CodedData < SDD/Primer

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SDD Part 0: Introduction and Primer to the SDD Standard

2.1 SDD for coded summary descriptions

Coded descriptions 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 2.1.1 - 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
101100000010

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

Coded summary descriptions record the range of characteristics found in a taxon (such as a family, genus, species etc). To record raw (sample) data for individual specimens, see the topic Using SDD for raw (sample) data?.

A coded sample description requires three essential items: the names of the taxa being described, a set of descriptors (characters and states) used to describe the taxa, and the coded descriptions themselves.

A simple SDD instance document for coded summary data has the basic structure shown below and in Example 2.1.1.

Example 2.1.1 - A simple coded description

<?xml version="1.0" encoding="UTF-8"?>
<Datasets xsi:schemaLocation="http://ns.tdwg.org/UBIF/2006/ 
  http://www.lucidcentral.org/2006/SDD/SDD1.1-RC1/SDD.xsd" 
  xmlns="http://ns.tdwg.org/UBIF/2006" 
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <Dataset xml:lang="en-us">
    <TaxonNames>
      <TaxonName id="t1">
        <Representation>
          <Label>Acanthaceae</Label>
        </Representation>
      </TaxonName>
          ...etc
    </TaxonNames>
    <Characters>
      <CategoricalCharacter id="c1">
        <Representation>
          <Label>Habit</Label>
        </Representation>
        <States>
          <StateDefinition id="s1">
            <Representation>
              <Label>tree</Label>
            </Representation>
          </StateDefinition>
          <StateDefinition id="s2">
            <Representation>
              <Label>shrub</Label>
            </Representation>
          </StateDefinition>
          <StateDefinition id="s3">
            <Representation>
              <Label>herb</Label>
            </Representation>
          </StateDefinition>
        </States>
      </CategoricalCharacter>
          ...etc
    </Characters>
    <CodedDescriptions>
      <CodedDescription id="cd1">
        <Representation>
          <Label>Acanthaceae</Label>
        </Representation>
        <Scope>
          <TaxonName ref="t1"/>
        </Scope>
        <SummaryData>
          <Categorical ref="c1">
            <State ref="s2"/>
            <State ref="s3"/>
          </Categorical>
        </SummaryData>
          ...etc
      </CodedDescription>
    </CodedDescriptions>
    <MediaObjects/>
  </Dataset>
</Datasets>

For more information on defining taxon names using the <TaxonNames> element, see the topic Defining taxon names. For more infirmation on defining characters and states using the <Characters> element, see the topic Defining characters and states.

Note that taxa and characters can also be arranged into hierarchies. See the topics Defining taxon hierarchies and Defining character hierarchies for more information.

The <Representation> element provides a label for the description. This may be useful if the instance document includes multiple descriptions for different purposes.

<Scope> describes the taxon or set of taxa to which the description applies.

Characters used in the description are listed under <SummaryData>. SDD distinguishes between different kinds of characters (see the topic Defining characters and states for more information). For categorical characters (characters with states) the states occurring in the taxon being described are listed by reference. In the example given above, the taxon Acanthaceae is described as being a shrub or herb (states s2 and s3 of character c1). Note that states that are not listed are inferred to not occur in the taxon being described.

States used in a description can also be modified using a predefined set of modifiers (such as "rare", "uncertain" etc.). See the topic <DescriptiveConcepts> for more information

-- Main.KevinThiele - 06 Jul 2006

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