1235 lines
48 KiB
Plaintext
1235 lines
48 KiB
Plaintext
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head 1.19;
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access;
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symbols;
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locks; strict;
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1.19
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date 2006.09.15.04.13.54; author KevinThiele; state Exp;
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branches;
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next 1.18;
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1.18
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date 2006.09.11.01.28.24; author KevinThiele; state Exp;
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branches;
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next 1.17;
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1.17
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date 2006.09.08.01.13.01; author KevinThiele; state Exp;
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branches;
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next 1.16;
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1.16
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date 2006.09.07.07.04.47; author DonovanSharp; state Exp;
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branches;
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next 1.15;
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1.15
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date 2006.08.29.02.03.43; author DonovanSharp; state Exp;
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branches;
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next 1.14;
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1.14
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date 2006.07.10.01.47.04; author DonovanSharp; state Exp;
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branches;
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next 1.13;
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1.13
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date 2006.07.07.00.38.28; author KevinThiele; state Exp;
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branches;
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next 1.12;
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1.12
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date 2006.07.06.09.32.55; author KevinThiele; state Exp;
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branches;
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next 1.11;
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1.11
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date 2006.07.06.05.58.04; author DonovanSharp; state Exp;
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branches;
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next 1.10;
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1.10
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date 2006.07.05.01.27.30; author DonovanSharp; state Exp;
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branches;
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next 1.9;
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1.9
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date 2006.07.04.04.52.23; author DonovanSharp; state Exp;
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branches;
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next 1.8;
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1.8
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date 2006.06.07.05.42.53; author DonovanSharp; state Exp;
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branches;
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next 1.7;
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1.7
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date 2006.06.07.05.33.55; author DonovanSharp; state Exp;
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branches;
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next 1.6;
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1.6
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date 2006.06.07.01.26.11; author DonovanSharp; state Exp;
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branches;
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next 1.5;
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1.5
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date 2006.06.05.05.39.18; author DonovanSharp; state Exp;
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branches;
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next 1.4;
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1.4
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date 2006.06.05.04.22.19; author DonovanSharp; state Exp;
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branches;
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next 1.3;
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1.3
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date 2006.06.02.04.54.10; author DonovanSharp; state Exp;
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branches;
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next 1.2;
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1.2
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date 2006.06.01.07.43.52; author DonovanSharp; state Exp;
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branches;
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next 1.1;
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1.1
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date 2006.06.01.02.38.28; author DonovanSharp; state Exp;
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branches;
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next ;
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desc
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@@
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1.19
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log
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@none
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@
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text
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@%META:TOPICINFO{author="KevinThiele" date="1158293634" format="1.1" version="1.19"}%
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%META:TOPICPARENT{name="SddContents"}%
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---++SDD Part 0: Introduction and Primer to the SDD Standard
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---+++Abstract
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SDD Part 0 is a non-normative introduction to the [[http://www.tdwg.org][Taxonomic Databases Working Group][Name:_blank]] 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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---+++Status of this document and version history
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See [[DocumentStatus][DocumentStatus]]
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---++1.0 Introduction
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---+++1.1 Background to the TDWG-SDD Subgroup
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In September 1998 the [[http://www.tdwg.org][Taxonomic Databases Working Group ][Name:_blank]] (TDWG) of the [[http://www.iubs.org][International Union of Biological Sciences][Name:_blank]] (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.
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Development of the SDD standard was initiated in response to recognition that the existing standard previously endorsed by TDWG – the [[http://delta-intkey.com/][DELTA][Name:_blank]] data standard developed at CSIRO in Canberra from 1971 and adopted by TDWG as a descriptive data standard in 1991 – had become inadequate [[SddFaq][(FAQ: Why not continue to use DELTA?)]].
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The SDD subgroup began discussing and scoping a standard through an email discussion group in November 1999 (see the [[http://listserv.nhm.ku.edu/archives/tdwg-sdd.html][SDD email list archives][Name:_blank]]). 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).
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---+++1.2 The nature of descriptive data in taxonomy
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In taxonomy, descriptive data takes a number of very different forms.
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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.
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----++++Box 1.2.1 - A typical natural language description
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<table bgcolor="#ddddff" cellspacing="2" cellpadding="2" border="1" width="80%">
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<tr>
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<td>
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<p align="left">
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<b>Red Knot (Calidris canutus)</b><br>
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Stout wader with bill same length as head, crown unstreaked, narrow white bar
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in wing, pale rump with grey barring, shortish olive legs. Non-breeding:
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grey above with narrow pale edging to feathers, pale eyebrow, smudged sides
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to neck with faint spotting. Juvenile: feathers of back edged white with
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dark subterminal bar, breast more heavily spotted pale buff and flanks
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barred, crown faintly streaked. Breeding: rufous underparts, feathers of
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back rufous patterned with black. Voice: 'knut-knut', `nyui , high-pitched `toowit-wit'.</p>
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<p align="right">
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from Slater, P., Slater, P. & Slater, R. (2001) The Slater Field Guide to
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Australian Birds (Reed New Holland: Sydney)</p>
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</td>
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</tr>
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</table>
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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.
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----++++Box 1.2.2 - A simple dichotomous key
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<div>
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<table bgcolor="#ddddff" border="1" cellpadding="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table8">
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<tr>
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<td style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: solid; border-top-width: 1px; border-bottom-style: none; border-bottom-width: medium" colspan="3">
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<b>Key to Australian skinks in the genus <i>Ctenotus</i></b></td>
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</tr>
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<tr>
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<td width="50" style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: solid; border-top-width: 1px; border-bottom-style: none; border-bottom-width: medium">1</td>
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<td style="border-left-style: none; border-left-width: medium; border-right-style: none; border-right-width: medium; border-top-style: solid; border-top-width: 1px; border-bottom-style: none; border-bottom-width: medium">Dark upper lateral zone with one or more distinct series of
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pale spots or blotches along the body</td>
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<td width="114" valign="bottom" align="right" style="border-left-style: none; border-left-width: medium; border-right-style: solid; border-right-width: 1px; border-top-style: solid; border-top-width: 1px; border-bottom-style: none; border-bottom-width: medium">2</td>
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</tr>
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<tr>
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<td width="50" style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">1a</td>
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<td style="border-style: none; border-width: medium">Dark upper lateral zone obscurely mottled or uniform with at
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most a few pale spots anteriorly</td>
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<td width="114" valign="bottom" align="right" style="border-left-style: none; border-left-width: medium; border-right-style: solid; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">3</td>
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</tr>
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<tr>
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<td width="50" style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">2</td>
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<td style="border-style: none; border-width: medium">Fewer than 25 lamellae under the fourth toe; supralabials 7-8 (usually 7); prefrontals separated</td>
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<td width="114" valign="bottom" align="right" style="border-left-style: none; border-left-width: medium; border-right-style: solid; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">
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<i>C. arcanus</i></td>
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</tr>
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<tr>
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<td width="50" style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">2a</td>
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<td style="border-style: none; border-width: medium">More than 25 lamellae under the fourth toe; supralabials 8-9
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(usually 8); prefrontals usually in contact</td>
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<td width="114" valign="bottom" align="right" style="border-left-style: none; border-left-width: medium; border-right-style: solid; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">
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<i>C. alleni</i></td>
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</tr>
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<tr>
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<td width="50" style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">3</td>
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<td style="border-style: none; border-width: medium">Pale mid-lateral stripe passes over the hindlimb to continue
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along the tail </td>
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<td width="114" valign="bottom" align="right" style="border-left-style: none; border-left-width: medium; border-right-style: solid; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: medium">
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<i>C. inornatus</i></td>
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</tr>
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<tr>
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<td width="50" style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: medium; border-top-style: none; border-top-width: medium; border-bottom-style: solid; border-bottom-width: 1px">3a</td>
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<td style="border-left-style: none; border-left-width: medium; border-right-style: none; border-right-width: medium; border-top-style: none; border-top-width: medium; border-bottom-style: solid; border-bottom-width: 1px">Pale mid-lateral stripe extends to groin, then continues
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along the front edge of the hindlimb</td>
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<td width="114" valign="bottom" align="right" style="border-left-style: none; border-left-width: medium; border-right-style: solid; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: solid; border-bottom-width: 1px">
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<i>C. coggeri</i></td>
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</tr>
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</table>
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</div>
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Coded descriptions (Box 1.2.3) comprise highly structured data used in computer identification and analysis programs such as Lucid ([[http://www.lucidcentral.org][www.lucidcentral.org]]) , DELTA ([[http://www.delta-intkey.com][www.delta-intkey.com]]) and phylogenetic analysis programs such as PAUP ([[http://www.paup.csit.fsu.edu][www.paup.csit.fsu.edu]]).
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----++++Box 1.2.3 - Simple examples of coded descriptions
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<div>
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<table bgcolor="#ddddff" border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table9">
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<tr>
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<td width="50%">
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<div>
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Lucid Interchange Format (LIF) file</div>
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#Lucid Interchange Format File v. 2.1<br>
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<br>
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[..Character List..]<br>
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Distribution by region<br>
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Tropical North<br>
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Subtropical and Temperate East and South<br>
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South West<br>
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Arid & Semi-arid (Central)<br>
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Island Territories<br>
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General habit<br>
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tree<br>
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shrub<br>
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climber (woody or herbaceous)<br>
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herb<br>
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grass- or sedge-like plant<br>
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Seasonal longevity<br>
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annual, biennial or ephemeral<br>
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perennial<br>
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<br>
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[..Taxon List..]<br>
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Acanthaceae<br>
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Aceraceae<br>
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Actinidiaceae<br>
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Agavaceae<br>
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Aizoaceae<br>
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Akaniaceae<br>
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Alangiaceae<br>
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Alismataceae<br>
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Aloaceae<br>
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Alseuosmiaceae<br>
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<br>
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[..Main Data (txs)..]<br>
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101101111111<br>
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100100000101<br>
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101000000010<br>
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011110111111<br>
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101111111111<br>
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100100000011<br>
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101101000011<br>
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011111011111<br>
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011100100111<br>
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101100000010</div>
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</td>
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<td width="50%">
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<div>
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DELTA file</div>
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*SHOW: Gentianella - character list. Last revised 16 April 1997.<br>
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<br>
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*CHARACTER LIST <br>
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<br>
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#1. plants/<br>
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1. monocarpic/<br>
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2. polycarpic/<br>
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<br>
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#2. <plants lifecycle>/<br>
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1. annual/<br>
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2. biennial/<br>
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3. perennial/<br>
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<br>
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#3. height in flower/<br>
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<> cm/<br>
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<br>
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#4. caudex/<br>
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1. unbranched/<br>
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2. branched/<br>
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<br>
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*ITEM DESCRIPTIONS <br>
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<br>
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# Gentianella amabilis/<br>
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1,2 2,3 3,3-13 4,1<br>
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<br>
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# Gentianella antarctica/<br>
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1,1 2,1<Godley 1982> 3,1.6-22.0<Godley 1982> 4,1<br>
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<br>
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# Gentianella antipoda/<br>
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|
|
1,1<Godley 1982> 2,2 3,3.5-9.8-24 4,1/2<depends on size of plant><br>
|
||
|
|
<br>
|
||
|
|
# Gentianella astonii/<br>
|
||
|
|
1,2 2,3 3,15 4,2<br>
|
||
|
|
<br>
|
||
|
|
# Gentianella cerina/<br>
|
||
|
|
1,2 2,3 3,9-17 4,1/2<br>
|
||
|
|
<br>
|
||
|
|
#Gentianella concinna/<br>
|
||
|
|
1,1 2,1 3,2.7-15.0 4,1<br>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
</td>
|
||
|
|
<td width="50%"> <p> </td>
|
||
|
|
</tr>
|
||
|
|
</table>
|
||
|
|
|
||
|
|
</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
|
||
|
|
|
||
|
|
<div>
|
||
|
|
<table bgcolor="#ddddff" border="1" width="80%" cellspacing="0" id="table10" cellpadding="0">
|
||
|
|
<tr>
|
||
|
|
<td rowspan="2" align="center">Specimen</td>
|
||
|
|
<td colspan="5" align="center">Spore length</td>
|
||
|
|
<td colspan="5" align="center">Spore width</td>
|
||
|
|
<td width="163" rowspan="2" align="center">Spore colour</td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="25" align="center">1</td>
|
||
|
|
<td width="25" align="center">2</td>
|
||
|
|
<td width="25" align="center">3</td>
|
||
|
|
<td width="25" align="center">4</td>
|
||
|
|
<td width="25" align="center">5</td>
|
||
|
|
<td width="25" align="center">1</td>
|
||
|
|
<td width="25" align="center">2</td>
|
||
|
|
<td width="25" align="center">3</td>
|
||
|
|
<td width="25" align="center">4</td>
|
||
|
|
<td width="25" align="center">5</td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td align="center">TJM45337</td>
|
||
|
|
<td width="25" align="center">12</td>
|
||
|
|
<td width="25" align="center">13</td>
|
||
|
|
<td width="25" align="center">12</td>
|
||
|
|
<td width="25" align="center">15</td>
|
||
|
|
<td width="25" align="center">11</td>
|
||
|
|
<td width="25" align="center">8</td>
|
||
|
|
<td width="25" align="center">8</td>
|
||
|
|
<td width="25" align="center">7</td>
|
||
|
|
<td width="25" align="center">6</td>
|
||
|
|
<td width="25" align="center">6</td>
|
||
|
|
<td width="163" align="center">brown</td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td align="center">TLM33466</td>
|
||
|
|
<td width="25" align="center">15</td>
|
||
|
|
<td width="25" align="center">18</td>
|
||
|
|
<td width="25" align="center">17</td>
|
||
|
|
<td width="25" align="center">17</td>
|
||
|
|
<td width="25" align="center">15</td>
|
||
|
|
<td width="25" align="center">10</td>
|
||
|
|
<td width="25" align="center">8</td>
|
||
|
|
<td width="25" align="center">9</td>
|
||
|
|
<td width="25" align="center">9</td>
|
||
|
|
<td width="25" align="center">10</td>
|
||
|
|
<td width="163" align="center">yellow</td>
|
||
|
|
</tr>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
---+++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:
|
||
|
|
|
||
|
|
* [[CodedData][Using SDD for coded summary descriptions]]
|
||
|
|
* [[CodedSampleDescription][Using SDD for coded raw (sample) descriptions]]
|
||
|
|
* [[NaturalLanguageDescriptions][Using SDD for natural language descriptions]]
|
||
|
|
* [[DichotomousKeys][Using SDD for dichotomous (or polytomous) identification keys]]
|
||
|
|
|
||
|
|
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:
|
||
|
|
|
||
|
|
* [[TechnicalMetadata][Describe metadata for a providing application]]
|
||
|
|
* [[DatasetMetadata][Describe metadata for an SDD dataset]]
|
||
|
|
* [[SddMedia][Attach media (images etc) to SDD items]]
|
||
|
|
|
||
|
|
-- Main.KevinThiele - 07 Jul 2006@
|
||
|
|
|
||
|
|
|
||
|
|
1.18
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="KevinThiele" date="1157938104" format="1.1" version="1.18"}%
|
||
|
|
d18 1
|
||
|
|
a18 1
|
||
|
|
Development of the SDD standard was initiated in response to recognition that the existing standard previously endorsed by TDWG – the [[http://biodiversity.uno.edu/delta/][DELTA][Name:_blank]] data standard developed at CSIRO in Canberra from 1971 and adopted by TDWG as a descriptive data standard in 1991 – had become inadequate [[SddFaq][(FAQ: Why not continue to use DELTA?)]].
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.17
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="KevinThiele" date="1157677981" format="1.1" reprev="1.17" version="1.17"}%
|
||
|
|
d9 1
|
||
|
|
a9 1
|
||
|
|
---+++Status of this document
|
||
|
|
a336 1
|
||
|
|
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.16
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1157612687" format="1.1" version="1.16"}%
|
||
|
|
d7 1
|
||
|
|
a7 1
|
||
|
|
SDD Part 0 is a non-normative introduction to the [[http://www.tdwg.org][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.
|
||
|
|
d16 1
|
||
|
|
a16 1
|
||
|
|
In September 1998 the [[http://www.tdwg.org][Taxonomic Databases Working Group ]] (TDWG) of the [[http://www.iubs.org][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.
|
||
|
|
d18 1
|
||
|
|
a18 1
|
||
|
|
Development of the SDD standard was initiated in response to recognition that the existing standard previously endorsed by TDWG – the [[http://biodiversity.uno.edu/delta/][DELTA]] data standard developed at CSIRO in Canberra from 1971 and adopted by TDWG as a descriptive data standard in 1991 – had become inadequate [[SddFaq][(FAQ: Why not continue to use DELTA?)]].
|
||
|
|
d20 1
|
||
|
|
a20 1
|
||
|
|
The SDD subgroup began discussing and scoping a standard through an email discussion group in November 1999 (see the [[http://listserv.nhm.ku.edu/archives/tdwg-sdd.html][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).
|
||
|
|
d337 1
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.15
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1156817023" format="1.1" reprev="1.15" version="1.15"}%
|
||
|
|
d18 1
|
||
|
|
a18 1
|
||
|
|
Development of the SDD standard was initiated in response to recognition that the existing standard previously endorsed by TDWG – the [[http://biodiversity.uno.edu/delta/][DELTA]] data standard developed at CSIRO in Canberra from 1971 and adopted by TDWG as a descriptive data standard in 1991 – had become inadequate [[SddFaq#DeltaFaq][(FAQ: Why not continue to use DELTA?)]].
|
||
|
|
a336 1
|
||
|
|
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.14
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1152496024" format="1.1" version="1.14"}%
|
||
|
|
d28 4
|
||
|
|
d34 1
|
||
|
|
a34 1
|
||
|
|
<td>Box 1.2.1 - A typical natural language description</div>
|
||
|
|
d53 3
|
||
|
|
d337 1
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.13
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="KevinThiele" date="1152232708" format="1.1" reprev="1.13" version="1.13"}%
|
||
|
|
d316 4
|
||
|
|
a319 4
|
||
|
|
* Using SDD for coded summary descriptions
|
||
|
|
* Using SDD for coded raw (sample) data
|
||
|
|
* Using SDD for natural language descriptions
|
||
|
|
* Using SDD for dichotomous (or polytomous) identification keys
|
||
|
|
d325 3
|
||
|
|
a327 3
|
||
|
|
* Describe metadata for a providing application
|
||
|
|
* Describe metadata for an SDD dataset
|
||
|
|
* Attach media (images etc) to SDD items
|
||
|
|
a329 1
|
||
|
|
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.12
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="KevinThiele" date="1152178375" format="1.1" version="1.12"}%
|
||
|
|
d30 1
|
||
|
|
a30 1
|
||
|
|
<td>Box 1.2.1 - Typical natural language descriptions</div>
|
||
|
|
d43 1
|
||
|
|
a43 19
|
||
|
|
<p>
|
||
|
|
<b>Discaria pubescens (Brongn.) Druce<br>
|
||
|
|
</b>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.</p>
|
||
|
|
</p>
|
||
|
|
<p align="right">
|
||
|
|
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)</td>
|
||
|
|
a48 67
|
||
|
|
<div>
|
||
|
|
<table bgcolor="#ddddff" border="0" cellpadding="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table7" >
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px; border-top-style: solid; border-top-width: 1px">
|
||
|
|
<b>Key to Ascomycete genera</b></td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px; border-top-style: solid; border-top-width: 1px"> </td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px; border-top-style: solid; border-top-width: 1px">
|
||
|
|
<br>
|
||
|
|
Ascus unitunicate</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px; border-top-style: solid; border-top-width: 1px"> </td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Clypeus present around ostiolar neck</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px"> </td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Clypeus poorly developed</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px">
|
||
|
|
<i>Glomerella</i></td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Clypeus well developed</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px">
|
||
|
|
<i>Hyllachora</i></td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Clypeus lacking</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px"> </td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Ascus widest in middle</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px">
|
||
|
|
<i>Physalospora</i></td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Ascus clavate or cylindrical</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px">
|
||
|
|
<i>Glomerella</i></td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Ascus bitunicate</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px"> </td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px">
|
||
|
|
Ascostroma uniloculate</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px">
|
||
|
|
<i>Guignardia</i></td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td width="409" style="border-left-style: solid; border-left-width: 1px; border-bottom-style: solid; border-bottom-width: 1px">
|
||
|
|
Ascostroma muliloculate</td>
|
||
|
|
<td align="right" style="border-right-style: solid; border-right-width: 1px; border-bottom-style: solid; border-bottom-width: 1px">
|
||
|
|
<i>Botryosphaeria</i></td>
|
||
|
|
</tr>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
<br>
|
||
|
|
d97 1
|
||
|
|
a97 1
|
||
|
|
Coded descriptions (Box 1.2.3) comprise highly structured data used in computer identification and analysis programs such as Lucid ([[http://www.lucidcentral.org][www.lucidcentral.org]]) , DELTA ([[http://www.delta-intkey.com][www.delta-intkey.com]]) and a suite of phylogenetic analysis programs such as PAUP ([[http://www.paup.csit.fsu.edu][www.paup.csit.fsu.edu]]).
|
||
|
|
d310 1
|
||
|
|
d312 1
|
||
|
|
a312 1
|
||
|
|
---+++1.4 Basic structure of a simple SDD instance document
|
||
|
|
d314 1
|
||
|
|
a314 1
|
||
|
|
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. 1.4.1, and its SDD representation in Example 1.4.1.
|
||
|
|
d316 4
|
||
|
|
a319 15
|
||
|
|
<div>
|
||
|
|
<table bgcolor="#ddddff" cellspacing="2" cellpadding="2" border="1" bordercolor="#a099cc" width="80%">
|
||
|
|
<tr>
|
||
|
|
<td style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: 1px; border-top-style: solid; border-top-width: 1px; border-bottom-style: solid; border-bottom-width: 1px">Box 1.4.1 - A simple description</td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: 1px">Viola hederacea Labill.</td>
|
||
|
|
</tr>
|
||
|
|
<tr>
|
||
|
|
<td style="border-left-style: solid; border-left-width: 1px; border-right-style: none; border-right-width: 1px; border-top-style: none; border-top-width: medium; border-bottom-style: none; border-bottom-width: 1px">Leaves simple</td>
|
||
|
|
</tr>
|
||
|
|
</table>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
---++++Example 1.4.1 - Description in Box 1.4.1 represented in SDD
|
||
|
|
d321 1
|
||
|
|
a321 1
|
||
|
|
<table bgcolor="#ddddff" border="0" width="100%" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111">
|
||
|
|
d323 1
|
||
|
|
a323 2
|
||
|
|
<tr>
|
||
|
|
<td>
|
||
|
|
d325 3
|
||
|
|
a327 1
|
||
|
|
<verbatim>
|
||
|
|
d329 1
|
||
|
|
a329 58
|
||
|
|
<?xml version='1.0' encoding='UTF-8'?>
|
||
|
|
<Datasets xmlns:xsi=
|
||
|
|
"http://www.w3.org/2001/XMLSchema-instance"
|
||
|
|
xmlns="http://www.tdwg.org/2005/UBIF"
|
||
|
|
xsi:schemaLocation=
|
||
|
|
"http://www.tdwg.org/2005/UBIF
|
||
|
|
http://www.tdwg.org/2005/SDD">
|
||
|
|
<Dataset>
|
||
|
|
<TechnicalMetadata created='2005-07-18T20:49:26'>
|
||
|
|
<Generator name='By Hand' version='v1'/>
|
||
|
|
</TechnicalMetadata>
|
||
|
|
<Metadata>
|
||
|
|
<Representation xml:lang='en'>
|
||
|
|
<Title>A simple description</Title>
|
||
|
|
</Representation>
|
||
|
|
</Metadata>
|
||
|
|
<TaxonNames>
|
||
|
|
<TaxonName id='t1'>
|
||
|
|
<Label xml:lang='en'>
|
||
|
|
<Text>Viola hederacea</Text>
|
||
|
|
</Label>
|
||
|
|
</TaxonName>
|
||
|
|
</TaxonNames>
|
||
|
|
<DescriptiveTerminology>
|
||
|
|
<Characters>
|
||
|
|
<CategoricalCharacter id='c1'>
|
||
|
|
<Label xml:lang='en'>
|
||
|
|
<Text>Leaf complexity</Text>
|
||
|
|
</Label>
|
||
|
|
<States>
|
||
|
|
<StateDefinition id='s1'>
|
||
|
|
<Label xml:lang='en'>
|
||
|
|
<Text>simple</Text>
|
||
|
|
</Label>
|
||
|
|
</StateDefinition>
|
||
|
|
<StateDefinition id='s2'>
|
||
|
|
<Label xml:lang='en'>
|
||
|
|
<Text>complex</Text>
|
||
|
|
</Label>
|
||
|
|
</StateDefinition>
|
||
|
|
</States>
|
||
|
|
</CategoricalCharacter>
|
||
|
|
</Characters>
|
||
|
|
</DescriptiveTerminology>
|
||
|
|
<CodedDescriptions>
|
||
|
|
<CodedDescription id='cd1'>
|
||
|
|
<Header>
|
||
|
|
<TaxonName ref='t1'/>
|
||
|
|
</Header>
|
||
|
|
<SummaryData>
|
||
|
|
<Categorical ref='c1'>
|
||
|
|
<State ref='s1'/>
|
||
|
|
</Categorical>
|
||
|
|
</SummaryData>
|
||
|
|
</CodedDescription>
|
||
|
|
</CodedDescriptions>
|
||
|
|
</Dataset>
|
||
|
|
</Datasets>
|
||
|
|
a330 25
|
||
|
|
</verbatim>
|
||
|
|
|
||
|
|
</td>
|
||
|
|
</tr>
|
||
|
|
|
||
|
|
</table>
|
||
|
|
|
||
|
|
In the SDD document in Box 2.0.1, data are wrapped in a [[SddDatasets][<Dataset>]] element. Several datasets may be wrapped in a single SDD document, in the [[SddDatasets][<Datasets>]] container element.
|
||
|
|
|
||
|
|
The [[TechnicalMetadata][<TechnicalMetadata>]] 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.
|
||
|
|
|
||
|
|
Metadata for the project that provided the data is given in the [[DatasetMetadata][<Metadata>]] element. In this case, only a title for the data set is provided.
|
||
|
|
|
||
|
|
The name of the taxon (Viola hederacea) is provided in the [[TaxonNames][<TaxonNames>]] element, while the names of the characters and states used to describe the taxon (character = Leaf complexity; states = simple and complex) are provided in the the [[DescriptiveTerminology][<DescriptiveTerminology>]] element. The [[CodedDescription][<CodedDescription>]] element contains the description itself, using references to identify the taxon, character and state being described.
|
||
|
|
|
||
|
|
[[SddFaq#VerboseFaq][FAQ: Why are SDD documents so verbose and complex?]]
|
||
|
|
|
||
|
|
---+++1.5 Beyond the simple instance...
|
||
|
|
|
||
|
|
Example 1.4.1 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, however, a number of fundamental SDD concepts and elements are common to all SDD documents. Use the links under SDD Fundamentals at left for an introduction to these basic concepts, then follow one or more of the streams. Other technical details of SDD are covered using the links in SDD Miscellaneous.
|
||
|
|
|
||
|
|
|
||
|
|
-- Main.DonovanSharp - 01 Jun 2006
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.11
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1152165484" format="1.1" version="1.11"}%
|
||
|
|
d154 1
|
||
|
|
a154 2
|
||
|
|
<td style="border-style: none; border-width: medium">Fewer than 25 lamellae under the fourth toe; supralabials
|
||
|
|
7-8 (usually 7); prefrontals separated</td>
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.10
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1152062850" format="1.1" reprev="1.10" version="1.10"}%
|
||
|
|
d417 5
|
||
|
|
d485 5
|
||
|
|
a507 1
|
||
|
|
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.9
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1151988743" format="1.1" version="1.9"}%
|
||
|
|
d11 1
|
||
|
|
a11 1
|
||
|
|
See DocumentStatus
|
||
|
|
d480 1
|
||
|
|
a480 1
|
||
|
|
In the SDD document in Box 2.0.1, data are wrapped in a [[SddDatasets][Dataset]] element. Several datasets may be wrapped in a single SDD document, in the [[SddDatasets][Datasets]] container element.
|
||
|
|
d482 1
|
||
|
|
a482 1
|
||
|
|
The TechnicalMetadata 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.
|
||
|
|
d484 1
|
||
|
|
a484 1
|
||
|
|
Metadata for the project that provided the data is given in the [[DatasetMetadata][Metadata]] element. In this case, only a title for the data set is provided.
|
||
|
|
d486 1
|
||
|
|
a486 1
|
||
|
|
The name of the taxon (Viola hederacea) is provided in the TaxonNames element, while the names of the characters and states used to describe the taxon (character = Leaf complexity; states = simple and complex) are provided in the the DescriptiveTerminology element. The CodedDescription element contains the description itself, using references to identify the taxon, character and state being described.
|
||
|
|
d498 1
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.8
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1149658973" format="1.1" reprev="1.8" version="1.8"}%
|
||
|
|
d428 1
|
||
|
|
a428 1
|
||
|
|
<Generator name='By Hand' version='1'/>
|
||
|
|
d436 1
|
||
|
|
a436 1
|
||
|
|
<TaxonName id='1'>
|
||
|
|
d444 1
|
||
|
|
a444 1
|
||
|
|
<CategoricalCharacter id='2'>
|
||
|
|
d449 1
|
||
|
|
a449 1
|
||
|
|
<StateDefinition id='3'>
|
||
|
|
d454 1
|
||
|
|
a454 1
|
||
|
|
<StateDefinition id='4'>
|
||
|
|
d464 1
|
||
|
|
a464 1
|
||
|
|
<CodedDescription id='0'>
|
||
|
|
d466 1
|
||
|
|
a466 1
|
||
|
|
<TaxonName ref='5'/>
|
||
|
|
d469 2
|
||
|
|
a470 2
|
||
|
|
<Categorical ref='2'>
|
||
|
|
<State ref='3'/>
|
||
|
|
a497 1
|
||
|
|
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.7
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1149658435" format="1.1" reprev="1.7" version="1.7"}%
|
||
|
|
a196 1
|
||
|
|
<div>
|
||
|
|
d198 1
|
||
|
|
a248 2
|
||
|
|
<div>
|
||
|
|
d299 1
|
||
|
|
a299 1
|
||
|
|
</div>
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.6
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1149643571" format="1.1" version="1.6"}%
|
||
|
|
d28 1
|
||
|
|
a28 1
|
||
|
|
<table bgcolor="#ddddff" cellspacing="2" cellpadding="2" border="1">
|
||
|
|
d67 1
|
||
|
|
a67 1
|
||
|
|
<div align="center">
|
||
|
|
d134 1
|
||
|
|
a134 1
|
||
|
|
<div align="center">
|
||
|
|
d189 1
|
||
|
|
a189 1
|
||
|
|
<div align="center">
|
||
|
|
d191 1
|
||
|
|
a191 1
|
||
|
|
<table bgcolor="#ddddff" border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="90%" id="table9">
|
||
|
|
d308 1
|
||
|
|
a308 1
|
||
|
|
<div align="center">
|
||
|
|
d403 1
|
||
|
|
a403 1
|
||
|
|
<div align="center">
|
||
|
|
d422 5
|
||
|
|
a426 2
|
||
|
|
<Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||
|
|
xmlns="http://www.tdwg.org/2005/UBIF" xsi:schemaLocation="http://www.tdwg.org/2005/UBIF
|
||
|
|
d500 1
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.5
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1149485958" format="1.1" version="1.5"}%
|
||
|
|
d11 1
|
||
|
|
a11 17
|
||
|
|
Version: 18 July 2005
|
||
|
|
|
||
|
|
Edited: <a href="mailto:k.thiele@@cbit.uq.edu.au">Kevin Thiele</a> (Centre for Biological Information Technology, University of Queensland), with financial support from the Gordon and Betty Moore Foundation ([[http://www.moore.org][www.moore.org]]).
|
||
|
|
|
||
|
|
Complete documentation of the SDD Schema is available on the [[http://160.45.63.11/Projects/TDWG-SDD/][SDD web site]].
|
||
|
|
|
||
|
|
To contribute to the discussion on the SDD Standard and to comment on this document, please join the [[http://efgblade.cs.umb.edu/twiki/bin/view/SDD/WebHome][SDD Wiki]] or [[http://160.45.63.11/Projects/TDWG-SDD/SDD-EmailList.html][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 [[http://www.bgbm.org/TDWG/CODATA/Schema/default.htm][Access to Biological Collections Data (ABCD)]] and [[http://www.soc.napier.ac.uk/tdwg/index.php][Taxonomic Concept Names]] standards. TDWG is developing a common, shared base schema for SDD and these related schemas, called [[http://efgblade.cs.umb.edu/twiki/bin/view/UBIF][UBIF]].
|
||
|
|
|
||
|
|
---+++SDD Version History
|
||
|
|
[[http://160.45.63.11/Projects/TDWG-SDD/Minutes/2003Lisbon_schema/SDD_09_DocuOverview.html][Version 0.9 beta]]: released for comment December 2003.
|
||
|
|
|
||
|
|
[[http://160.45.63.11/Projects/TDWG-SDD/Minutes/2004NZ_schema/DocuOverview.html][Version 1.0 beta]]: released August 2004
|
||
|
|
|
||
|
|
Version 1.0 was ratified at the TDWG St. Petersburg Meeting in September 2005
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.4
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1149481339" format="1.1" reprev="1.4" version="1.4"}%
|
||
|
|
d396 19
|
||
|
|
a512 1
|
||
|
|
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.3
|
||
|
|
log
|
||
|
|
@@
|
||
|
|
text
|
||
|
|
@d1 1
|
||
|
|
a1 1
|
||
|
|
%META:TOPICINFO{author="DonovanSharp" date="1149224050" format="1.1" reprev="1.3" version="1.3"}%
|
||
|
|
d484 1
|
||
|
|
a484 1
|
||
|
|
[[SddFaq#DeltaFaq][FAQ: Why are SDD documents so verbose and complex?]]
|
||
|
|
@
|
||
|
|
|
||
|
|
|
||
|
|
1.2
|
||
|
|
log
|
||
|
|
@@
|
||
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@d1 1
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%META:TOPICINFO{author="DonovanSharp" date="1149147832" format="1.1" reprev="1.2" version="1.2"}%
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d23 1
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a23 3
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Version 0.9 beta: released for comment December 2003.
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Version 1.0 beta: released August 2004
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Version 1.0 was ratified at the TDWG St. Petersburg Meeting in September 2005
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1.0 Introduction
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1.1 Background to the TDWG-SDD Subgroup
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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.
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d27 1
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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?).
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d29 2
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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).
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a32 2
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1.2 The nature of descriptive data in taxonomy
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In taxonomy, descriptive data takes a number of very different forms.
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a34 1
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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.
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a36 3
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Box 1.2.1 - Typical natural language descriptions
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Red Knot (Calidris canutus)
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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'.
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d38 1
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a38 1
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from Slater, P., Slater, P. & Slater, R. (2001) The Slater Field Guide to Australian Birds (Reed New Holland: Sydney)
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d40 1
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a40 2
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Discaria pubescens (Brongn.) Druce
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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.
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d44 36
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a79 2
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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)
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a84 5
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<div class="Example">
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<div class="exampleHeader">Box 1.2.2 - Typical dichotomous keys</div>
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<br>
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<div align="center">
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<table border="0" cellpadding="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table7" >
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<table border="1" cellpadding="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table8">
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d197 1
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</div>
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<br></div>
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Coded descriptions (Box 1.2.2) comprise highly structured data used in computer identification and analysis programs such as Lucid (www.lucidcentral.org) , DELTA (www.delta-intkey.com) and a suite of phylogenetic analysis programs such as PAUP (www.paup.csit.fsu.edu).
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a200 2
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<div class="Example">
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<div class="exampleHeader">Box 1.2.3 - Simple examples of coded descriptions</div>
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<table border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="90%" id="table9">
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a210 2
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<div class="Example">
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<div class="exampleHeader">
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<p>
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a265 2
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<div class="Example">
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<div class="exampleHeader">
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<p>
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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.
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Box 1.2.4 - Example of raw (specimen) descriptive data
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<div class="Example">
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<div class="exampleHeader">Box 1.2.4 - Example of raw (specimen) descriptive
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data</div>
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<br>
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<table border="1" width="80%" cellspacing="0" id="table10" cellpadding="0">
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<br>
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</div>
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1.3 Goals of SDD
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The SDD Standard:
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provides a flexible, platform-independent data structure for the capture and storage of taxonomic descriptions
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comprises a superset of data requirements of all existing programs
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provides extension beyond existing programs where data requirements can be predicted
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is readily extensible to account for future developments and data requirements
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is human-readable (although it is assumed that in almost all cases standard descriptions will be machine-generated and processed)
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is XML-based, and provides a schema for validation of documents.
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It facilitates:
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lossless porting of data between standard-aware applications
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achievable progressive markup of legacy descriptions, particularly natural-language descriptions
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comparability and, if possible, combinability of alternate descriptions of any one taxon
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efficient multi-tasking of descriptions (one description serving alternate purposes)
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archiving and sharing of raw and processed data
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1.4 Basic structure of a simple SDD instance document
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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.
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<div class="Example">
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<div class="exampleHeader">Box 2.0.1 - A simple description</div>
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<p>Viola hederacea Labill.<br>
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Leaves simple</p>
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</div>
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a396 59
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<div class="Example">
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<div class="exampleHeader">Example 2.0.1 - Description in Box 2.0.1 represented in SDD</div>
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<p>
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<pre><?xml version='1.0' encoding='UTF-8'?>
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<Datasets xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance">http://www.w3.org/2001/XMLSchema-instance</a>"
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xmlns="http://www.tdwg.org/2005/UBIF" xsi:schemaLocation="http://www.tdwg.org/2005/UBIF
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http://www.tdwg.org/2005/SDD">
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<Dataset>
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<TechnicalMetadata created='2005-07-18T20:49:26'>
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<Generator name='By Hand' version='1'/>
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</TechnicalMetadata>
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<Metadata>
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<Representation xml:lang='en'>
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<Title>A simple description</Title>
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</Representation>
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</Metadata>
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<TaxonNames>
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<TaxonName id='1'>
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<Label xml:lang='en'>
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<Text>Viola hederacea</Text>
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</Label>
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</TaxonName>
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</TaxonNames>
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<DescriptiveTerminology>
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<Characters>
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<CategoricalCharacter id='2'>
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<Label xml:lang='en'>
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<Text>Leaf complexity</Text>
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</Label>
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<States>
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<StateDefinition id='3'>
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<Label xml:lang='en'>
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<Text>simple</Text>
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</Label>
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</StateDefinition>
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<StateDefinition id='4'>
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<Label xml:lang='en'>
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<Text>complex</Text>
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</Label>
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</StateDefinition>
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</States>
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</CategoricalCharacter>
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</Characters>
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</DescriptiveTerminology>
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<CodedDescriptions>
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<CodedDescription id='0'>
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<Header>
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<TaxonName ref='5'/>
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</Header>
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<SummaryData>
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<Categorical ref='2'>
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<State ref='3'/>
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</Categorical>
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</SummaryData>
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</CodedDescription>
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</CodedDescriptions>
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</Dataset>
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</Datasets>
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</pre>
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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.
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The <TechnicalMetadata> 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.
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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.
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The name of the taxon (Viola hederacea) is provided in the <TaxonNames> element, while the names of the characters and states used to describe the taxon (character = Leaf complexity; states = simple and complex) are provided in the the <DescriptiveTerminology> element. The <CodedDescription> element contains the description itself, using references to identify the taxon, character and state being described.
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FAQ: Why are SDD documents so verbose and complex?
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d478 11
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a488 2
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1.5 Beyond the simple instance...
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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.
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@
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1.1
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log
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@@
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text
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@d1 1
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%META:TOPICINFO{author="DonovanSharp" date="1149129508" format="1.1" reprev="1.1" version="1.1"}%
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SDD Part 0: Introduction and Primer to the SDD Standard
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a5 2
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Abstract
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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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Status of this document
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Edited: Kevin Thiele (Centre for Biological Information Technology, University of Queensland), with financial support from the Gordon and Betty Moore Foundation (www.moore.org).
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Complete documentation of the SDD Schema is available on the SDD web site.
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To contribute to the discussion on the SDD Standard and to comment on this document, please join the SDD Wiki or SDD discussion list.
|
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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.
|
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SDD Version History
|
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@
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