) comprise highly structured data used in computer identification and analysis programs such as Lucid (www.lucidcentral.org) , DELTA (www.delta-intkey.com) and phylogenetic analysis programs such as PAUP (www.paup.csit.fsu.edu).

Box 1.2.3 - Simple examples of coded descriptions

Lucid Interchange Format (LIF) file
#Lucid Interchange Format File v. 2.1

[..Character List..]
Distribution by region
  Tropical North
  Subtropical and Temperate East and South
  South West
  Arid & Semi-arid (Central)
  Island Territories
General habit
  tree
  shrub
  climber (woody or herbaceous)
  herb
  grass- or sedge-like plant
Seasonal longevity
  annual, biennial or ephemeral
  perennial

[..Taxon List..]
Acanthaceae
Aceraceae
Actinidiaceae
Agavaceae
Aizoaceae
Akaniaceae
Alangiaceae
Alismataceae
Aloaceae
Alseuosmiaceae

[..Main Data (txs)..]
101101111111
100100000101
101000000010
011110111111
101111111111
100100000011
101101000011
011111011111
011100100111
101100000010div
DELTA file
*SHOW: Gentianella - character list. Last revised 16 April 1997.

*CHARACTER LIST

#1. plants/
1. monocarpic/
2. polycarpic/

#2. <plants lifecycle>/
1. annual/
2. biennial/
3. perennial/

#3. height in flower/
<> cm/

#4. caudex/
1. unbranched/
2. branched/

*ITEM DESCRIPTIONS

# Gentianella amabilis/
1,2 2,3 3,3-13 4,1

# Gentianella antarctica/
1,1 2,1<Godley 1982> 3,1.6-22.0<Godley 1982> 4,1

# Gentianella antipoda/
1,1<Godley 1982> 2,2 3,3.5-9.8-24 4,1/2<depends on size of plant>

# Gentianella astonii/
1,2 2,3 3,15 4,2

# Gentianella cerina/
1,2 2,3 3,9-17 4,1/2

#Gentianella concinna/
1,1 2,1 3,2.7-15.0 4,1
 div 		 

 

Raw data descriptions (Box 1.2.4) usually comprise repeated measurements of parts of individual specimens, and are the basis from which the more abstracted descriptions in natural language and coded descriptions are derived. Few taxonomists consistently record and archive their raw data in a standardised format.

Box 1.2.4 - Example of raw (specimen) descriptive data

Specimen Spore length Spore width Spore colour
1 2 3 4 5 1 2 3 4 5
TJM45337 12 13 12 15 11 8 8 7 6 6 brown
TLM33466 15 18 17 17 15 10 8 9 9 10 yellow

1.3 Goals of SDD

The goal of the SDD standard is to allow capture, transport, caching and archiving of descriptive data in all the forms shown above, using a platform- and application-independent, international standard. Such a standard is crucial to enabling lossless porting of data between existing and future software platforms including identification, data-mining and analysis tools, and federated databases.

The SDD Standard:

  • provides a flexible, platform-independent data structure for the capture and storage of taxonomic descriptions
  • comprises a superset of data requirements of all existing programs
  • provides extension beyond existing programs where data requirements can be predicted
  • is readily extensible to account for future developments and data requirements
  • is human-readable (although it is assumed that in almost all cases standard descriptions will be machine-generated and processed)
  • is XML-based, and provides a schema for validation of documents.

It facilitates:

  • lossless porting of data between standard-aware applications
  • achievable progressive markup of legacy descriptions, particularly natural-language descriptions
  • comparability and, if possible, combinability of alternate descriptions of any one taxon
  • efficient multi-tasking of descriptions (one description serving alternate purposes)
  • archiving and sharing of raw and processed data

SDD documents may include all or some of the following:

  • Terminologies (characters, states, modifiers, char. trees, higher concepts)
  • Structured (coded) data
  • Sample data (e. g., measurements)
  • Unstructured natural language data
  • Natural language data with markup
  • Dichotomous or polytomous keys
  • Resources associated with descriptions (e. g., images, references, links)

SDD is currently not designed to accommodate:

  • Molecular sequence and other genetic data (future plans exist)
  • Occurrence and specimen data (e. g., distribution maps)
  • Complex ecological data such as models and ecological observations
  • Organism interactions (host-parasite, plant-pollinator, predator-prey, etc.)
  • Nomenclatural and formal systematic (rank) information

1.4 SDD Streams

This Primer is structured into several streams, each describing how SDD can help you with a specific task. For each stream, the Primer describes the core elements of SDD used to capture information related to the task, and provides examples extending from simple to complex.

The four main tasks (uses) of SDD are as follows:

Choose a link above to enter one of the SDD streams.

In addition to the streams, a number of SDD elements are common to all streams. Choose a link below to find out how to:

-- Main.KevinThiele - 07 Jul 2006