On Feb 25, 2013, at 5:50 PM, Alan Ruttenberg wrote:



On Mon, Feb 25, 2013 at 5:35 PM, Erick Antezana <erick.antezana@gmail.com> wrote:
I would think the owl2obo for that term should look like the following
(assuming that "alternative term"  (IAO) = exact synonym):

[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant  that is a bearer of quality  and realizable entity
 entities, in which other entities inhere and which itself cannot
inhere in anything." []
property_value: example_of_usage "a chair" xsd:string
property_value: example_of_usage "a heart" xsd:string
property_value: example_of_usage "a leg" xsd:string
property_value: example_of_usage "a person" xsd:string
property_value: example_of_usage "a symphony orchestra" xsd:string
property_value: example_of_usage "an organism" xsd:string
property_value: example_of_usage "the bottom right portion of a human
torso" xsd:string
property_value: example_of_usage "the lawn and atmosphere in front of
our building" xsd:string
synonym: "substantial entity" EXACT []
is_a: BFO:0000002 ! continuant

Why the extra "property value:" and xsd:string noise?
 

or something like the following if we have extra instances or terms:

[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant  that is a bearer of quality  and realizable entity
 entities, in which other entities inhere and which itself cannot
inhere in anything." []
property_value: example_of_usage chair
property_value: example_of_usage heart
property_value: example_of_usage leg
property_value: example_of_usage person
property_value: example_of_usage symphony_orchestra
property_value: example_of_usage organism
property_value: example_of_usage XYZ:0000011
property_value: example_of_usage XYZ:0000012
synonym: "substantial entity" EXACT []
is_a: BFO:0000002 ! continuant

where 'chair', 'heart', 'leg', ..., XYZ:0000011 (=the lawn...) are IDs
of an instance or term/universal...

I think that some terms will have other kind of example_of_usage's
where their type could be a date (xsd:date) or a positive integer
(xsd:positiveInteger)... if so, explicitly having xsd:string might
still be useful...


I agree that having type information is useful. But default the common case, which is xsd:string. Or better have some way to map strings to instances, so the mapping can be imported in different places. Or use the approach that manchester syntax does, which is that if it looks like a number it, it *is* a number. Could do the same with dates.

OWL can't do defaulting or dwimming, but OBO can. 

This would be a non-backwards compatible change. I'm hesitant to do this unless there's strong demand.

 

cheers,
Erick

On 25 February 2013 05:26, Alan Ruttenberg <alanruttenberg@gmail.com> wrote:
> I was looking at an OORT generated OBO version of OBI and was struck by how
> unnecessarily (afaik) unpleasant rendering. Here's the example:
>
> Before:
>
> [Term]
> id: BFO:0000004
> name: independent continuant
> def: "A continuant  that is a bearer of quality  and realizable entity
> entities, in which other entities inhere and which itself cannot inhere in
> anything." []
> property_value: IAO:0000111 "independent continuant" xsd:string
> property_value: IAO:0000112 "a chair" xsd:string
> property_value: IAO:0000112 "a heart" xsd:string
> property_value: IAO:0000112 "a leg" xsd:string
> property_value: IAO:0000112 "a person" xsd:string
> property_value: IAO:0000112 "a symphony orchestra" xsd:string
> property_value: IAO:0000112 "an organism" xsd:string
> property_value: IAO:0000112 "the bottom right portion of a human torso"
> xsd:string
> property_value: IAO:0000112 "the lawn and atmosphere in front of our
> building" xsd:string
> property_value: IAO:0000118 "substantial entity" xsd:string
> is_a: BFO:0000002 ! continuant
>
> Here's  what I think it should look like. Comments below. Is there a reason
> it can't look like this? It seems that the benefit of OBO, something that we
> should retain, is that it's possible to read and author it in a text editor.
>
> [Term]
> id: BFO:0000004
> name: independent continuant
> def: "A continuant  that is a bearer of quality  and realizable entity
> entities, in which other entities inhere and which itself cannot inhere in
> anything." []
> example_of_usage: "a chair"
> example_of_usage: "a heart"
> example_of_usage: "a leg"
> example_of_usage: "a person"
> example_of_usage: "a symphony orchestra"
> example_of_usage: "an organism"
> example_of_usage: "the bottom right portion of a human torso"
> example_of_usage: "the lawn and atmosphere in front of our building"
> synonym: "substantial entity" EXACT
> is_a: BFO:0000002 ! continuant
>
> Notes:
> Don't repeat name as IAO:0000111 - they mean the same thing.
> IAO:0000118 'alternative term' means the same thing as exact synonym
> property_value: IAO:0000112 means example of usage. I use a tag that says
> that. Is there a reason that the generic tag is necessary/desirable in
> someone's view?
> One doesn't need to ever write xsd:string, since that's the only type of
> string there is. When there is provision for language tags that will merit
> some extra markup.
>
> While there may be some controversy on a small set of the IAO metadata tags,
> particularly non-exact "synonyms", most of the metadata terms we envisioned
> as fitting comfortably in OBO syntax. The other ones I would add as built-in
> tags are (perhaps not exclusively - but these make sense on quick glance)
>
> editor-note:
> curation-note:
> curation-status:
> term-editor:
> obsolescence-reason:
> imported-from:
> denotator-type:
> first-order-logic-expression:
>
> While the field values of some of these are supposed to be taken from
> enumerated sets (e.g. curation_status is (currently) one of {'example to be
> eventually removed' , 'metadata complete' , 'organizational term' , 'ready
> for release' , 'metadata incomplete' , uncurated , 'pending final vetting' ,
> 'to be replaced with external ontology term' , 'requires discussion'}
> there's no reason why the translation rules can't take these from strings to
> their instances.
>
> Some of these tags could be construed to be equivalent to properties in
> other vocabularies, e.g. 'alternative term' -> skos:altLabel. When there was
> a wider discussion of this issue a number of years ago, the thought was 1)
> The other vocabulary terms are often poorly defined or ambiguous 2) that we
> should have, at least, annotation properties that are defined how we want
> them to be 3) That we should, in those cases where we defined a property
> that has a close cognate in a popular semweb vocabulary,  as a matter of
> courtesy, have property assertions for both the foundry defined annotation
> property as well as the external vocabulary property. Hence OBI mirrors
> labels (via script) between 'editor preferred name' and refs:label. Our
> OBO->OWL mapping could do the same.
>
> -Alan
>
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