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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.
Status of this document
Version: 17 Oct. 2004
Edited: Kevin Thiele (Centre for Biological Information Technology, University of Queensland), with financial support from the Gordon and Betty Moore Foundation (www.moore.org).
Complete documentation of the SDD Schema is available on the SDD web site.
To contribute to the discussion on the SDD Standard and to comment on this document, please join the SDD Wiki or SDD discussion list.
Relationship between SDD and other TDWG standards
TDWG maintains and is developing other standards that relate to the SDD standard, including the Access to Biological Collections Data (ABCD) and Taxonomic Concept Names standards. TDWG is developing a common, shared base schema for SDD and these related schemas, called UBIF.
SDD Version History
Version 0.9 beta: released for comment December 2003.
Version 1.0
beta: released August 2004
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.
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)
Discaria pubescens (Brongn.) Druce
Rigid, spreading shrub to c. 1 m high and wide; stems glabrous. Leaves soon
deciduous, c. oblong, to 10 mm long, 3 mm wide, obtuse or minutely mucronate
within an apical notch, margins minutely toothed, surfaces glabrous or a few
hairs present near tip; stipules dark reddish-brown, c. 1 mm long, often
shallowly joined around the node, pubescent on inner face; spines stout, 1.5-4
cm long. Flowers white, solitary or in few-flowered axillary cymes, sometimes
congested on short apical shoots; pedicels 2-3 mm long; hypanthium c. 1.5 mm
long; sepals somewhat spreading, 1-1.5 mm long; petals attached at throat of
hypanthium, c. 1 mm long; stamens subequal to and weakly hooded by petals;
disc prominent, lining base of hypanthium, obscurely 5-angled; style minute.
Capsule prominently 3-lobed, 4-5 mm diam., the valves separating incompletely
at maturity and splitting dorsally and medially.
from Walsh, N.G. (1999) Rhamnaceae, in N.G.Walsh & T.J.Entwisle, Flora of Victoria Volume 4, Dicotyledons, Cornaceae to Asteraceae (Inkata Press: Melbourne)
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.
| Key to Ascomycete genera | |
|
Ascus unitunicate |
|
| Clypeus present around ostiolar neck | |
| Clypeus poorly developed | Glomerella |
| Clypeus well developed | Hyllachora |
| Clypeus lacking | |
| Ascus widest in middle | Physalospora |
| Ascus clavate or cylindrical | Glomerella |
| Ascus bitunicate | |
| Ascostroma uniloculate | Guignardia |
| Ascostroma muliloculate | Botryosphaeria |
| 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 1.2.2) comprise highly structured data used in computer identification and analysis programs such as Lucid (www.lucidcentral.org) , DELTA (hyperlink) and a suite of phylogenetic analysis programs such as PAUP (hyperlink).
|
Lucid Interchange Format (LIF) file
#Lucid Interchange Format File v. 2.1 |
DELTA file
*SHOW: Gentianella - character list. Last revised 16 April 1997. |
|
Raw data descriptions (Box 1.2.3) 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.
| 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
2.0 Basic structure of a simple SDD instance document
The simplest possible description comprises a single descriptive statement about an organism, taxon or object. An example of such a description is given in Box. 2.0.1, and its SDD representation in Example 2.0.1.
Viola hederacea Labill.
Leaves simple
<?xml version='1.0' encoding='UTF-8'?> <Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.tdwg.org/2004/UBIF" xsi:schemaLocation="http://www.tdwg.org/2004/UBIF SDD.xsd"> <Dataset> <Derivation datetime='2004-10-17T06:50:13'> <Generator name='By Hand' version='1'/> </Derivation> <ExternalDataInterface> <ClassNames> <ClassName id='1'> <Label> <Representation language='en'> <Text>Viola hederacea</Text> </Representation> </Label> </ClassName> </ClassNames> <Agents> <Agent id='1'> <Label> <Representation language='en'> <Text>A. Botanist</Text> </Representation> </Label> </Agent> </Agents> </ExternalDataInterface> <Metadata> <Description> <Representation language='en'> <Title>Descriptive statement for a Viola</Title> </Representation> </Description> </Metadata> <DescriptiveData> <Terminology> <Characters> <CategoricalCharacter id='1'> <Label> <Representation language='en'> <Text>Leaf complexity</Text> </Representation> </Label> <States> <StateDefinition id='1'> <Label> <Representation language='en'> <Text>simple</Text> </Representation> </Label> </StateDefinition> </States> </CategoricalCharacter> </Characters> </Terminology> <CodedDescriptions> <CodedDescription id='0'> <Header> <ClassName ref='1'/> </Header> <SummaryData> <Categorical ref='1'> <State ref='1'/> </Categorical> </SummaryData> </CodedDescription> </CodedDescriptions> </DescriptiveData> </Dataset> </Datasets>
In the SDD document in Box 2.0.1, data are wrapped in a <Dataset> element. Several datasets may be wrapped in a single SDD document, in the <Datasets> container element.
The <Derivation> element provides information about the way in which the data were created, including the date and time stamp at which the data was generated, and the application or other method by which the document was created.
The <ExternalDataElement> is used to wrap data that may be provided by an external web service (in this case, the data are internal to the document). In this element, the name of the taxon (Viola hederacea) is provided in the <Classes> element, and the name of the author of the document in the <Agents> element
Metadata for the project that provided the data is given in the <Metadata> element. In this case, only a title for the data set is provided.
The description is provided in the <DescriptiveData> element, using a character and state (character = Leaf complexity; state = simple) defined in the <Terminology> element. The <CodedDescription> element contains the description itself, using references to identify the taxon (class), character and state being described.
FAQ: Why are SDD documents so verbose and complex?
3.0 Beyond the simple instance...
Example 2.0.1 describes only the most simple of SDD structures. To go
further, the Primer provides several pathways or streams, depending on what
you wish to use SDD for. On each stream, the Primer will introduce the basic
concepts first, then branch to more complex examples.
Before entering the first stream, you should understand the
<Derivation> and
<ExternalDataInterface>
elements.
For more information on the relationships between the SDD and UBIF schemas, read the topic SDD and UBIF Schemas.
The streams are:
Using SDD for coded data
Using SDD for natural language descriptions
Using SDD for dichotomous keys
Using SDD for raw observation data
KRT Last Edit: 16 Jan 04
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