steve
/
wiki-archive
mirror of https://github.com/tdwg/wiki-archive.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
wiki-archive/twiki/temp-gjr/BDI/SDD/Primer/CodedData.txt,v

1081 lines
33 KiB
Plaintext
Raw Permalink Normal View History

Archive entire twiki setup from owl as of today
2016-02-24 10:46:01 +00:00
head 1.22;
access;
symbols;
locks; strict;
1.22
date 2009.11.20.02.02.02; author LeeBelbin; state Exp;
branches;
next 1.21;
1.21
date 2008.11.24.05.26.30; author GregorHagedorn; state Exp;
branches;
next 1.20;
1.20
date 2006.08.29.02.06.18; author DonovanSharp; state Exp;
branches;
next 1.19;
1.19
date 2006.07.11.02.32.03; author DonovanSharp; state Exp;
branches;
next 1.18;
1.18
date 2006.07.07.09.49.18; author KevinThiele; state Exp;
branches;
next 1.17;
1.17
date 2006.07.07.06.07.29; author DonovanSharp; state Exp;
branches;
next 1.16;
1.16
date 2006.07.07.03.38.04; author DonovanSharp; state Exp;
branches;
next 1.15;
1.15
date 2006.07.07.02.26.10; author KevinThiele; state Exp;
branches;
next 1.14;
1.14
date 2006.07.07.00.08.01; author DonovanSharp; state Exp;
branches;
next 1.13;
1.13
date 2006.07.06.05.15.14; author KevinThiele; state Exp;
branches;
next 1.12;
1.12
date 2006.07.06.02.30.28; author DonovanSharp; state Exp;
branches;
next 1.11;
1.11
date 2006.07.06.02.25.54; author KevinThiele; state Exp;
branches;
next 1.10;
1.10
date 2006.07.06.02.17.34; author DonovanSharp; state Exp;
branches;
next 1.9;
1.9
date 2006.07.06.01.48.29; author KevinThiele; state Exp;
branches;
next 1.8;
1.8
date 2006.07.05.11.42.11; author KevinThiele; state Exp;
branches;
next 1.7;
1.7
date 2006.07.05.01.48.33; author DonovanSharp; state Exp;
branches;
next 1.6;
1.6
date 2006.06.09.03.15.16; author DonovanSharp; state Exp;
branches;
next 1.5;
1.5
date 2006.06.07.07.15.37; author DonovanSharp; state Exp;
branches;
next 1.4;
1.4
date 2006.06.07.05.47.11; author DonovanSharp; state Exp;
branches;
next 1.3;
1.3
date 2006.06.07.05.46.29; author DavidDickson; state Exp;
branches;
next 1.2;
1.2
date 2006.06.02.04.51.36; author DonovanSharp; state Exp;
branches;
next 1.1;
1.1
date 2006.06.01.05.25.23; author DonovanSharp; state Exp;
branches;
next ;
desc
@@
1.22
log
@none
@
text
@%META:TOPICINFO{author="LeeBelbin" date="1258682522" format="1.1" version="1.22"}%
%META:TOPICPARENT{name="SddContents"}%
---++Main.BDI Part 0: Introduction and Primer to the Main.BDI Standard
---+++2.1 Main.BDI for coded summary descriptions
Coded descriptions 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]]).
----++++Box 2.1.1 - Simple examples of coded descriptions
<div>
<table bgcolor="#ddddff" border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table9">
<tr>
<td width="50%">
<div>
Lucid Interchange Format (LIF) file</div>
#Lucid Interchange Format File v. 2.1<br>
<br>
[..Character List..]<br>
Distribution by region<br>
&nbsp; Tropical North<br>
&nbsp; Subtropical and Temperate East and South<br>
&nbsp; South West<br>
&nbsp; Arid &amp; Semi-arid (Central)<br>
&nbsp; Island Territories<br>
General habit<br>
&nbsp; tree<br>
&nbsp; shrub<br>
&nbsp; climber (woody or herbaceous)<br>
&nbsp; herb<br>
&nbsp; grass- or sedge-like plant<br>
Seasonal longevity<br>
&nbsp; annual, biennial or ephemeral<br>
&nbsp; perennial<br>
<br>
[..Taxon List..]<br>
Acanthaceae<br>
Aceraceae<br>
Actinidiaceae<br>
Agavaceae<br>
Aizoaceae<br>
Akaniaceae<br>
Alangiaceae<br>
Alismataceae<br>
Aloaceae<br>
Alseuosmiaceae<br>
<br>
[..Main Data (txs)..]<br>
101101111111<br>
100100000101<br>
101000000010<br>
011110111111<br>
101111111111<br>
100100000011<br>
101101000011<br>
011111011111<br>
011100100111<br>
101100000010</div>
</td>
<td width="50%">
<div>
DELTA file</div>
*SHOW: Gentianella - character list. Last revised 16 April 1997.<br>
<br>
*CHARACTER LIST <br>
<br>
#1. plants/<br>
1. monocarpic/<br>
2. polycarpic/<br>
<br>
#2. &lt;plants lifecycle&gt;/<br>
1. annual/<br>
2. biennial/<br>
3. perennial/<br>
<br>
#3. height in flower/<br>
&lt;&gt; cm/<br>
<br>
#4. caudex/<br>
1. unbranched/<br>
2. branched/<br>
<br>
*ITEM DESCRIPTIONS <br>
<br>
# Gentianella amabilis/<br>
1,2 2,3 3,3-13 4,1<br>
<br>
# Gentianella antarctica/<br>
1,1 2,1&lt;Godley 1982&gt; 3,1.6-22.0&lt;Godley 1982&gt; 4,1<br>
<br>
# Gentianella antipoda/<br>
1,1&lt;Godley 1982&gt; 2,2 3,3.5-9.8-24 4,1/2&lt;depends on size of plant&gt;<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>
&nbsp;</div>
</td>
<td width="50%">&nbsp;<p>&nbsp;</td>
</tr>
</table>
</div>
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 [[SampleData][Using Main.BDI 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 Main.BDI instance document for coded summary data has the basic structure shown below and in Example 2.1.1.
<img src="%ATTACHURLPATH%/coded_summary_descriptions.gif"/>
----++++Example 2.1.1 - A simple coded description
<div>
<table bgcolor="#ddddff" border="0" width="80%" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111">
<pre>
<tr>
<td>
<verbatim>
<?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>
</verbatim>
</td>
</tr>
</pre>
</table>
</div>
For more information on defining taxon names using the &lt;TaxonNames&gt; element, see the topic [[TaxonNames][Defining taxon names]].
For more infirmation on defining characters and states using the &lt;Characters&gt; element, see the topic [[SddCharacters][Defining characters and states]].
Both taxa and characters can be arranged into hierarchies; see [[TaxonHierarchies][Defining taxon hierarchies]] and [[CharacterHierarchies][Defining character hierarchies]] for more information.
The &lt;Representation&gt; element provides a label for the description. This reflects the fact that a single taxon may have several descriptions. In a butterfly, "Gonepteryx rhamni, male" and "Gonepteryx rhamni, female", and "caterpillar of Gonepteryx rhamni" may be three different descriptions. Other examples are descriptions scoped to a geographic region ("in Australia"), to a small number of defined specimens, or to a given publication (which may have been kept separate because less trusted). Each coded description in Main.BDI may express these scopes of a description in the Scope element. To allow human users a simple and consistent access to descriptions, the separate description label is provided.
One problem that Main.BDI cannot solve itself is the fact that while some data models make a distinction between a taxon and multiple descriptions, many do not. Most current programs either have no formal taxon name (e.g. DELTA, Xper, etc. are careful to avoid the name "taxon description") or they handle male/female as pseudo-taxa (Lucid, ETI-Linneaus II). Software importing and exporting Main.BDI therefore needs to take care to accept both datasets that have only a Description Label and those that have explicit Taxon names.
&lt;Scope&gt; describes the taxon or set of taxa to which the description applies.
Characters used in the description are listed under &lt;SummaryData&gt;. Main.BDI distinguishes between different kinds of characters (see the topic [[SddCharacters][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][&lt;DescriptiveConcepts&gt;]] for more information
-- Main.KevinThiele - 06 Jul 2006
%META:FILEATTACHMENT{name="coded_summary_descriptions.gif" attr="" autoattached="1" comment="" date="1152237087" path="coded_summary_descriptions.gif" size="9347" user="Main.KevinThiele" version="3"}%
@
1.21
log
@none
@
text
@d1 1
a1 1
%META:TOPICINFO{author="GregorHagedorn" date="1227504390" format="1.1" version="1.21"}%
d3 1
a3 1
---++SDD Part 0: Introduction and Primer to the SDD Standard
d5 1
a5 1
---+++2.1 SDD for coded summary descriptions
d120 1
a120 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 [[SampleData][Using SDD for raw (sample) data]].
d124 1
a124 1
A simple SDD instance document for coded summary data has the basic structure shown below and in Example 2.1.1.
d207 1
a207 1
The &lt;Representation&gt; element provides a label for the description. This reflects the fact that a single taxon may have several descriptions. In a butterfly, "Gonepteryx rhamni, male" and "Gonepteryx rhamni, female", and "caterpillar of Gonepteryx rhamni" may be three different descriptions. Other examples are descriptions scoped to a geographic region ("in Australia"), to a small number of defined specimens, or to a given publication (which may have been kept separate because less trusted). Each coded description in SDD may express these scopes of a description in the Scope element. To allow human users a simple and consistent access to descriptions, the separate description label is provided.
d209 1
a209 1
One problem that SDD cannot solve itself is the fact that while some data models make a distinction between a taxon and multiple descriptions, many do not. Most current programs either have no formal taxon name (e.g. DELTA, Xper, etc. are careful to avoid the name "taxon description") or they handle male/female as pseudo-taxa (Lucid, ETI-Linneaus II). Software importing and exporting SDD therefore needs to take care to accept both datasets that have only a Description Label and those that have explicit Taxon names.
d213 1
a213 1
Characters used in the description are listed under &lt;SummaryData&gt;. SDD distinguishes between different kinds of characters (see the topic [[SddCharacters][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.
@
1.20
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1156817178" format="1.1" reprev="1.20" version="1.20"}%
a15 2
d205 3
a207 1
Note that taxa and characters can also be arranged into hierarchies. See the topics [[TaxonHierarchies][Defining taxon hierarchies]] and [[CharacterHierarchies][Defining character hierarchies]] for more information.
d209 1
a209 1
The &lt;Representation&gt; element provides a label for the description. This may be useful if the instance document includes multiple descriptions for different purposes.
@
1.19
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152585123" format="1.1" version="1.19"}%
d9 1
a9 1
----++++Box 1.2.3 - Simple examples of coded descriptions
d130 2
a131 1
Example 2.1.1 - A simple coded description
@
1.18
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="KevinThiele" date="1152265758" format="1.1" reprev="1.18" version="1.18"}%
d214 1
a214 1
States used in a description can also be modified using a predefined set of modifiers (such as "rare", "uncertain" etc.). See the topic Using [[SDDModifiers][Modifiers]] in SDD for more information
@
1.17
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152252449" format="1.1" version="1.17"}%
d8 113
@
1.16
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152243484" format="1.1" version="1.16"}%
d69 1
a69 1
<TaxonName ref="t1">
d73 2
a74 2
<State ref="s2">
<State ref="s3">
@
1.15
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="KevinThiele" date="1152239170" format="1.1" reprev="1.15" version="1.15"}%
d99 1
a99 1
Characters used in the description are listed under &lt;SummaryData&gt;. SDD distinguishes between different kinds of characters (see the topic [[SddCharacters][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 taxonbeing described.
@
1.14
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152230881" format="1.1" reprev="1.14" version="1.14"}%
a5 1
---++++2.1.1 What are coded summary descriptions?
d7 1
a7 1
Coded descriptions (Box 2.1.1.1) 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]]).
d9 1
a9 1
In SDD coded descriptions may comprise summary data (descriptions recording the range of characteristics found in a taxon such as a genus, species etc) or [[SampleData][sample data]] (descriptions recording direct observations or measurements of an individual specimen).
a10 109
----++++Box 2.1.1.1 - Simple examples of coded summary descriptions
<div>
<table bgcolor="#ddddff" border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="80%" id="table9">
<tr>
<td width="50%">
<b>Lucid Interchange Format (LIF) file</b>
#Lucid Interchange Format File v. 2.1<br>
<br>
[..Character List..]<br>
Habit<br>
&nbsp; tree<br>
&nbsp; shrub<br>
&nbsp; climber (woody or herbaceous)<br>
&nbsp; herb<br>
&nbsp; grass- or sedge-like plant<br>
Seasonal longevity<br>
&nbsp; annual, biennial or ephemeral<br>
&nbsp; perennial<br>
Distribution by region<br>
&nbsp; Tropical North<br>
&nbsp; Subtropical and Temperate East and South<br>
&nbsp; South West<br>
&nbsp; Arid &amp; Semi-arid (Central)<br>
<br>
[..Taxon List..]<br>
Acanthaceae<br>
Aceraceae<br>
Actinidiaceae<br>
Agavaceae<br>
Aizoaceae<br>
Akaniaceae<br>
Alangiaceae<br>
Alismataceae<br>
Aloaceae<br>
Alseuosmiaceae<br>
<br>
[..Main Data (txs)..]<br>
101101111111<br>
100100000101<br>
101000000010<br>
011110111111<br>
101111111111<br>
100100000011<br>
101101000011<br>
011111011111<br>
011100100111<br>
101100000010</div>
</td>
<td width="50%">
<b>DELTA file</b>
*SHOW: Gentianella - character list. Last revised 16 April 1997.<br>
<br>
*CHARACTER LIST <br>
<br>
#1. plants/<br>
1. monocarpic/<br>
2. polycarpic/<br>
<br>
#2. &lt;plants lifecycle&gt;/<br>
1. annual/<br>
2. biennial/<br>
3. perennial/<br>
<br>
#3. height in flower/<br>
&lt;&gt; cm/<br>
<br>
#4. caudex/<br>
1. unbranched/<br>
2. branched/<br>
<br>
*ITEM DESCRIPTIONS <br>
<br>
# Gentianella amabilis/<br>
1,2 2,3 3,3-13 4,1<br>
<br>
# Gentianella antarctica/<br>
1,1 2,1&lt;Godley 1982&gt; 3,1.6-22.0&lt;Godley 1982&gt; 4,1<br>
<br>
# Gentianella antipoda/<br>
1,1&lt;Godley 1982&gt; 2,2 3,3.5-9.8-24 4,1/2&lt;depends on size of plant&gt;<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>
&nbsp;</div>
</td>
<td width="50%">&nbsp;<p>&nbsp;</td>
</tr>
</table>
</div>
---++++2.1.2 Elements of structured summary data in SDD.
d14 1
d13 1
a13 2
In SDD taxa are listed in [[TaxonNames][&lt;TaxonNames&gt;]], characters and states are defined in [[DescriptiveTerminology][&lt;SDD-DescriptiveTerminology&gt;]], while the coded descriptions themselves are recorded in [[CodedDescription][&lt;SDD-DescriptiveData&gt;]], using references to identify the taxon and characters and states used in the descriptions.
In SDD taxa are listed in [[TaxonNames][&lt;TaxonNames&gt;]], characters and states are defined in [[DescriptiveTerminology][&lt;DescriptiveTerminology&gt;]], while the coded descriptions themselves are recorded in [[CodedDescription][&lt;CodedDescription&gt;]], using references to identify the taxon and characters and states used in the descriptions.
d15 1
a15 3
%ATTACHURL%/codeddata.jpg
d93 1
An SDD instance document for coded summary data has the basic structure shown in Example 2.1.2.1.
d17 1
a17 2
---++++Example 2.1.2.1 - SDD structure of coded descriptions
d27 2
a28 1
xmlns="http://ns.tdwg.org/UBIF/2006" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
d73 1
a74 1
<State ref="s2">
d90 13
d105 1
a105 2
%META:FILEATTACHMENT{name="coded_data.gif" attachment="coded_data.gif" attr="" comment="" date="1152233923" path="coded_data.gif" size="11884" stream="coded_data.gif" user="Main.KevinThiele" version="2"}%
%META:FILEATTACHMENT{name="codeddata.jpg" attachment="codeddata.jpg" attr="" comment="" date="1152230880" path="codeddata.jpg" size="14661" stream="codeddata.jpg" user="Main.DonovanSharp" version="6"}%
@
1.13
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="KevinThiele" date="1152162914" format="1.1" reprev="1.13" version="1.13"}%
d204 1
a204 1
%META:FILEATTACHMENT{name="codeddata.jpg" attachment="codeddata.jpg" attr="" comment="" date="1152152254" path="codeddata.jpg" size="19778" stream="codeddata.jpg" user="Main.DonovanSharp" version="3"}%
@
1.12
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152153028" format="1.1" version="1.12"}%
d5 2
a6 2
---+++2.1 SDD for coded descriptions
---++++2.1.1 What are coded descriptions?
d10 1
a10 1
In SDD coded descriptions may comprise [[SummaryData][summary data]] (descriptions recording the range of characteristics found in a taxon such as a genus, species etc) or [[SampleData][sample data]] (descriptions recording direct observations or measurements of an individual specimen).
d25 1
a25 7
Distribution by region<br>
&nbsp; Tropical North<br>
&nbsp; Subtropical and Temperate East and South<br>
&nbsp; South West<br>
&nbsp; Arid &amp; Semi-arid (Central)<br>
&nbsp; Island Territories<br>
General habit<br>
d34 5
d119 1
d121 1
a121 2
SampleData descriptions (Box 2.1.1.2) 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.
d123 1
a123 1
----++++Box 1.2.4 - Example of sample (specimen) descriptive data
d125 1
a125 50
<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>
d127 1
d129 1
a129 3
---+++2.1.2 Elements of structured data in SDD.
d179 1
%ATTACHURL%/codeddata.jpg
a130 5
An SDD instance document for coded summary data has the basic structure shown in Example 4.4.1.
An SDD instance document for coded data has the basic structure shown in Example 2.1.2.
---++++Example 2.1.2 - SDD structure of coded descriptions
d149 4
d137 5
a141 3
<Datasets>
<Dataset>
d143 6
a148 1
... provides a list of the entities (usually taxa) described
d150 25
a174 14
<TaxonHierarchies>
... describes relationships between entities
</TaxonHierarchies>
<Specimens>
... provides a list of the objects (usually specimens) described
</Specimens>
<DescriptiveTerminology>
... provides the terminology and ontology used to describe the
entities (see DescriptiveConcepts, SddCharacters, CharacterTrees)
</DescriptiveTerminology>
d176 15
a190 1
... the actual data
d192 1
a192 6
<MediaResources>
... provides media (images, video, audio etc.) associated with
any of the above
</MediaResources>
a200 2
A coded description requires three essential items: the names of the taxa or objects being described are recorded in [[TaxonNames][&lt;TaxonNames&gt;]]; the characters and states used to describe the taxa or objects are recorded in [[DescriptiveTerminology][&lt;DescriptiveTerminology&gt;]], while the coded descriptions themselves are recorded in [[CodedDescription][&lt;CodedDescription&gt;]], using references to identify the taxon or object and characters and states used in the descriptions.
@
1.11
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="KevinThiele" date="1152152754" format="1.1" reprev="1.11" version="1.11"}%
@
1.10
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152152254" format="1.1" reprev="1.10" version="1.10"}%
d187 1
a187 1
<table bgcolor="#ddddff" border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111">
a188 2
a217 1
d226 1
a226 1
A coded description requires three essential items: the names of the taxa or objects being described are recorded in [[TaxonNames][&lt;TaxonNames&gt;]]; the characters and states used to describe the taxa or objects are recorded in [[DescriptiveTerminology][&lt;DescriptiveTerminology&gt;]], while the coded descriptions themselves are recorded in [[CodedDescription][&lt;CodedDescription&gt;]], using references to identify the taxon or object and characters and states.
@
1.9
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="KevinThiele" date="1152150509" format="1.1" reprev="1.9" version="1.9"}%
d187 1
d189 9
a197 5
d219 2
&lt;Datasets&gt;
&lt;Dataset&gt;
&nbsp;
&lt;TaxonNames&gt;
d199 3
a201 3
&lt;/TaxonNames&gt;
&nbsp;
&lt;TaxonHierarchies&gt;
d203 3
a205 3
&lt;/TaxonHierarchies&gt;
&nbsp;
&lt;DescriptiveTerminology&gt;
d208 3
a210 3
&lt;/DescriptiveTerminology&gt;
&nbsp;
&lt;CodedDescriptions&gt;
d212 14
a225 10
&lt;/CodedDescriptions&gt;
&nbsp;
&lt;MediaResources&gt;
... provides media (images, video, audio etc.) associated with any of the
above
&lt;/MediaResources&gt;
&nbsp;
&lt;/Dataset&gt;
&nbsp;
&lt;/Datasets&gt;
d227 1
a228 1
</table>
d230 1
d235 1
a235 1
%META:FILEATTACHMENT{name="codeddata.jpg" attachment="codeddata.jpg" attr="" comment="" date="1149664537" path="codeddata.jpg" size="19800" stream="codeddata.jpg" user="Main.DonovanSharp" version="1"}%
@
1.8
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="KevinThiele" date="1152099731" format="1.1" reprev="1.8" version="1.8"}%
d5 2
a6 2
---+++2.1 SDD for coded data
---++++2.1.1 What is coded data?
d8 1
a8 1
Coded descriptions (Box 2.1.1.1) 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]]).
d20 1
a21 6
<div>
Lucid Interchange Format (LIF) file</div>
a69 2
@
1.7
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1152064113" format="1.1" reprev="1.7" version="1.7"}%
d10 1
a10 1
Coded data may describe various different types of data. [[SummaryData][Summary data]] is data describing an organism (e.g. genus or species) and expresses the range found in that organism. [[SampleData][Sample data]] records direct observations or measurements made to individual specimens.
@
1.6
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1149822916" format="1.1" reprev="1.6" version="1.6"}%
d10 1
a10 1
Coded data may describe various different types of data. SummaryData is data describing an organism (e.g. genus or species) and expresses the range found in that organism. SampleData records the diract observations or measurements made to individual specimens.
d242 1
a242 1
Coded data are effectively represented in SDD using three high level elements, the name of the taxon (e.g. Viola hederacea) is provided in the TaxonNames element, while the names of the characters and states used to describe the taxon (e.g. Leaf complexity with the 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.
@
1.5
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1149664537" format="1.1" reprev="1.5" version="1.5"}%
d10 1
a10 1
Coded data may describe various different types of data. SummaryData is data describing an organism (e.g. genus or species) and expresses the range found in that organism. RawData records the diract observations or measurements * made to individual specimens.
d127 1
a127 1
RawData descriptions (Box 2.1.1.2) 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.
d129 1
a129 1
----++++Box 1.2.4 - Example of raw (specimen) descriptive data
d131 1
a131 1
<div align="center">
@
1.4
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1149659231" format="1.1" version="1.4"}%
d196 2
a204 2
&lt;Dataset&gt;
&nbsp;
d208 2
d221 1
a221 1
&lt;/ClassHierarchies&gt;
d248 3
@
1.3
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DavidDickson" date="1149659189" format="1.1" version="1.3"}%
d14 1
a14 1
<div align="center">
d16 1
a16 1
<table bgcolor="#ddddff" border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="90%" id="table9">
a21 1
<div>
d23 1
a73 2
<div>
d124 1
a124 1
</div>
@
1.2
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1149223896" format="1.1" reprev="1.2" version="1.2"}%
a247 1
@
1.1
log
@@
text
@d1 1
a1 1
%META:TOPICINFO{author="DonovanSharp" date="1149139523" format="1.1" reprev="1.1" version="1.1"}%
d3 1
a3 1
SDD Part 0: Introduction and Primer to the SDD Standard
d5 2
a6 2
2.1 SDD for coded data
2.1.1 What is coded data?
d8 1
a8 1
Coded descriptions (Box 2.1.1.1) 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).
d10 1
a10 1
Coded data may describe various different types of data. Summary data is data describing an organism (e.g. genus or species) and expresses the range found in that organism. Raw data records the diract observations or measurements made to individual specimens.
d12 1
a12 2
<div class="Example">
<div class="exampleHeader">Box 2.1.1.1 - Simple examples of coded summary descriptions</div>
d14 3
a16 1
<table border="0" cellpadding="5" cellspacing="5" style="border-collapse: collapse" bordercolor="#111111" width="90%" id="table9">
a19 2
<div class="Example">
<div class="exampleHeader">
d21 3
a24 1
<p>
d73 2
a74 2
<div class="Example">
<div class="exampleHeader">
a76 1
<p>
d78 1
d126 1
d129 1
a129 1
Raw data descriptions (Box 2.1.1.2) 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.
d131 2
a132 4
<div class="Example">
<div class="exampleHeader">Box 2.1.1.2 - Example of raw (specimen) descriptive
data</div>
<br>
d134 1
a134 1
<table border="1" width="80%" cellspacing="0" id="table10" cellpadding="0">
a182 2
<br>
</div>
a183 1
d186 2
a187 1
2.1.2 Elements of structured data in SDD.
d190 6
a195 5
comprises a superset of the 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 a computer-based intermediary will be used)
is XML-based, and provides a schema for validation of documents.
d198 1
a198 3
<div class="Example">
<div class="exampleHeader">Example 2.1.2 - SDD structure of coded descriptions</div>
<p><pre>
d200 3
d208 1
a208 1
... describes the generating application, see (<a href="SDD_Technical_Metadata.htm">Technical Metadata</a>)
d212 1
a212 1
... describes the dataset, see (<a href="SDD_Dataset_Metadata.htm">Dataset metadata</a>)
d216 1
a216 2
... provides a list of the entities (usually taxa) described,
see (<a href="SDD_taxon_names.htm">Taxon names</a>)
d220 1
a220 1
... describes relationships between entities, see(<a href="SDD_taxon_hierarchies.htm">Hierarchies</a>)
d225 1
a225 1
entities (see <a href="SDD_descriptive.htm">Descriptive Concepts</a>, <a href="SDD_characters.htm">Characters</a>, <a href="SDD_char_hierarchies.htm">Character Trees</a>)
d234 1
a234 1
above (see <a href="SDD_Media.htm">Media</a>)
d241 2
a242 2
</div></p>
Coded data are effectively represented in SDD using three high level elements, the name of the taxon (e.g. Viola hederacea) is provided in the <TaxonNames> element, while the names of the characters and states used to describe the taxon (e.g. Leaf complexity with the 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.
@