BioSB PhD Retreat 2017 Introduction to SPARQL http://www.youngcb.nl/events/biosb-phd-retreat-2017/

1. SPARQL
SPARQL Protocol And RDF Query Language
Amrapali Zaveri, Ph.D.

2. What is SPARQL?
SPARQL (pronounced sparkle) stands for: SPARQL Protocol And
RDF Query Language
• SPARQL 1.0 W3C-RecommendaFon since January 15th 2008
• SPARQL 1.1 W3C-RecommendaFon since March 21st 2013
• Query language to query instances in RDF documents
• Great pracFcal importance (almost all applicaFons need it)

3. SPARQL Example
SELECT
*
WHERE
{
?subject ?predicate ?object .
}
Similar to SQL !

4. SPARQL Components
A SPARQL query comprises, in order:
• PREFIX declaraFons, for abbreviaFng URIs
• Dataset defini;on, staFng what RDF graph(s) are being queried
• A result clause, idenFfying what informaFon to return from the
query
• The query pa@ern, specifying what to query for in the
underlying dataset
• Query modifiers, slicing, ordering, and otherwise rearranging
query results

5. SPARQL Components
# prefix declara;ons
PREFIX foo: <h`p://example.com/resources/>
# dataset defini;on
FROM
# result clause
SELECT
# query pa@ern
WHERE {
...
}
# query modifiers
ORDER BY ...

6. SPARQL Example
SELECT * WHERE {
?book rdf:type <h`p://dbpedia.org/ontology/Book> .
}
Try it yourself: dbpedia.org/sparql/

7. SPARQL Example
PREFIX dbo:<h@p://dbpedia.org/ontology/>
SELECT * WHERE {
?book a dbo:Book .
?book dbo:author ?author.
}
Try it yourself: dbpedia.org/sparql/

8. SPARQL Example
PREFIX dbo:<h@p://dbpedia.org/ontology/>
SELECT * WHERE {
?book a dbo:Book .
?book dbo:author ?author.
} LIMIT 10
Try it yourself: dbpedia.org/sparql/

9. SPARQL Example
PREFIX dbo:<h@p://dbpedia.org/ontology/>
SELECT ?author WHERE {
?book a dbo:Book .
?book dbo:author ?author.
} LIMIT 10
Try it yourself: dbpedia.org/sparql/

10. Filter in SPARQL
• Keyword FILTER, followed by filter expression in parentheses
• Filter condiFons output truth values (and possibly errors)
• Many filter funcFons are not specified by RDF
funcFons
• partly taken from XQuery/XPath-Standard for XML

11. Filter Functions
Comparison operators: <, =, >, <=, >=, !=
• Comparison of data literals according to natural order
• Support for numerical data types, xsd:dateTime, xsd:string
(alphabeFc ordering), xsd:Boolean (1>0)
• For other types and other RDF-elements, only = and != are
available
• Comparison of literals of incompaFble types (e.g. xsd:string and
xsd:integer) is not allowed
ArithmaFc operators: +, -, *, /
• Support for numerical data types
• Used to combine values in filter condiFons Ex.: FILTER(?weight/
(?size*?size)>=25)

12. SPARQL Example
PREFIX dbo:<h`p://dbpedia.org/ontology/>
SELECT ?author WHERE {
?book a dbo:Book .
?book dbo:author ?author.
?book dbo:numberOfPages ?pages.
FILTER (?pages > 500)
} LIMIT 10
Try it yourself: dbpedia.org/sparql/

13. Special Filter Functions
Other RDF-specific filter funcFons:
sameTERM(A,B) true, if A and B are the same RDF-terms.
langMATCHES(A,B) true, if the language specificaFon A fits the pa`ern B
REGEX(A,B)
true, if the character string A contains the regular
expression B

14. SPARQL Example
PREFIX dbo:<h`p://dbpedia.org/ontology/>
PREFIX dbp:<h@p://dbpedia.org/property/>
SELECT * WHERE {
?book a dbo:Book .
?book dbo:author ?author.
?book dbo:numberOfPages ?pages.
?book dbp:name ?name.
FILTER (?pages > 500)
FILTER (langMATCHES(LANG(?name),"en))
} LIMIT 10
Try it yourself: dbpedia.org/sparql/

15. Filter Functions: Boolean
operators
Filter condiFons can be linked with boolean operators: &&, ||, !
• ParFally also expressible through graph pa`ern:
• ConjuncFon corresponds to specificaFons of several filters
• DisjuncFon corresponds to applicaFon of filters in alternaFve
pa`erns

16. Filter Functions: Boolean
operators
UnFl now, only basic formaong seong for results:
• How can one retrieve defined parts of the output set?
• How are the results ordered?
• Can duplicate result rows be removed instantaneously?

17. Result Sorting
PREFIX dbo:<h`p://dbpedia.org/ontology/>
PREFIX dbp:<h`p://dbpedia.org/property/>
SELECT * WHERE {
?book a dbo:Book .
?book dbo:author ?author.
?book dbo:numberOfPages ?pages.
?book dbp:name ?name.
FILTER (?pages > 500)
FILTER (langMATCHES(LANG(?name),"en))
} ORDER BY ?pages LIMIT 10
Try it yourself: dbpedia.org/sparql/

18. Resulting Sorting
• SorFng same as with filter comparison operators
• SorFng of URIs alphabeFcally as sequence of characters
Other possible specificaFons:
• ORDER BY DESC(?price): descending
• ORDER BY ASC(?price): ascending, default seong
• ORDER BY DESC(?price), ?Ftle: hierarchical classificaFon criteria

19. LIMIT, OFFSET, DISTINCT
RestricFon of output set:
• LIMIT: maximal number of results (table rows)
• OFFSET: posiFon of the first delivered result
• SELECT DISTINCT: removal of duplicate table rows
LIMIT and OFFSET only make sense with ORDER BY!

20. Hands-on Bio2RDF
• SPARQL endpoint
• http://sparql.openlifedata.org/
• Datasets
• http://download.bio2rdf.org/release/3/
release.html

21. Hands-on DIY -1
DESCRIBE
<http://bio2rdf.org/drugbank:DB00088>
The DESCRIBE query result clause allows the server to return
whatever RDF it wants that describes the given resource(s).

22. Hands-on Bio2RDF -2
<http://bio2rdf.org/drugbank:DB00088>
• Retrieve title, affected organism, target and group
of this Drug
TIP: View it as NTriples to construct your query!

23. Hands-on Bio2RDF - 3
SELECT * WHERE {
?drug a
<http://bio2rdf.org/drugbank_vocabulary:Drug>. }
• filter for drugs starting with A

24. Hands-on Bio2RDF -3
SELECT * WHERE {
?drug a
<http:bio2rdf.orgdrugbank_vocabulary:Drug>. }
• filter for drugs starting with A
• FILTER regex(?title, "A")

25. Hands-on Bio2RDF -3
SELECT * WHERE {
?drug a
<http://bio2rdf.org/drugbank_vocabulary:Drug>. }
• filter for drugs starting with A
• FILTER regex(?title, “A")
• sort them alphabetically

26. Hands-on DIY
• Get 100 drug-metabolizing enzymes
• Get phenotypes and genes associated with
OMIM diseases
• Retrieve unique diseases and publications
associated with the BRCA1 gene

27. Hands-on DIY
• Get 100 drug-metabolizing enzymes
• Get phenotypes and genes associated with
OMIM diseases
• Retrieve unique diseases and publications
associated with the BRCA1 gene
TIPS:
- View the resource as NTriples to construct your query
- Use prefix.cc to look up prefixes
- Always use LIMIT
- Start by getting results one triple at a time and build up.

28. Answer 1
PREFIX dv: <http://bio2rdf.org/drugbank_vocabulary:>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT distinct ?enzyme_name ?drug_name
{
?s a dv:Enzyme-Relation .
?s dv:enzyme/dct:title ?enzyme_name .
?s dv:drug/dct:title ?drug_name .
}
LIMIT 100

29. Answer 2
PREFIX om: <http://bio2rdf.org/omim_vocabulary:>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX b: <http://bio2rdf.org/bio2rdf_vocabulary:>
SELECT * {
?s a om:Phenotype .
?s dct:title ?name .
?s om:clinical-synopsis ?cs .
?cs om:feature ?f .
?f om:x-umls/b:identifier ?umls .
?f om:x-hp/dct:identifier ?hp .
?s om:phenotype-map ?pm .
?pm om:gene-symbol ?gene.
} LIMIT 10

30. Answer 3
PREFIX om: <http://bio2rdf.org/omim_vocabulary:>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX hgnc:<http://bio2rdf.org/hgnc.symbol>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?geneName ?name ?pubmedArticle{
?s a om:Phenotype .
?s dct:title ?name .
?s om:phenotype-map ?pm .
?pm om:gene-symbol ?gene.
?gene dct:title ?geneName.
?s om:article ?pubmed.
?pubmed dct:title ?pubmedArticle.
FILTER regex(?gene, “BRCA1") }

31. SPARQL Components
# prefix declara;ons
PREFIX foo: <h`p://example.com/resources/>
# dataset defini;on
FROM
# result clause
SELECT
# query pa@ern
WHERE {
...
}
# query modifiers
ORDER BY ...

32. Summary
BASIC Structure
PREFIX
WHERE
GRAPH Pattern
simple graph pattern
{…}
OPTIONAL
UNION
FILTER
LANG
DATATYPE
REGEX
OUTPUT Format
SELECT
CONSTRUCT
ASK
DESCRIBE
MODIFIERS
ORDER BY
LIMIT
OFFSET
DISTINCT

33. THANK YOU!
QUESTIONS?
@AmrapaliZ
amrapali.j.zaveri@maastrichtuniversity.nl
Contact me if you are interested in doing a project
at the Institute of Data Science, Uni Maastricht!