transitivity of reference and position with begin/end

[nlwashington]

In the example below, I have two features that are defined by regions that span 500-600 and 1000-2000 on the same reference. Then, I want to add a new feature's region (mybigregion) that is defined in terms of those other regions. But at the time that I process mybigregion, I don't know the coordinates of the 5prime and 3prime regions, I only know the ids of those regions. I want it to represent the region that could be computed to span 500-2000. Right now, I can say the following:

  _:my5primeregion a Region
    faldo:begin _:position500
    faldo:end  _:position600

  _:my3primeregion a Region
    faldo:begin _:position1000
    faldo:end _:position2000

  _:mybigregion a Region
    faldo:begin _:beginOf5primeRegion
    faldo:end _:endOf3primeRegion

  _:beginOf5primeRegion a FuzzyPosition
    faldo:reference _:my5primeRegion

  _:endOf3primeRegion a FuzzyPosition
    faldo:reference _:my3primeRegion

  _:position500 a Position
    faldo:position 500
    faldo:reference _:myChromosome

  _:position600 a Position
    faldo:position 600
    faldo:reference _:myChromosome
  
  _:position1000 a Position
    faldo:position 1000
    faldo:reference _:myChromosome

  _:position2000 a Position
    faldo:position 2000
    faldo:reference _:myChromosome

What is the status of the transitivity of position and reference for begin/end properties? would the faldo:end of _:my3primeRegion transitively be the faldo:end of _:mybigregion, and similarly for the faldo:begin of the _:my5primeRegion ?

tagging @mbrush, @cmungall

[JervenBolleman]

Currently these are not transitive. A new transitive begin property could be mined, but I am not sure about the real use case?

The cases where we thought this would happen is when you don't know the start and end precisely.
i.e. starts between 500-600 ends between 1000-2000
Here it seems you do, know it starts at 500 and ends at 2000. However, at the point of generating the triple you can't access it. However, instead of using OWL to postprocess to fix it could you use any other cheaper method?

[cmungall]

transitivity of begin is provable (given my formal definition of begin) - do you have a counter-example where it isn't?

What we can do is make a bridge to RO which has a more complete axiomatization. I think we can declare faldo:begin to be an equivalentProperty of
http://purl.obolibrary.org/obo/RO_0002516

This part of RO hasn't been as well fleshed out as the temporal counterpart:
http://purl.obolibrary.org/obo/RO_0002224

[JervenBolleman]

@cmungall I was worrying that changing the begin to be transitive, would give an issue with inexact positions. But that won't happen as they use the after/before predicates instead of begin/end.
So considering this begin can be a transitive property. Let me make a branch for testing.

[JervenBolleman]

@nlwashington there is now a branch#27 that contains the change. Would you mind testing it to make sure it works as intended.