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OneOfPosition, how to point to the actual positions? #37

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ljgarcia opened this issue Aug 10, 2018 · 5 comments
Open

OneOfPosition, how to point to the actual positions? #37

ljgarcia opened this issue Aug 10, 2018 · 5 comments

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@ljgarcia
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Hi all,

Let's suppose we have a site that has a location at either 143 or 144. I will link that site to a OneOfPosition element via faldo:location. Now, what would be the right predicate from the OneOfPosition element and the actual positions?

If my OneOfPosition is , I would have to do something like
- faldo:location - faldo:ExactPosition - faldo:Position - 143
- faldo:location - faldo:ExactPosition - faldo:Position - 144

Seems a bit long. Should not be easier having a predicate to directly link to OneOfPosition to the actual positions?

@JervenBolleman
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Hi @ljgarcia,

Very good question. Right now as documented it would be

Right now as documented it would be.

<mything> faldo:location [
    a faldo:OneOfPosition ;
    faldo:location <option143> , <option144> .
]

<option143> a faldo:ExactPosition ;
    faldo:position 143 ;
    faldo:reference <mysequence> .


<option144> a faldo:ExactPosition ;
    faldo:position 144 ;
    faldo:reference <mysequence> . 

At somepoint I was thinking about .

<mything> faldo:location [
    a faldo:OneOfPosition ;
    faldo:possiblePosition <option143> , <option144> .
]

But this was not added to FALDO, now I am thinking should that be done afterall?

@peterjc peterjc changed the title OneOfPosition, how to point to the actula possitions? OneOfPosition, how to point to the actual positions? Aug 11, 2018
@ljgarcia
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Using faldo:possiblePosition seems easier and cleaner. What would be the way for this to make it to the ontology? Do you need a supporting use case?

@JervenBolleman
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I think discussing a pull request with a fix of this of the tll on the mailing list will be best.

ljgarcia added a commit to ljgarcia/FALDO that referenced this issue Aug 31, 2018
It is currently not straight forward to model possible positions for OneOfPosition, see OBF#37. The new property possiblePositions makes it simpler.
The second new property for FuzzyPosition, probability, cover cases as those of PTMs in IntAct where a probability is assigned to a fuzzy position.
@ljgarcia
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@JervenBolleman please find a pull request in this regard, see #38

@ljgarcia
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ljgarcia commented Nov 1, 2018

Hi all, @JervenBolleman

Any news on PR #38? I saw on an email that faldo:possbilePosition would be ok but faldo:probablePossition maybe not too much. I am happy to modify the PR to get at least the possible position in place. Could you please comment on the PR what changes are needed in order to get this included in FALDO?

Thanks,

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