Package "sparqlprog_wikidata"

Title:	SPARQLprog bindings for WikiData
Rating:	Not rated. Create the first rating!
Latest version:	0.0.3
SHA1 sum:	52cd638fea49af2fbc2ed8b078afd7073ea0dea4
Author:	Chris Mungall <cmungall@gmail.com>
Packager:	Chris Mungall <cmungall@gmail.com>
Home page:	https://github.com/cmungall/sparqlprog_wikidata
Download URL:	https://github.com/cmungall/sparqlprog_wikidata/releases/*.zip
Requires:	dcgutils
	regex
	sparqlprog

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Details by download location

Version	SHA1	#Downloads	URL
0.0.1	b98c0c575900b89162f3cadceead488524995d30	7	https://github.com/cmungall/sparqlprog_wikidata/archive/v0.0.1.zip
0.0.2	446a607e627ef66eff20b815b34bba05b9feba4e	1	https://github.com/cmungall/sparqlprog_wikidata/archive/v0.0.2.zip
0.0.3	52cd638fea49af2fbc2ed8b078afd7073ea0dea4	49	https://github.com/cmungall/sparqlprog_wikidata/archive/v0.0.3.zip


Query wikidata using logic predicates

This is a module for sparqlprog that provides convenience predicates for making sparql queries over wikidata using logic programming terms. It allows you to define reusable query predicates, and to integrate programming constructs with queries in a declarative way.

Examples (command line):

All cities over a certain population size together with their continents:

pq-wikidata -l -L enlabel "city(City),part_of_continent(City,Continent),population(City,Pop),Pop>10000000"

yields:

City	Continent	Population	City Name	Continent Name	Pop Name
wd:Q174	wd:Q18	12106920	São Paulo	South America	$null$
wd:Q649	wd:Q46	12500123	Moscow	Europe	$null$
wd:Q1355	wd:Q48	10535000	Bangalore	Asia	$null$
wd:Q1156	wd:Q48	12442373	Mumbai	Asia	$null$
wd:Q406	wd:Q48	14657434	Istanbul	Asia	$null$
wd:Q406	wd:Q46	14657434	Istanbul	Europe	$null$
wd:Q85	wd:Q15	19500000	Cairo	Africa	$null$
wd:Q15174	wd:Q48	11908400	Shenzhen	Asia	$null$
wd:Q956	wd:Q48	21710000	Beijing	Asia	$null$
wd:Q1353	wd:Q48	26495000	Delhi	Asia	$null$

The -l argument auto-adds labels for every column (this is meaningless for the population column but this is included for consistency)

Create a file city_ontology.pro with a single line:

big_city(City) :- city(City),population(City,Pop),Pop>10000000.

Now the big_city/1 predicate can be reused in queries:

pq-wikidata --consult city_ontology.pro -l -L enlabel "big_city(City),part_of_continent(City,Continent)"

yields:

city	continent	city label	continent label
wd:Q956	wd:Q48	Beijing	Asia
wd:Q15174	wd:Q48	Shenzhen	Asia
wd:Q1353	wd:Q48	Delhi	Asia
wd:Q649	wd:Q46	Moscow	Europe
wd:Q406	wd:Q48	Istanbul	Asia
wd:Q406	wd:Q46	Istanbul	Europe
wd:Q1156	wd:Q48	Mumbai	Asia
wd:Q85	wd:Q15	Cairo	Africa
wd:Q1355	wd:Q48	Bangalore	Asia
wd:Q174	wd:Q18	São Paulo	South America

Qualified properties may be represented by n-ary predicates, such as population_at/3:

$ pq-wikidata -f tsv --consult tests/city_ontology.pro -l -L enlabel 'big_city(City),population_at(City,Pop,At),in_time_interval("2010-01-01"^^xsd:dateTime,"2013-01-01"^^xsd:dateTime,At)' | tbl2ghwiki

|City|Pop|Time|City Name|---|---| |---|---|---|---|---|---| |wd:Q1353|16787941|2011-01-01T00:00:00Z|Delhi|$null$|$null$ |wd:Q406|13624240|2011-01-01T00:00:00Z|Istanbul|$null$|$null$ |wd:Q649|11856578|2012-01-01T00:00:00Z|Moscow|$null$|$null$ |wd:Q3630|9607787|2010-01-01T00:00:00Z|Jakarta|$null$|$null$ |wd:Q404763|12010000|2011-01-01T00:00:00Z|Nanyang|$null$|$null$ |wd:Q649|11979529|2013-01-01T00:00:00Z|Moscow|$null$|$null$ |wd:Q649|11503501|2010-01-01T00:00:00Z|Moscow|$null$|$null$ |wd:Q11746|10220000|2013-01-01T00:00:00Z|Wuhan|$null$|$null$ |wd:Q406|14160467|2013-01-01T00:00:00Z|Istanbul|$null$|$null$ |wd:Q649|11776764|2011-01-01T00:00:00Z|Moscow|$null$|$null$ |wd:Q42622|10465994|2010-01-01T00:00:00Z|Suzhou|$null$|$null$ |wd:Q174|11316149|2011-01-01T00:00:00Z|São Paulo|$null$|$null$ |wd:Q406|13255685|2010-01-01T00:00:00Z|Istanbul|$null$|$null$ |wd:Q406|13854740|2012-01-01T00:00:00Z|Istanbul|$null$|$null$ |wd:Q1355|8425970|2011-01-01T00:00:00Z|Bangalore|$null$|$null$ |wd:Q174|11253503|2010-01-01T00:00:00Z|São Paulo|$null$|$null$ |wd:Q1490|13159388|2010-01-01T00:00:00Z|Tokyo|$null$|$null$ |wd:Q15174|10628900|2013-01-01T00:00:00Z|Shenzhen|$null$|$null$ |wd:Q3838|9464000|2012-01-01T00:00:00Z|Kinshasa|$null$|$null$ |wd:Q373346|10820000|2011-01-01T00:00:00Z|Linyi|$null$|$null$ |wd:Q1352|4646732|2011-01-01T00:00:00Z|Chennai|$null$|$null$ |wd:Q11739|7129629|2010-01-01T00:00:00Z|Lahore|$null$|$null$ |wd:Q1156|12442373|2011-01-01T00:00:00Z|Mumbai|$null$|$null$

Location queries:

Find all forests around San Francisco in a 100 mile radius

$ pq-wikidata -l -L enlabel  -f tsv "coordinate_location(wd:'Q62',Loc),geolocation_around(Loc,100,X),forest(X)"

The entity_search/2 predicate provides access to the Wikibase EntitySearch function. The following example finds all subclasses of a symptom by name:

$ pq-wikidata -l -L enlabel "entity_search(vomiting,Match),subclass_of_transitive(Symptom,Match)"

|Match|Symptom|Match Label|Symptom Label| |---|---|---|---| |wd:Q127076|wd:Q127076|vomiting|vomiting |wd:Q127076|wd:Q2635499|vomiting|Projectile vomiting |wd:Q127076|wd:Q21993813|vomiting|chronic vomiting |wd:Q127076|wd:Q23012213|vomiting|glowing vomit |wd:Q127076|wd:Q5140942|vomiting|coffee ground vomiting |wd:Q127076|wd:Q54974197|vomiting|anticipatory vomiting |...|...|...|...|

$ pq-wikidata -f tsv -l -L enlabel "subclass_of_transitive(S,wd:'Q127076'),has_cause(S,C)" | tbl2ghwiki

Note that affixing _transitive to a predicate will always translate to the reflexive transitive version of that predicate. Here we find all known causes of different kinds of vomiting in Wikidata:

|S|C|S Label|C Label| |---|---|---|---| |wd:Q1570161|wd:Q1495657|hematemesis|gastrointestinal bleeding |wd:Q1938763|wd:Q16244733|fecal vomiting|intestinal obstruction |wd:Q5140942|wd:Q1883970|coffee ground vomiting|upper gastrointestinal bleeding |wd:Q127076|wd:Q133823|vomiting|migraine |wd:Q127076|wd:Q121041|vomiting|appendicitis |wd:Q127076|wd:Q164778|vomiting|rotavirus |wd:Q127076|wd:Q943897|vomiting|gastroparesis |wd:Q127076|wd:Q974135|vomiting|chemotherapy

Installation

Docker

To run queries on the command line:

alias pq-wikidata="docker run cmungall/sparqlprog_wikidata pq-wikidata

To run a service:

docker run -p 9083:9083 cmungall/sparqlprog_wikidata

Within SWI Environment

Install SWI-Prolog from http://www.swi-prolog.org

pack_install(sparqlprog_wikidata)

How it works

For each class in the defined subset, for example Country, multiple predicates will be defined:

• city/1 - any instance of City, or its subclasses
• city_direct/1 - any instance of City (ignoring subclasses)
• city_iri/1 - IRI for City in WikiData

For example, the query

city(City)

will be expanded to:

SELECT ?city WHERE {
  ?city (<http://www.wikidata.org/prop/direct/P31>/<http://www.wikidata.org/prop/direct/P279>*) <http://www.wikidata.org/entity/Q515>
}

For each predicate in the defined subset, for example, regulates (molecular biology), the following predicates will be defined:

• regulates/2 - direct assertion between regulator and regulated
• regulates_transitive/2 - transitive version of above
• regulates_iri/1 - IRI for regulates

Further predicates will be defined that utilize the wikidata reification model.

• $predicate_eiri/1 - Entity IRI for predicate
• $predicate_e2s - links entity to statement
• $predicate_s2v - links value from statement
• $predicate_s2q - links qualifier statement

To illustrate consider the definition of the following 3-ary predicate, based on the positive therapeutic predictor predicate in wikidata. These triples can be qualified by medical condition treated.

positive_therapeutic_predictor_for_condition(V,D,C) :-
        positive_therapeutic_predictor_e2s(V,S),
        medical_condition_treated_s2q(S,C),
        positive_therapeutic_predictor_s2v(S,D).

The following query:

pq-wikidata -C "positive_therapeutic_predictor_for_condition(Var,Drug,Condition)"

will be translated to:

SELECT ?var ?drug ?condition WHERE {
  ?var <http://www.wikidata.org/prop/P3354> ?v0 .
  ?v0 <http://www.wikidata.org/prop/qualifier/P2175> ?condition .
  ?v0 <http://www.wikidata.org/prop/statement/P3354> ?drug
}

(use -C to generate the SPARQL without executing it

Other Queries

Location of San Francisco:

$ pq-wikidata -l -L enlabel  "geolocation(wd:'Q62',Lat,Long,Precision,Globe)"
37.766667,-122.433333,1.0E-6,wd:Q2,$null$,$null$,$null$,Earth

Supported subsets of Wikidata

Currently on a small subset of the overall Wikidata schema is exposed, mostly a subset focused around life science and geoscience/geographic use cases. More can be added on request.

In future we may translate the entire Wikidata model (i.e. all classes and properties) into sparqlprog predicates.

More examples

See [bin/wikidata-examples.sh](bin/wikidata-examples.sh)

TODO

Document API calls, search, etc

Uses

See: environments2wikidata

Contents of pack "sparqlprog_wikidata"

Pack contains 18 files holding a total of 63.8K bytes.