Based on the CHEBI ontology perspective, alcohol is a class with subclasses like 'aromatic alcohol' which has subclasses like 'benzyl alcohols' which has subclasses like 'methylbenzyl alcohol' and so on. These relationships seem worth capturing and subclass seems like a reasonable way to do it. If not, would another property be better? Check out CHEBI here: http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=alcohol&que… -Ben On Thu, Sep 25, 2014 at 10:52 AM, Alain Cuvillier < alain.cuvillier(a)gmail.com&gt; wrote: _______________________________________________ Wikidata-l mailing list Wikidata-l(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata-l

Hi, I fully agree with Thomas and the other replies given here. Let me give some other views on these topics (partly overlapping with what was said before). It's important to understand these things to get the subclass of/instance of thing right -- and it would be extremely useful if we could get this right in our data :-) What is a class and what is an item is often a matter of perspective, and it is certainly accepted in the ontology modelling community that one thing may need to be both. The important thing is that "subclass of" is a relation between *similar* things (usually of the same type): * "sports car" subclass of "car" * "Porsche Carrera" subclass of "sports car" * "Porsche 356" subclass of "Porsche Carrera" Use "A subclass of B" if it makes sense to say "all A's are also B's" as in "all Porsche Carreras are sports cars". In contrast, "instance of" is between things that are very *different* in nature: * "Douglas Adams" instance of "human" * "human" instance of "species" Subclass naturally forms chains, like in my example. You can leave out some part of the chain and the result is still meaningful: * "Porsche Carrera" subclass of "car" [makes sense] For instance of, this does not work: * "Douglas Adams" instance of "species" [bogus] So if you want to organise things in a hierarchy (specific to general), then you need "subclass of". If you just describe the type of one thing, then you need "instance of". It is perfectly possible that one thing participates in both types of relationships. In addition to these general guidelines, I would say that a well-modelled ontology should be organised in "levels": whenever you use instance of, you go to a higher level; if you use subclass of, you stay on your current level. Each thing should belong to only one level. Here is an example where this is violated: * "Porsche Carrera" subclass of "sports car" * "Porsche 356" subclass of "Porsche Carrera" * "Porsche 356" instance of "sports car" Each of these makes sense individually, but the combination is weird. We should make up our mind if we want to treat Porsche 356 as a class (on the same level as sports car) or as an instance (on a lower level than sports car), but not do both at the same time. I think "subclass of" usually should be preferred in such a case (because if it is possible to use subclass of, then it is usually also quite likely that more specific items occur later [Porsche 356 v1 or whatever], and we really will need subclass of to build a hierarchy then). Cheers, Markus On 25.09.2014 20:10, Thomas Douillard wrote: _______________________________________________ Wikidata-l mailing list Wikidata-l(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata-l

The statement "ethanol *instance of* chemical compound" is ontologically incorrect. Importantly, it is also incompatible with ChEBI, the most widely-used chemistry ontology. The matter of how to apply *instance of* (P31, rdf:type) and *subclass of* (P279, rdfs:subClassOf) on Wikidata in relation to chemical entities has been, as Thomas puts it, a long discussion [1-5]. Hopefully with a wider audience and experts like Markus Krötzsch and Denny Vrandečić now interested, we can come to a resolution at least in the particular domain of chemical compounds. Since it concerns interoperability with another large Semantic Web project, I have copied Janna Hastings and Alan Ruttenberg on this discussion. Janna coordinates ChEBI. Alan coordinates BFO, the upper ontology used by ChEBI and many other major ontologies in the natural sciences, like Gene Ontology and Disease Ontology. Denny indicates how the statement "Porsche 356 *instance of *car" would be incorrect in Wikidata even though "Porsche 356 *is a* car" is acceptable in everyday speech. Similarly, "ethanol *instance of* chemical compound" is incorrect in Wikidata even though "ethanol *is a* chemical compound" is acceptable in less formal contexts. A key difference between talk about cars and talk about chemicals is that, with cars, we have familiar terms like "car model" that distinguish concrete instances (that *particular* car you see on the street) from abstract "instances" (i.e. metaclasses, classes that are also instances, the *kind* of car that you see on the street). We do not have a well-known term like "chemical model" or "chemical compound type" to distinguish classes (types) of chemicals and instances (tokens) of chemicals. When one speaks of the properties of ethanol or hydrogen, it is understood that the subject is *all concrete, particular, spatiotemporal tokens, i.e. instances *of ethanol and hydrogen -- not just a specific ethanol molecule floating in that container before you on a Saturday with friends, but all molecules that we label "ethanol" everywhere. Thus, in order to formally classify ethanol itself as opposed to some particular ethanol molecule, we must say for an item like http://www.wikidata.org/wiki/Q153: "ethanol *subclass of* chemical compound" and not "ethanol *instance of* chemical compound". (On Wikidata, the statement is more precisely "ethanol *subclass of *alcohol", but it is entailed from the statements "alcohol *subclass of* organic compound" and "organic compound *subclass of* chemical compound" that "ethanol *subclass of* chemical compound".) A common defense of statements like "ethanol *instance of* chemical compound" is that Wikidata will never have items about any concrete molecules of ethanol, so, since ethanol is a "leaf node" in our concept taxonomy, it makes sense to state that ethanol is an instance. That interpretation of "instance" is short-sighted. It precludes us from ever talking about particular tokens of ethanol, or particular aggregates of such objects, without overhauling our chemistry ontology. Excluding consideration of metaclasses like "chemical compound type", the fact that an entity is a leaf node in a concept hierarchy is a necessary but not sufficient condition for using *instance of*. Another common suggestion is that we should state something like "ethanol *instance of* chemical compound type" and "ethanol *subclass of* chemical compound". To see where that gets us, try wrapping your head around this: https://commons.wikimedia.org/wiki/File:Atom_classes.svg. Really, take a look. If we want Wikidata's concept hierarchy to be seen as of dauntingly complex, pervasively applying that kind of three-layer classification scheme will do. The kind of explicit metamodeling seen when punning things like cars and car models, ships and ship classes, biological taxa and organisms, etc. works reasonably well in certain domains. But, while we hold that hammer in one hand, we should be careful not to see everything as a nail. Outside domains that have established vocabulary for metaclasses, imposing explicit metamodeling with statements like "ethanol *instance of* chemical compound type" or "hydrogen *instance of* atom type" will strike users as unduly complex. Without such metamodeling, though, querying for a list of chemical compounds becomes murkier. Surely we would want to return "ethanol" and not "organic compound" in such a list. How about "alcohol"? Relatedly, if we don't state "oxygen *instance of *chemical element", then how can we easily query for all the elements in the Periodic Table of Elements without including in the results of any potential subclasses of oxygen (e.g., isotopes of oxygen like oxygen-16, oxygen-17, etc.)? There are ways to achieve that in SPARQL using rdfs:subClassOf / P279 / *subclass of*, but they require adhering to certain conventions. When faced with requiring many potential query users to learn some Wikidata MetaObject Protocol, though, I'm inclined to make some sacrifices for simplicity, ontological correctness, and consistency with major existing ontologies. In summary, this ball has punted for over a year now. Because of the impasse in how to classify chemical entities, we now have showcase items that have obvious problems like entailing that something is both a class and an instance of chemical compound. We need input from a wider group of people knowledgeable about ontology or chemistry, ideally both. Hopefully with a Wikimedian in Residence at the Royal Society of Chemistry [6] we'll get some more focused resources on this. All major scientific ontologies use *subclass of* (rdfs:subClassOf), not *instance of* (rdf:type), to classify such things. In my opinion, Wikidata should maintain technical and philosophical compatibility with ontologies like ChEBI and remove statements like "ethanol *instance of* chemical compound". This would improve interoperability between Wikidata and the rest of the Semantic Web. Thanks, Eric https://www.wikidata.org/wiki/User:Emw 1. https://www.wikidata.org/wiki/Wikidata:Project_chat/Archive/2014/07#Forth_a… 2. https://www.wikidata.org/wiki/Wikidata:Project_chat/Archive/2014/05#chemica… . 3. https://www.wikidata.org/wiki/Wikidata_talk:WikiProject_Chemistry#Germanium…. 4. https://www.wikidata.org/wiki/Wikidata:Project_chat/Archive/2014/07#Subclas… 5. https://www.wikidata.org/wiki/Help_talk:Basic_membership_properties#Proposi… 6. http://pigsonthewing.org.uk/wikimedian-residence-royal-society-chemistry/ _______________________________________________ Wikidata-l mailing list Wikidata-l(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata-l

Hi David, How does your treatise relate to the fact that https://www.wikidata.org/wiki/Q153 has statements that entail the following? [1] ethanol *instance of* chemical compound *subclass of* chemical compound How would it resolve that specific problem? Such statements make Wikidata incompatible with ChEBI and other major ontologies, like Gene Ontology and Disease Ontology, which use *instance of* (i.e. rdf:type, P31) and *subclass of* (i.e. rdfs:subClassOf, P279, is_a) as recommended in the Relation Ontology (RO) [2] and the Basic Formal Ontology (BFO). For Wikidata to be interoperable with other major ontologies in the Semantic Web, we cannot "scrap everything and start again from the beginning". We must stand on the shoulders of giants. Doing away with "entity" [3] as a the top of the *subclass of* hierarchy and introducing a raft of idiosyncratic ontological constructs like "identifiables", "cognizables", "negentropy" and "system survival-oriented direction" to Wikidata is probably not the way to go. Regarding your concerns about the ability of existing approaches to represent emergent properties and natural language, I recommend perusing [4], an influential paper that informs DOLCE and BFO -- particularly the section on "The Role of Identity Criteria". I also highly recommend lectures 3 and 1 in http://ontology.buffalo.edu/smith/IntroOntology_Course.html for gaining a perspective on how BFO maintainers think about things like distinguishing objects and representations, and that upper ontology's philosophical roots. Given your interest in phenomenology and Husserl, you may also be interested in what BFO maintainers have written on those subjects in e.g. [5] with regard to ontology. Best, Eric [1] https://www.wikidata.org/wiki/Q153 currently states "ethanol *subclass of* alcohol", but given "alcohol *subclass of* organic compound" and "organic compound *subclass of* chemical compound", it is entailed that "ethanol *subclass of* chemical compound". [2] Barry Smith et al. (2005). *Relations in Biomedical Ontologies*. http://genomebiology.com/2005/6/5/r46 [3] "Entity" item on Wikidata. https://www.wikidata.org/wiki/Q35120. Mapped to owl:Thing. [4] Nicola Guarino (1998). *Some Ontological Principles for Designing Upper Level Lexical Resources*. http://arxiv.org/pdf/cmp-lg/9809002v1 [5] Barry Smith (1989). *Husserl: Logic and Formal Ontology*. http://ontology.buffalo.edu/smith/articles/lfo.html

wrote:

It is a mistake to have ethanol both subclass and instance of chemical compound. if chemical compound is a class, then it cannot be a metaclass.

wrote:

Sorry Micru, I read your document, but I can't see a relation beetween ethanol, negenthropy, and Wikidata's survival :)

I have removed the statement *"instance of* chemical compound" from ethanol (Q153) [1]. A few proposals have been made in this thread about how -- or whether -- to use *instance of* (i.e. rdf:type, P31) to classify 'ethanol' and other chemical compounds, but there seems to be consensus that "*instance of* chemical compound" is not the way to do it. Summary of proposals: 1. *Do not use instance of for chemical compounds*. Such statements make Wikidata incompatible with many major scientific ontologies, like ChEBI, Gene Ontology and Disease Ontology, which use *instance of* as defined in the Relation Ontology (RO) [2]. Note that RO defines instances as particular things that have a unique location in space and time, whereas classes are universal, general entities which have particular instances. Instances and classes are thus disjoint, so RO-based ontologies cannot have entities that have both *instance of* (rdf:type, P31) and *subclass of* (rdfs:subClassOf, P279) statements as is possible in OWL 2 DL via punning. 2. *Use statements like "instance of type of chemical compound" for chemical compounds*. Doing so makes it easier to generate lists of chemical compounds, and is valid in OWL 2 DL -- it is metamodeling via punning. Let's build consensus for how (or whether) we want to use *instance of* for chemical compounds before any mass edits to remove or replace the 14969 other "*instance of* chemical compound" claims [3] or adding statements like "*instance of *type of chemical compound" to ethanol. Micru has a different proposal for how to model items, which incidentally does not represent "ethanol" as an instance [4]. However, that proposal is clearly a more radical vision for Wikidata, and probably warrants a separate thread for discussion. Eric https://www.wikidata.org/wiki/User:Emw [1] Removal of "*instance of* chemical compound" from ethanol: https://www.wikidata.org/w/index.php?title=Q153&diff=162563849&oldi… [2] Barry Smith et al. (2005). *Relations in Biomedical Ontologies*. http://genomebiology.com/2005/6/5/r46 [3] All "*instance of* chemical compound" claims on Wikidata. http://tools.wmflabs.org/wikidata-todo/autolist.html?q=claim[31:11173] [4] "'ethanol' is no longer an instance, but a class". https://lists.wikimedia.org/pipermail/wikidata-l/2014-October/004691.html _______________________________________________ Wikidata-l mailing list Wikidata-l(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata-l

Hi David, How does your treatise relate to the fact that https://www.wikidata.org/wiki/Q153 has statements that entail the following? [1] ethanol *instance of* chemical compound *subclass of* chemical compound How would it resolve that specific problem? Such statements make Wikidata incompatible with ChEBI and other major ontologies, like Gene Ontology and Disease Ontology, which use *instance of* (i.e. rdf:type, P31) and *subclass of* (i.e. rdfs:subClassOf, P279, is_a) as recommended in the Relation Ontology (RO) [2] and the Basic Formal Ontology (BFO). For Wikidata to be interoperable with other major ontologies in the Semantic Web, we cannot "scrap everything and start again from the beginning". We must stand on the shoulders of giants. Doing away with "entity" [3] as a the top of the *subclass of* hierarchy and introducing a raft of idiosyncratic ontological constructs like "identifiables", "cognizables", "negentropy" and "system survival-oriented direction" to Wikidata is probably not the way to go. Regarding your concerns about the ability of existing approaches to represent emergent properties and natural language, I recommend perusing [4], an influential paper that informs DOLCE and BFO -- particularly the section on "The Role of Identity Criteria". I also highly recommend lectures 3 and 1 in http://ontology.buffalo.edu/smith/IntroOntology_Course.html for gaining a perspective on how BFO maintainers think about things like distinguishing objects and representations, and that upper ontology's philosophical roots. Given your interest in phenomenology and Husserl, you may also be interested in what BFO maintainers have written on those subjects in e.g. [5] with regard to ontology. Best, Eric [1] https://www.wikidata.org/wiki/Q153 currently states "ethanol *subclass of* alcohol", but given "alcohol *subclass of* organic compound" and "organic compound *subclass of* chemical compound", it is entailed that "ethanol *subclass of* chemical compound". [2] Barry Smith et al. (2005). *Relations in Biomedical Ontologies*. http://genomebiology.com/2005/6/5/r46 [3] "Entity" item on Wikidata. https://www.wikidata.org/wiki/Q35120. Mapped to owl:Thing. [4] Nicola Guarino (1998). *Some Ontological Principles for Designing Upper Level Lexical Resources*. http://arxiv.org/pdf/cmp-lg/9809002v1 [5] Barry Smith (1989). *Husserl: Logic and Formal Ontology*. http://ontology.buffalo.edu/smith/articles/lfo.html _______________________________________________ Wikidata-l mailing list Wikidata-l(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata-l