Publishing Taxonomies - Revision history

Hilmar: /* Use Cases */

2009-11-11T15:30:44Z

Use Cases

← Older revision		Revision as of 15:30, 11 November 2009
Line 34:		Line 34:
	== Use Cases ==		== Use Cases ==

	This overlaps with ~~Taxo~~ Reasoning		This overlaps with Taxon Reasoning.

	* Give me the most recent common ancestor		* Give me the most recent common ancestor

Hilmar: /* Taxa are Logical Individuals with Parent/Child Links */

2009-11-11T15:26:32Z

Taxa are Logical Individuals with Parent/Child Links

← Older revision		Revision as of 15:26, 11 November 2009
Line 28:		Line 28:
	This seems like a more practical approach in that it is less likely to become broken by rogue publisher. We can then induce useful class hierarchies through restriction.		This seems like a more practical approach in that it is less likely to become broken by rogue publisher. We can then induce useful class hierarchies through restriction.

	Much of this is summed up in ~~this~~ [~~http://www.evoio.org/wiki/File~~:Class-based-taxonomy.pdf pdf]		Much of this is summed up in [[Media:Class-based-taxonomy.pdf\|this pdf]]

	This is the preferred option for publishing classification - but we need to work on it.		This is the preferred option for publishing classification - but we need to work on it.

Hilmar: /* Monophyly Class Examples */

2009-11-11T15:24:02Z

Monophyly Class Examples

← Older revision		Revision as of 15:24, 11 November 2009
Line 22:		Line 22:
	=== Monophyly Class Examples ===		=== Monophyly Class Examples ===

	This is described in [[Monophyly in DL]].		This is described in [[VoCamp1/Monophyly in DL]].

	== Taxa are Logical Individuals with Parent/Child Links ==		== Taxa are Logical Individuals with Parent/Child Links ==

Hilmar: /* Monophyly Class Examples */

2009-11-11T15:23:14Z

Monophyly Class Examples

← Older revision		Revision as of 15:23, 11 November 2009
Line 22:		Line 22:
	=== Monophyly Class Examples ===		=== Monophyly Class Examples ===

	This is described ~~on another page.~~		This is described in [[Monophyly in DL]].

	[[~~Monophyly_in_DL~~] ~~[http://www.evoio~~.~~org/wiki/VoCamp/Monophyly_in_DL]]~~

	== Taxa are Logical Individuals with Parent/Child Links ==		== Taxa are Logical Individuals with Parent/Child Links ==

Hilmar at 15:22, 11 November 2009

2009-11-11T15:22:30Z

← Older revision		Revision as of 15:22, 11 November 2009
Line 1:		Line 1:
	What 'format' should we ask publishers to make their biological classification available in?		What 'format' should we ask publishers to make their biological classification available in?

	Candidates include		'''Candidates include'''
	* Don't define anything - client's must do all the conversion to a class hierarchy.		* Don't define anything - client's must do all the conversion to a class hierarchy.
	* Use a generic RDF vocabulary that doesn't imply a class hierarchy		* Use a generic RDF vocabulary that doesn't imply a class hierarchy
Line 7:		Line 7:
	* Use a defined class hierarchy based on rdfs:subClassOf (see [http://www.hyam.net/publications/LinkedTaxaTutorial/ Roger Hyam's Linked Data Tutorial])		* Use a defined class hierarchy based on rdfs:subClassOf (see [http://www.hyam.net/publications/LinkedTaxaTutorial/ Roger Hyam's Linked Data Tutorial])

	~~----~~		'''Outcomes:'''
	Outcomes		* A recommendation document

	A recommendation document


	== Simple Subsumption Hierarchy ==		== Simple Subsumption Hierarchy ==

Hilmar at 15:21, 11 November 2009

2009-11-11T15:21:45Z

← Older revision		Revision as of 15:21, 11 November 2009
Line 4:		Line 4:
	* Don't define anything - client's must do all the conversion to a class hierarchy.		* Don't define anything - client's must do all the conversion to a class hierarchy.
	* Use a generic RDF vocabulary that doesn't imply a class hierarchy		* Use a generic RDF vocabulary that doesn't imply a class hierarchy
	* Use SKOS		* Use [http://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)
	* Use a defined class hierarchy based on rdfs:subClassOf (~~This approach is defined here:~~ http://www.hyam.net/publications/LinkedTaxaTutorial/)		* Use a defined class hierarchy based on rdfs:subClassOf (see [http://www.hyam.net/publications/LinkedTaxaTutorial/ Roger Hyam's Linked Data Tutorial])

	----		----

Hilmar at 15:20, 11 November 2009

2009-11-11T15:20:15Z

New page

What 'format' should we ask publishers to make their biological classification available in?

Candidates include
* Don't define anything - client's must do all the conversion to a class hierarchy.
* Use a generic RDF vocabulary that doesn't imply a class hierarchy
* Use SKOS
* Use a defined class hierarchy based on rdfs:subClassOf (This approach is defined here: http://www.hyam.net/publications/LinkedTaxaTutorial/)

----
Outcomes

A recommendation document

== Simple Subsumption Hierarchy ==

In this approach we would represent taxonomic hierarchies as subsumption hierarchies. Each taxon would be an RDFS class and joined to the others with rdfs:subClassOf links.

Strength of this is that it seems "natural". Many would consider taxonomy and possibly phylogenetic hierarchies as being a series of nested sets (classes) of individuals.

Weakness is that if anyone makes an assertion directly about a class then OWL reasoners will consider it to be simultaneously an individual and a class - which is OWL Full and therefore not guaranteed to be decidable. It also makes it difficult to think about. To avoid this all properties that have the class resource as a subject must be declared owl:annotationProperties which excludes them from inference (except possibly under OWL 2.0). People may wish to infer over these classes.

Using class based publishing 'format' may be dangerous as if some data suppliers 'polluted' their data with assertions about classes it would prevent their data being imported directly into systems that relied on inference.

=== Monophyly Class Examples ===

This is described on another page.

[[Monophyly_in_DL] [http://www.evoio.org/wiki/VoCamp/Monophyly_in_DL]]

== Taxa are Logical Individuals with Parent/Child Links ==

This seems like a more practical approach in that it is less likely to become broken by rogue publisher. We can then induce useful class hierarchies through restriction.

Much of this is summed up in this [http://www.evoio.org/wiki/File:Class-based-taxonomy.pdf pdf]

This is the preferred option for publishing classification - but we need to work on it.

== Use Cases ==

This overlaps with Taxo Reasoning

* Give me the most recent common ancestor
* Give me all the specimens that have been identified to this taxon
* Give me specimens identified to this taxon or a synonym of this taxon or a taxon with the same name in another classification or a synonym of that taxon - as a class hierarchy.
* Give me give me give me

----

OWL / RDF skill
Biological Taxonomists
Ecologists please.
----

We are currently playing with some test data and failing to get it into Protege.

If this doesn't work we will try hand coding "Hello World" type data type to test the theories.