[Tcs-lc] Human Readable - the thread formally known as 'Name of NomenCode'

[Kennedy, Jessie]

Roger wrote:

What is the relationship type between a species and it's genus? Is it 'included in' or 'child of' and would the user agent expect the reciprocal relationships to be marked up i.e. 'includes' and 'is parent of'?  
 
It depends on how the species was defined. If it is as say a revision of a genus then each species is a "child of" the genus being revised.
 (of course one could interpret this to mean the genus includes the species but as Bob says this is implied - the relationship would be child of - agree with Bob's interpretation)
 
If someone comes along and defines a new speices for a genus and are saying the genus is the "parent of" the species. This in no way redefines the genus as described by the original author - so there should be no cascading. However someone working on the genus in future would want to consider the species that was defined to have the genus as it's parent so they might in their revision of the genus redefine it to include that species. 
Of course the author might have explicitly said they were redefining the genus by accepting the previous definition (and all of its species as is) and adding a new species in which case we would have a revision of the genus and the relationship could then in this case be "child of".
 
 
Would all software agents:


1.	expect only up pointing links. 

2.	expect only down pointing links. 

3.	expect both to be present for the link to be valid.


4.	allow the use of a mixture of the two, relationship sometime shown with 'includes' and sometimes with 'included in'.  

they should expect a mixture - as either are possible depending on what was meant by the taxonomist doing the work. 
Nico gave a good summary answer - I agree with him on this. 
This is why we need different types of relationships with different semantics to allow us to choose to traverse them or not in dffierent situations.
If I have have a revision of a family F1 according to X say and produce a hierarchy of the genera it contains (g1..G3) and for each of these the species they contain (s1-s3),(s4-s7) (s8). If someone,Y, later came along and said that they had found a new species s9 and placed it in G3 then this would not change the definition of G3 or F1 as defined by X. 
If I I wanted to know what species were in the family according to X then I would get s1...s8 as these were all defined by X.However if I wanted to know all the species that were in F1(nominal) then I would get s1-s9. There are several ways to implement this but that would be my interpretation of the semantics. 
 
I define relationships between a species concept and it's genus concept but what about the subgenus and sectional stuff? 
I could:


1.	mark the species as belonging to the section and section to subgenus and subgenus to genus and not specify any other relationships 

2.	 join the species to section, subgenus and genus as well as joining up the section to subgenus and genus and subgenus to genus. i.e. all the includes relationships. 

3.	do a mixture of the two. Species always in genus but other things not.
 

again this depends on what the taxonomist did - if the taxonomist defined a classification using section and subgenus then the relationships would be most appropriately marked as described in 1. However for nomenclatural purposes placement of species in genus is required so there would be a relationship between species and genus but of a different type (placed in ?? as we used in Prometheus)
 
I am in agreement with Sally and Paul's repsonses on this.
 
Confused? I am and I am just doing this manually! I find the thought of writing software to consume this more scary than handling the links to the publications and specimens. Even if we define how these relationships should be encoded there is no way for the schema to validate it so we will have to write checking code and try and handle graceful degradation etc. I think we need to nail this thing down a bit - there should only really be one way of encoding a basic taxonomic hierarchy and that should be enforced by the schema I think. What do you all think? 
 
well it depends on whether we are modelling how taxonomy should be done or how it has been done and how we want it to be done in future. If we want to cover best practice for futrue and deal with legacy data and approaches then we can't write rules expressing how it should've been done. 

 Jessie 


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