Hi Peter,
The community-defined meaning of
subclass of (P279) is that of rdfs:subClassOf [1]. Similarly, the community-defined meaning of
instance of (P31) is that of rdf:type [2, 3].
There are some open problems with how to handle qualifiers on
instance of and
subclass of in RDF/OWL exports of P31 as rdf:type and P279 as rdfs:subClassOf, but that does not negate the community's decision to tie its two most basic membership properties to those W3C standard properties. In the current RDF/OWL exports that follow the community interpretation of P31 and P279, e.g. wikidata-taxonomy.nt.gz and wikidata-instances.nt.gz in [4], statements that have qualifiers on either of those properties are simply omitted.
The community's definition of disease is less established. However, there is consensus that diseases like cancer (Q12078) and malaria (Q12156) are classes. An instance of disease would be a particular case of a disease, i.e. a particular case of an abnormal condition in a particular organism. For example, it would be the particular case of throat cancer that caused U.S. President Ulysses S. Grant to die, as reflected in the Wikidata statement "Ulysses S. Grant cause of death throat cancer" [5].
Wikidata has no items on actual instances of disease to my knowledge -- although it does have at least one item about an instance of a symptom [6]. That of course does not mean that such instances of disease do not exist or that they could not theoretically be modeled in some local Wikibase installation (e.g. in a physician's office or a hospital) that uses Wikidata vocabulary to track actual instances of disease, e.g. a particular case of pancreatic cancer in a patient.
If you have questions or concerns regarding how diseases are modeled, I would recommend contacting Wikidata editor and disease ontologist Elvira Mitraka (Emitraka) [7], as well as WikiProject Medicine [8] or WikiProject Molecular Biology [9].
Regarding how outsiders can become aware of modeling methodology, I recommend reading
https://www.wikidata.org/wiki/Help:Basic_membership_properties and engaging with particular domain modeling groups on Wikidata, e.g. the wikiprojects mentioned above. This mailing list and Wikidata Project Chat [10] are also good places to ask questions.
Finally, regarding your question "Is Wikidata uniform in applying this methodology?", the answer is no. Wikidata's use of
subclass of and
instance of varies among (and sometimes within) different domains of knowledge like human occupations, creative work genres, cuisines, and sports. The basic difference in usage among those domains is using
instance of where others would use
subclass of.
For example, pizza (
https://www.wikidata.org/wiki/Q177) is currently modeled as an instance of food and (transitively) a subclass of food. Problematic indeed! Disease modeling achieves the same goal of easy queryability by making statements like "malaria
subclass of disease" and "malaria
subclass of parasitic protozoa infectious disease" [11], where the latter value transitively resolves to disease. This is not only rather redundant, but also makes the
subclass of hierarchy cyclic and thus not a directed acyclic graph (DAG) due to the situation you note in the item about disease itself. But at least it avoids the more severe problem of being ontologically incorrect as seen in the item on pizza -- and all chemical elements, e.g. hydrogen (Q556) [12].
Regards,
3. is a -> instance of.
https://www.wikidata.org/w/index.php?title=Property_talk:P31&oldid=254073736#is_a_-.3E_instance_of4.
http://tools.wmflabs.org/wikidata-exports/rdf/index.php?content=dump_download.php&dump=201509285. Ulysses S. Grant: cause of death.
https://www.wikidata.org/wiki/Q34836#P5096. George H. W. Bush vomiting incident.
https://www.wikidata.org/wiki/Q55401127.
https://www.wikidata.org/wiki/User:Emitraka8. WikiProject Medicine on Wikidata.
https://www.wikidata.org/wiki/Wikidata_talk:WikiProject_Medicine9. Wikiproject Molecular Biology on Wikidata.
https://www.wikidata.org/wiki/Wikidata:WikiProject_Molecular_biology10.
https://www.wikidata.org/wiki/Wikidata:Project_chat