RE: [ANN] OTTR: RDF/OWL modelling framework release, ISWC tutorial from Cox, Simon (L&W, Clayton) on 2019-11-06 (semantic-web@w3.org from November 2019)

From: Cox, Simon (L&W, Clayton) <Simon.Cox@csiro.au>
Date: Wed, 6 Nov 2019 05:06:04 +0000
To: Simon Steyskal <simon.steyskal@gmail.com>, Martin G. Skjæveland <martige@ifi.uio.no>
CC: Chris Mungall <cjmungall@lbl.gov>, Dan Brickley <danbri@danbri.org>, Martynas Jusevičius <martynas@atomgraph.com>, "Semantic Web" <semantic-web@w3.org>, "holger@topquadrant.com" <holger@topquadrant.com>
Message-ID: <ME2PR01MB53620348F28CB12E0B1CF26388790@ME2PR01MB5362.ausprd01.prod.outlook.com>
Thanks Simon – yeah, I had seen that and had a go at getting it running in TBCME, but failed ☹
The doco didn’t help me get over that hump (a couple of years ago now tho.)

From: Simon Steyskal <simon.steyskal@gmail.com>
Sent: Wednesday, 6 November, 2019 15:54
To: Martin G. Skjæveland <martige@ifi.uio.no>; Cox, Simon (L&W, Clayton) <Simon.Cox@csiro.au>
Cc: Chris Mungall <cjmungall@lbl.gov>; Dan Brickley <danbri@danbri.org>; Martynas Jusevičius <martynas@atomgraph.com>; Semantic Web <semantic-web@w3.org>; holger@topquadrant.com
Subject: Re: [ANN] OTTR: RDF/OWL modelling framework release, ISWC tutorial

@Simon Cox<mailto:simon.cox@csiro.au>
> SPIN had the advantage that it supported SPARQL CONSTRUCT.
> This is still hinted at in SHCAL but I haven’t found it implemented.

@Martin G. Skjæveland<mailto:martige@ifi.uio.no>
> As already pointed out in this thread, SHACL and ShEX, as constraint
> languages, do not support /generating/ patterns, "only" describing
> them. SPIN on the other hand is a more generic language that as a rule
> language also supports generating patterns.

SHACL Rules (similar to SPIN Rules):
Defined here -> https://www.w3.org/TR/shacl-af/#rules (not part of the core SHACL Rec., but published as W3C Note)
Implemented e.g., by TopBraid's SHACL API -> https://github.com/TopQuadrant/shacl


(pinging @Holger Knublauch<mailto:holger@topquadrant.com> for that matter)

- simon

Am Di., 5. Nov. 2019 um 20:31 Uhr schrieb Martin G. Skjæveland <martige@ifi.uio.no<mailto:martige@ifi.uio.no>>:
As already pointed out in this thread, SHACL and ShEX, as constraint
languages, do not support /generating/ patterns, "only" describing
them. SPIN on the other hand is a more generic language that as a rule
language also supports generating patterns.

OTTR has a more narrow focus than SPIN, aiming to be language for
representing reusable modelling patterns for RDF and OWL. These
templates are intended to be made available in libraries of
interconnected templates. OTTR templates are compositional in design,
meaning a template is defined based on other templates -- "it's
templates all the way down".  A template instance is "transformed" to
RDF by recursively expanding the instance to instances of the /base
template/ ottr:Triple, which represents an RDF triple. The relative
simple structure of OTTR templates permits automatic analysis of
template libraries to discover possibly unwanted redundancies like
overlap or containment between templates. Other possibly
distinguishing features of OTTR are a custom-built type system that is
used to type check template definitions and instances and can for
instance be used to disallow punning, and list arguments to support
variable length arguments.

This is an example of an OTTR template representing a pattern
implicitly used in the Pizza ontology:

ex:NamedPizza [ owl:Class ?pizza,
                 ? owl:NamedIndividual ?country,
                 NEList<ottr:IRI> ?toppings] :: {
   ax:SubClassOf(?pizza, ex:NamedPizza),
   ax:SubObjectHasValue(?pizza, ex:hasCountryOfOrigin, ?country),
   ax:SubObjectAllValuesFrom(?pizza, ex:hasTopping, _:toppingsUnion),
   rstr:ObjectUnionOf(_:toppingsUnion, ?toppings),
   cross | ax:SubObjectSomeValuesFrom(?pizza, ex:hasTopping, ++?toppings)
} .

and these are two instances of the template:

ex:NamedPizza(ex:Margherita, ex:Italy, (ex:Mozzarella, ex:Tomato)) .
ex:NamedPizza(ex:Hawaii, none, (ex:Cheese, ex:Ham, ex:Pineapple)) .

These are found in the interactive examples on http://ottr.xyz. Click
"Run" to see their expansion.

OTTR at its core does not support manipulating terms, e.g.,
concatenating two strings to form a URI. While this is of course a
necessary feature, we believe it should not be part of the *modelling
pattern* as this makes the pattern description in many cases too
specific to the input data. Data cleansing and preparation we believe
should be placed outside the template. (To support data ingestion, we
have introduced a simple mapping language that translates query
answers to OTTR template instances --- allowing for data preparation
in the query over the sources, see
http://spec.ottr.xyz/pOTTR/0.1/04-etl-bottr.html.)

We believe that the design of OTTR makes these templates easy to use
and maintain, but we have yet to evaluate this. Our belief is that
OTTR templates are well suited especially for large scale/long term
ontology development as the availability of a well managed library of
reusable and instantiable modelling patterns will pay off in the long
run. An initial library of basic patterns are available, and
maintenance procedures for template libraries are in development.

Martin

On 05/11/2019 06:47, Cox, Simon (L&W, Clayton) wrote:
> SPIN had the advantage that it supported SPARQL CONSTRUCT.
>
> This is still hinted at in SHCAL but I haven’t found it implemented.
>
> *From:* Chris Mungall <cjmungall@lbl.gov<mailto:cjmungall@lbl.gov>>
> *Sent:* Tuesday, 5 November, 2019 12:25
> *To:* Dan Brickley <danbri@danbri.org<mailto:danbri@danbri.org>>
> *Cc:* Simon Steyskal <simon.steyskal@gmail.com<mailto:simon.steyskal@gmail.com>>; Martin G. Skjæveland
> <martige@ifi.uio.no<mailto:martige@ifi.uio.no>>; Martynas Jusevičius <martynas@atomgraph.com<mailto:martynas@atomgraph.com>>;
> Semantic Web <semantic-web@w3.org<mailto:semantic-web@w3.org>>
> *Subject:* Re: [ANN] OTTR: RDF/OWL modelling framework release, ISWC
> tutorial
>
> AFAIK shape languages can't be used in a generative capacity. OTTR seems
> more in the family of templating languages such as OPPL[1], ROBOT
> templates[2], or Dead Simple OWL Design Paterns[3]
>
> [1] https://github.com/owlcs/OPPL2

>
> [2] http://robot.obolibrary.org/template R.C. Jackson, J.P. Balhoff, E.
> Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for
> automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019.
> https://link.springer.com/epdf/10.1186/s12859-019-3002-3

>
> [3] Dead Simple OWL Design Patterns David Osumi-Sutherland, Melanie
> Courtot, James P. Balhoff and Christopher Mungall Journal of Biomedical
> Semantics 2017 8:18 DOI:10.1186/s13326-017-0126-0
> https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0126-0

>
> On Fri, Nov 1, 2019 at 1:45 AM Dan Brickley <danbri@danbri.org<mailto:danbri@danbri.org>
> <mailto:danbri@danbri.org<mailto:danbri@danbri.org>>> wrote:
>
>     Or, for that matter, ShEx?
>
>     https://shex.io/

>
>     A good comparison could help clarify the entire design space.
>
>     (academics looking for good semweb topics for students, please take
>     note!)
>
>     On Fri, 1 Nov 2019 at 05:59, Simon Steyskal
>     <simon.steyskal@gmail.com<mailto:simon.steyskal@gmail.com> <mailto:simon.steyskal@gmail.com<mailto:simon.steyskal@gmail.com>>> wrote:
>
>         or SHACL?
>
>         https://www.w3.org/TR/shacl/#sparql-constraint-components

>
>         https://www.w3.org/TR/shacl-af/

>
>         - simon
>
>         On Fri, 25 Oct 2019, 09:09 Martynas Jusevičius,
>         <martynas@atomgraph.com<mailto:martynas@atomgraph.com> <mailto:martynas@atomgraph.com<mailto:martynas@atomgraph.com>>> wrote:
>
>             Hi Martin,
>
>             how does OTTR compare to SPIN templates?
>             https://spinrdf.org/spin.html#spin-templates

>
>
>             Martynas
>
>             On Fri, Oct 25, 2019 at 5:02 AM Martin G. Skjæveland
>             <martige@ifi.uio.no<mailto:martige@ifi.uio.no> <mailto:martige@ifi.uio.no<mailto:martige@ifi.uio.no>>> wrote:
>              >
>              > Hi all,
>              >
>              > Lutra, the open source reference implementation of OTTR
>             templates, is
>              > now available in release version 0.6.
>              >
>              > OTTR (Reasonable Ontology Templates) allows RDF/OWL
>             modelling patterns
>              > to be precisely defined and instantiated and support
>             desirable modelling
>              > principles such as
>              >
>              >   - layered abstractions
>              >   - encapsulating complexity
>              >   - uniform modelling
>              >   - DRY don't repeat yourself
>              >   - separation of design and content
>              >
>              > Lutra and OTTR supports many convenient language constructs:
>              >   - nested template definitions
>              >   - typing system adapted to RDF and OWL
>              >   - optional arguments
>              >   - list arguments
>              > and support bulk loading data from spreadsheets and
>             databases.
>              >
>              > To see and learn what this means, visit the project page:
>              > http://ottr.xyz and the primer
>             http://spec.ottr.xyz/pOTTR/0.1/

>              > containing many interactive examples.
>              >
>              > If you are attending ISWC 2019, please come to our
>             tutorial "Scalable
>              > construction of sustainable knowledge bases" tomorrow,
>             Saturday October
>              > 26: http://ottr.xyz/event/2019-10-267-iswc/

>              >
>              > On behalf of the OTTR team,
>              > Martin
>              >
>
Received on Wednesday, 6 November 2019 05:06:26 UTC