Hi Markus, Thanks for your responses. Markus, I think the point that Sebastian was raising has more to do with practices for communities working on data modeling for wikidata than specifically about OWL semantics. Let me explain a little further. We are a group of 3-7 (depending on the week) people working collaboratively on the task of loading wikidata with content linking genes, diseases, and drugs. Even amongst this small group, we have struggled to keep our data modeling discussions orderly and productive - even before entering into these discussions with the broader community. Its a constant struggle to see the big picture. One of the main reasons for this (IMHO) is the lack of ways to view the structure of the model that we are assembling as its being figured out. This is a consequence of wikidata's schema-free design. e.g. on Freebase this problem was addressed using their Type system. For a given kind of thing, you could create/find a Type to describe it and there you could argue about what set of properties were most useful for representing things of that Type. Wikidata seems to want to deal with things one property at a time - which is fine until you want to come up with a coherent collection of a number of related properties and associated constraints that cover a particular domain. For that purpose an ontology and tools for looking at and thinking about the ontology become very useful. So.. currently we are experimenting with webprotege as a place to collaboratively work through our data models before entering into discussions on wikidata itself. Thoughts on that as a pattern for collaboration would be helpful - could/should we be doing this all in wikidata? Would some interface improvements be possible that facilitated schema-level views and discussions?
The idea of working in OWL (though note that we are not currently using any semantics beyond RDF-S) provides the added potential bonuses of facilitating import/export and mappings to other linked data sources, but this is really secondary to the social management challenge. Emw, We have not explicitly attempted to force alignment with BFO or OBO - though we have been in touch with Chris Mungall about this and would welcome help with such alignments either on webprotege or on wiki. We are driven very pragmatically based on the requirements generated by the data sources that are next on the list for import but, as the ontology discussion should indicate, want to do our best to help generate a clean and effective model for the community to build upon. -Ben On Mon, Apr 6, 2015 at 1:03 PM, Markus Krötzsch < mar...@semantic-mediawiki.org> wrote: > On 06.04.2015 22:02, Markus Krötzsch wrote: > >> Dear Sebastian, >> >> Using OWL is surely a nice idea when the semantics is appropriate (i.e., >> where you want Open-World entailment, not constraints) and here the >> > > Possibly misleading typo: I meant "where", not "here" ;-) -- Markus > > > > expressiveness is enough. This is much more difficult, however, than one >> might at first think it is. For a simple example, the common Wikidata >> constraint that a property is /symmetric/ can not be expressed in OWL. >> The reason is that, in order to represent statements with references and >> qualifiers in OWL (i.e., in RDF), one needs to introduce auxiliary >> individuals for statements. I discussed some of these limitations of OWL >> in my keynote at the "OWL: Experiences and Directions" workshop 2012, >> but it seems the slides are not on the web site. I will try if I can >> track them down and publish them somewhere. >> >> Maybe you already have observed these limitations yourself? I was not >> sure from your email (and the linked documents) how exactly you envision >> the use of OWL. One thing that is clear is that OWL does cannot be used >> on Wikidata directly, but only on an RDF version of it. For this reason, >> you should also have a look at the (many) ongoing discussions about the >> final details of this RDF model. You can find related issue reports on >> Phabricator. I think it is also fairly safe to base your work on the >> published RDF export (see our paper at ISWC 2014): there will be >> changes, but the basic structural aspects that matter for creating OWL >> statements will most likely be the same. The paper also contains some >> discussion of how current Wikidata constraints can be mapped to OWL >> (which of course is not the semantics that constraints have). >> >> >> Maybe I should explain this again in detail, since some of these issues >> do not seem to be completely clear to the Wikidata community right now. >> For example, you can see things like Wikidata's "instance of" (P31) >> being declared to be "equivalent" (P1628) to rdf:type. Of course, this >> "equivalence" is only an informal notion that refers to the common ideas >> of classification that are embodied in both "properties" (note that they >> are both called "properties" but that there are fundamental differences >> between RDF properties and Wikidata properties -- again, they are >> closely related in spirit but not in a precise formal way). In >> particular, there is no semantic framework where P31 and rdf:type >> coexist, so it does not make sense to declare them "equivalent" in any >> stronger way. The best we can do is to translate Wikidata data into RDF, >> but after this translation, there is no "P31" any more: instead, there >> are several RDF properties that are used together to encode P31 >> statements, and none of these RDF properties is "equivalent" to rdf:type. >> >> OWL is part of the RDF world, and it only has meaning in this context -- >> you cannot apply OWL to Wikidata contents directly. You can certainly >> apply OWL to RDF exported from Wikidata. However, it you want the >> resulting conclusions to be "first class" statements in the Wikidata >> world (as you seem to suggest), then you need to use an RDF encoding >> that faithfully captures all data in Wikidata. This is the reason why >> OWL can express the symmetry of RDF properties, but not the symmetry of >> Wikidata properties. >> >> Best regards, >> >> Markus >> >> >> On 03.04.2015 11:16, Sebastian Burgstaller wrote: >> >>> Hello all, >>> >>> Wikidata consists of millions of single data items, which is great. In >>> order to facilitate modeling the interactions between the single items, >>> we hereby suggest using OWL based ontologies >>> (http://en.wikipedia.org/wiki/Web_Ontology_Language). >>> >>> We think that using ontologies brings several advantages: >>> -Looking at an ontology (could collaboratively be generated e.g. on >>> webprotege.stanford.edu <http://webprotege.stanford.edu>) gives a very >>> clear overview of how data is interconnected. This would allow for >>> modeling of even very large and/or complex interactions. >>> -Layouting a data integration project in an ontology first, before >>> really integrating data into WD facilitates property proposal, as a >>> ontology with its properties could first be designed and then the >>> ontology with all its properties and classes could be generated as a >>> whole. >>> -Data could be queried/exported from WD based on an ontology by simply >>> selecting the whole or parts of an ontology. >>> >>> This approach has been suggested and discussed by Benjamin Good, Elvira >>> Mitraka, Andra Wagmeester, Andrew Su and me. As an example, we put >>> together draft properties for gene disease interactions, which allows >>> for WD community discussion of this apporach. A preliminary version can >>> be found here: >>> https://www.wikidata.org/wiki/User:ProteinBoxBot/GeneDiseaseIteraction_ >>> Discussion >>> >>> >>> Best regards, >>> >>> Sebastian >>> >>> >>> _______________________________________________ >>> Wikidata-l mailing list >>> Wikidata-l@lists.wikimedia.org >>> https://lists.wikimedia.org/mailman/listinfo/wikidata-l >>> >>> >> > > _______________________________________________ > Wikidata-l mailing list > Wikidata-l@lists.wikimedia.org > https://lists.wikimedia.org/mailman/listinfo/wikidata-l >
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