wiki-archive/twiki/data/SDD/CIPResDevelopment.txt,v

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date	2009.11.25.03.14.31;	author GarryJolleyRogers;	state Exp;
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date	2004.06.23.21.37.00;	author BobMorris;	state Exp;
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@%META:TOPICINFO{author="GarryJolleyRogers" date="1259118871" format="1.1" version="1.5"}%
%META:TOPICPARENT{name="ImplementationsOfBDI.SDD"}%
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[[http://www.phylo.org/index.html][CIPRes]] is a major multi-institutional research initiative in phyloinformatics and computational phylogenetics. One of their staff, Main.ShirleyCohen, has begun evaluating SDD for its utility to various aspects of the CIPRes effort and has produced a rather interesting spreadsheet, attached, comparing SDD to current CIPRes representations. The spreadsheet is based, where it can be, on criteria elucidated by Mike Dallwitz [[http://biodiversity.uno.edu/delta/www/compdata.htm][comparing DELTA to NEXUS]] facilities.

Shirley's analysis was based on 0.91b16, but most things of interest to her haven't changed. I've spent a little time with her going over some of SDD 0.91b25; the attachment represents a few changes from her original. Herewith I make subtopics for the few issues in the spreadsheet where she couldn't see how to represent the concept in SDD. Some we clearly can do and I just ran out of time in our discussion. Some I don't see how to do, some I don't understand what's meant, and some we don't do (but maybe could easily). The major one we agreed(?) not to address in SDD 1.0 is character and state inheritance.
Because a version of this spreadsheet is and may circulate on the cipres-dev list, I have added a local version number in case it evolves here

 |*row*|*feature*          |*intent*|*sdd feature*|*sdd ver*|*spreadsheet ver*|
 |23   |CharacterKeywords  |unordered character sets|Concept Trees|0.91b25|1.0 23June2004|
 |44   |StructureOfTaxonNames|???|???|???|1.0 23June2004|
 |45   |<nop>ImplicitValues|?| [see note 1]| |1.0 23June2004|
 |46   |IndefiniteValues   |?| | |1.0 23June2004|
 |47   |AttributeWeights   |?| | |1.0 23June2004|
 |48   |AttributePassedUp  |inheritance| | |1.0 23June2004|
 |49   |AttributePassedDown|inheritance| | |1.0 23June2004|
 |52   |TaxonKeywords      |unordered taxon sets|Class Hierarchy|0.91b25|1.0 23June2004|

Note 1: Implicit values are difficult, since in DELTA they have two meanings: a) Default values to be inserted globally into the data matrix (this will not be supported, but replaced with data passed up/passed down features, implicit values are simply those passed down from the root). b) values inserted, but then removed from natural language output because they are considered implicit by the human reader (plants are generally green so the absence of green is reported, but protozoa generally not green, so presence of green is reported!) -- Gregor

For some comparison between DELTA and SDD, see [[http://www.DiversityCampus.net/Projects/TDWG-SDD/SDD_DELTA_CompComplexity.html][Complexity of SDD versus DELTA]] and [[http://www.DiversityCampus.net/Projects/TDWG-SDD/SDD_DELTA_Export2BDI.SDD.html][Exporting DELTA to SDD]]). Note that these documents refer to SDD 0.9, some of the outer structures have changed since. I will try to update the documents as soon as I have time. -- Gregor

   * [[%ATTACHURL%/ComparisonMatrix.xls][ComparisonMatrix.xls]]: Comparison of SDD with CIPRes/NEXUS

-- Main.BobMorris / [[Main.GregorHagedorn][Gregor Hagedorn]] - 23 Jun 2004

Please someone add some semantics to <nop>StructureOfTaxonNames in the table above. For me this is too ambiguous: whether an atomization of the name itself, or the arrangement of names into a class hierarchy, or something else is meant - then delete this note! -- Gregor

%META:FILEATTACHMENT{name="ComparisonMatrix.xls" attr="" comment="Comparison of SDD with CIPRes/NEXUS" date="1088026159" path="C:\Documents and Settings\ram\Desktop\ComparisonMatrix.xls" size="19456" user="BobMorris" version="1.1"}%
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[[http://www.phylo.org/index.html][CIPRes]] is a major multi-institutional research initiative in phyloinformatics and computational phylogenetics. One of their staff, Main.ShirleyCohen, has begun evaluating BDI.SDD for its utility to various aspects of the CIPRes effort and has produced a rather interesting spreadsheet, attached, comparing BDI.SDD to current CIPRes representations. The spreadsheet is based, where it can be, on criteria elucidated by Mike Dallwitz [[http://biodiversity.uno.edu/delta/www/compdata.htm][comparing DELTA to NEXUS]] facilities.
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Shirley's analysis was based on 0.91b16, but most things of interest to her haven't changed. I've spent a little time with her going over some of BDI.SDD 0.91b25; the attachment represents a few changes from her original. Herewith I make subtopics for the few issues in the spreadsheet where she couldn't see how to represent the concept in BDI.SDD. Some we clearly can do and I just ran out of time in our discussion. Some I don't see how to do, some I don't understand what's meant, and some we don't do (but maybe could easily). The major one we agreed(?) not to address in BDI.SDD 1.0 is character and state inheritance.
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For some comparison between DELTA and BDI.SDD, see [[http://www.DiversityCampus.net/Projects/TDWG-BDI.SDD/SDD_DELTA_CompComplexity.html][Complexity of BDI.SDD versus DELTA]] and [[http://www.DiversityCampus.net/Projects/TDWG-BDI.SDD/SDD_DELTA_Export2BDI.SDD.html][Exporting DELTA to BDI.SDD]]). Note that these documents refer to BDI.SDD 0.9, some of the outer structures have changed since. I will try to update the documents as soon as I have time. -- Gregor
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   * [[%ATTACHURL%/ComparisonMatrix.xls][ComparisonMatrix.xls]]: Comparison of BDI.SDD with CIPRes/NEXUS
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[[http://www.phylo.org/index.html][CIPRes]] is a major multi-institutional research initiative in phyloinformatics and computational phylogenetics. One of their staff, Main.ShirleyCohen, has begun evaluating SDD for its utility to various aspects of the CIPRes effort and has produced a rather interesting spreadsheet, attached, comparing SDD to current CIPRes representations. The spreadsheet is based, where it can be, on criteria elucidated by Mike Dallwitz [[http://biodiversity.uno.edu/delta/www/compdata.htm][comparing DELTA to NEXUS]] facilities.
d7 1
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Shirley's analysis was based on 0.91b16, but most things of interest to her haven't changed. I've spent a little time with her going over some of SDD 0.91b25; the attachment represents a few changes from her original. Herewith I make subtopics for the few issues in the spreadsheet where she couldn't see how to represent the concept in SDD. Some we clearly can do and I just ran out of time in our discussion. Some I don't see how to do, some I don't understand what's meant, and some we don't do (but maybe could easily). The major one we agreed(?) not to address in SDD 1.0 is character and state inheritance.
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 |*row*|*feature*			 |*intent*|*sdd feature*|*sdd ver*|*spreadsheet ver*|
 |23	|CharacterKeywords  |unordered character sets|Concept Trees|0.91b25|1.0 23June2004|
 |44	|StructureOfTaxonNames|???|???|???|1.0 23June2004|
 |45	|<nop>ImplicitValues|?| [see note 1]| |1.0 23June2004|
 |46	|IndefiniteValues	|?| | |1.0 23June2004|
 |47	|AttributeWeights	|?| | |1.0 23June2004|
 |48	|AttributePassedUp  |inheritance| | |1.0 23June2004|
 |49	|AttributePassedDown|inheritance| | |1.0 23June2004|
 |52	|TaxonKeywords		|unordered taxon sets|Class Hierarchy|0.91b25|1.0 23June2004|
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For some comparison between DELTA and SDD, see [[http://www.DiversityCampus.net/Projects/TDWG-SDD/SDD_DELTA_CompComplexity.html][Complexity of SDD versus DELTA]] and [[http://www.DiversityCampus.net/Projects/TDWG-SDD/SDD_DELTA_Export2SDD.html][Exporting DELTA to SDD]]). Note that these documents refer to SDD 0.9, some of the outer structures have changed since. I will try to update the documents as soon as I have time. -- Gregor
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	* [[%ATTACHURL%/ComparisonMatrix.xls][ComparisonMatrix.xls]]: Comparison of SDD with CIPRes/NEXUS
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%META:TOPICINFO{author="BobMorris" date="1088026620" format="1.0" version="1.1"}%
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 |*row*|*feature*|*intent*|*sdd feature*|*sdd ver*|*spreadsheet ver*|
 |23|CharacterKeywords|unordered character sets|Concept Trees?|0.91b25|1.0 23June2004|
 |44|StructureOfTaxonNames|???|???|???|1.0 23June2004|
 |45|ImplicitValues|?| | |1.0 23June2004|
 |46|IndefiniteValues|?| | |1.0 23June2004|
 |47|AttributeWeights|?| | |1.0 23June2004|
 |48|AttributePassedUp|inheritance| | |1.0 23June2004|
 |49|AttributePassedDown|inheritance| | |1.0 23June2004|
 |52|TaxonKeywords|unordered taxon sets|Concept Trees?|0.91b25|1.0 23June2004|
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-- Main.BobMorris - 23 Jun 2004
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