This document provides an introduction to bio-ontologies and the semantic web. It discusses what ontologies are and how they are used in the bio domain through initiatives like the OBO Foundry. It introduces key semantic web technologies like RDF, URIs, Turtle syntax, and SPARQL query language. It provides examples of ontologies like the Gene Ontology and how ontologies can be represented and queried using these semantic web standards.

1. Introduction to Bio Ontologies
and The Semantic Web
M. Devisscher
Biological Databases

2. Overview
• Bio ontologies
• Semantic technologies
• SPARQL in practice

3. Introduction
• Ontologies: what are ontologies ?
• Ontologies in the bio domain: OBO Foundry
• Ontologies in the semantic web
• OBO
• RDF, IRI, TTL, SPARQL, OWL

4. What is an ontology ?
• Ontology = a specification of a
conceptualization (Gruber 1993)
• In practice: controlled vocabularies
– Disambiguation (e.g. Bank, Running)
– Language/species independence
• Very useful in biology – complex hierarchies of
terms

5. Ontologies in the bio Domain
• OBO Foundry - open Biological and
Biomedical Ontologies
• Common principles
• List of ontologies at
http://www.obofoundry.org
• OBO is also a data format .obo

6. SideTrack – The Gene Ontology
• The mother of bio-ontologies: the GO
– Oldest bio – ontology
– Many practical applications:
• Cross species studies
• Overrepresentation studies (RNASeq)
• GO is an OBO ontology

7. SideTrack – The Gene Ontology
• Collection of terms

8. SideTrack – The Gene Ontology
• Relationships between terms:
– Subsumption: is_a
– Partonomic: part_of
• These terms are transitive
• Terms form a DAG (directed, acyclic graph)
• Some information can be inferred

9. SideTrack – The Gene Ontology

10. SideTrack – The Gene Ontology

11. SideTrack – The Gene Ontology
• Know more: www.geneontology.org
• AMIGO : the GO browser

12. Gene Ontology Annotation
• Gene ontology annotations GOA = entities
labeled with GO terms
– E.g. Uniprot-GOA

13. Semantic Technologies
• The semantic web: Tim Berners Lee et al,
Scientific American 2001

14. Semantic Technologies
• W3C: a set of specifications
http://www.w3.org/standards/semanticweb/
• A mature toolset
– Dedicated data formats
– Storage
– Query language

15. Resource Description Framework
• A standard model for data interchange on the
(semantic) web
• Basic data element = a Triple
– A mini sentence
– Contains three Terms:
• Subject Predicate Object

16. • Representation of triples
– Basic data format: RDF/XML
– All data expressed in RDF (Resource Description
Framework)
– Several compatible syntaxes: TTL (Terse Triple
Language) most human readable
Resource Description Framework

17. Example

18. The Turtle Syntax
• Basic Triple
<http://bioinformatics.be/entities#martijn>
<http://bioinformatics.be/relations#has_favorite_beer>
<http://bioinformatics.be/entities#karmeliet>.

19. The Turtle Syntax
• Prefix
@prefix b4x: <http:bioinformatics.be/terms#>
b4x:martijn b4x:has_favorite_beer b4x:karmeliet.

20. The Turtle Syntax
• Predicate lists
@prefix b4x: <http:bioinformatics.be/terms#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
b4x:martijn b4x:has_favorite_beer b4x:karmeliet;
foaf:name “Martijn Devisscher”.

21. The Turtle Syntax
• Object lists
@prefix b4x: <http:bioinformatics.be/terms#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
b4x:martijn b4x:has_favorite_beer b4x:karmeliet,
b4x:chimay_blauw;
foaf:name “Martijn Devisscher”.

22. IRI’s and Literals
• Terms can be either IRI’s, Literals or blank nodes
• IRI = Internationalized Resource Identifier
• Unique id – a virtual URI
– Example: <http://bioinformatics.be/terms#martijn>
– There is no requirement for resolving
– Now: Open Data initiatives: please do use resolvable
URI’s http://linkeddata.org
– Unique identifiers can be registered on
http://identifiers.org

23. Introduction
• Literals: can be typed, allowed types from the
XSD namespace:
– E.g. “This is a string example”^^xsd:string
– E.g. “5”^^xsd:integer
• IRI’s are used for entities and attributes
• Literals are used for attribute values that
aren’t entities

24. The Turtle Syntax
• Typed literals
@prefix b4x: <http:bioinformatics.be/terms#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
b4x:martijn b4x:has_favorite_beer b4x:karmeliet,
b4x:chimay_blauw;
b4x:length “184”^^xsd:integer;
foaf:name “Martijn Devisscher”^^xsd:string.

25. The Turtle Syntax
• Blank nodes
@prefix b4x: <http:bioinformatics.be/terms#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
b4x:martijn b4x:has_favorite_beer b4x:karmeliet,
b4x:chimay_blauw;
b4x:length “184”^^xsd:integer;
foaf:name “Martijn Devisscher”^^xsd:string;
b4x:owns_cat [ b4x:color “Gray” ].

26. Classes and Individuals
• rdf:type
@prefix b4x: <http:bioinformatics.be/terms#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
b4x:martijn rdf:type foaf:Person.

27. Classes and Individuals
• Shorthand: a
@prefix b4x: <http:bioinformatics.be/terms#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
b4x:martijn a foaf:Person;
foaf:knows b4x:geert.
b4x:geert a foaf:Person.

28. Example
<http://xmpl/entities#martijn>
<http://xmpl/relations#has_favorite_beer>
<http://xmpl/entities#karmeliet>.

29. Semantic Technologies
• Sets of triples form a Graph

30. Graphs
• Triples are building blocks of Graphs
• Combining sets of triples allows the
construction of arbitrarily complex graphs
b4x:martijn b4x:karmeliethas_favorite_beer

31. Graph of graphs
• Combining RDF datasets can be considered a
slightly bigger graph, a knowledge cloud
• Key is interoperability: same format used for
disclosing information, independent of
backend

32. RDF dataset examples
• The LOD cloud http://lod-cloud.net : overview
of interlinked, RDF compatible datasources

33. RDF dataset examples
• Closer to home
https://data.stad.gent/devzone/docs/linked-
open-data

34. Add meaning !
• Reuse terms from existing, well defined
vocabularies – ontologies (foaf, dc, go, so)
• Describe new terms = Ontologies
• Contain
– A crisp human definition
– Some machine readable facts

35. Metadata
• Ontologies are also described in RDF
– RDFS: RDF - Schema
– OWL: Web Ontology Language
– Also expressed in RDF
• For clarity, file extension can be .rdfs or .owl

36. RDFS Essentials
• Descriptions
– rdfs:label
– rdfs:comment

37. RDFS
• Relationships between properties, classes
– rdfs:Class
– rdfs:subClassOf
– rdf:Property
– rdfs:subPropertyOf
– rdfs:range
– rdfs:domain

38. RDFS: Example
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
b4x:karmeliet a b4x:Tripel .
b4x:Beer a rdfs:Class .
b4x:Tripel a rdfs:Class .
b4x:Tripel rdfs:subClassOf b4x:Beer .
b4x:has_favorite_beer a rdf:Property ;
rdfs:domain foaf:Person ;
rdfs:range b4x:Beer .
b4x:Beer rdfs:subClassOf b4x:Drink .

39. Analogy
• RDF = database = data
• RDFS/OWL = schema = metadata
• Both are described in RDF, but have a different
scope

40. Semantic Technologies
• Inference
– Enhance dataset using knowledge from metadata
(e.g. rdfs, owl)
• Types of inference engines
– RDFS inference
• RDFS entailment regime
– OWL inference
• Under active research
• Engines exist for specific subsets of OWL (OWL-DL)

41. RDFS Entailment

42. RDFS: Inference
b4x:kevin b4x:has_favorite_beer b4x:stella
Q: What can we infer from this using RDFS
entailment ?

43. RDFS: Inference
b4x:kevin b4x:has_favorite_beer b4x:stella
Inferred triples:
b4x:kevin a foaf:Person [from domain]
b4x:stella a b4x:Beer [from range]
b4x:stella a b4x:Drink [from subClassOf]

44. DuckTyping
• Watch out with inference !
Example: You want to express that people can
have lengths
b4x:length a rdf:Property;
rdfs:domain foaf:Person;
rdfs:range xsd:integer.

45. DuckTyping
• Problem:
ex:VW_Transporter b4x:length “600”^xsd:integer.
• Would infer that VW_Transporter is a Person !
• This is called DuckTyping
If it looks like a duck, swims like a duck, and
quacks like a duck, then it probably is a duck

46. Task
• Find a solution: express in rdfs that people can
have lengths

47. Task
• Find a solution: express in rdfs that people can
have lengths
b4x:havingLenght a rdfs:Class.
b4x:length a rdf:Property;
rdfs:domain b4x:havingLength;
rdfs:range xsd:integer.
foaf:Person rdfs:subClassOf b4x:havingLength.

48. Storing RDF
• As an RDF file for download
• In a Triplestore
– Database optimised for storing triples
– Examples: BlazeGraph, Fuseki, Sesame

49. Semantic Technologies
• Querying over RDF data: SPARQL
• Cool features:
– Distributed querying = actual distribution of data
and computing resources
– SPARQL/Update: modify data
• SPARQL endpoints: SPARQL over HTTP

50. SPARQL Query Syntax
• First example:
SELECT ?subject ?predicate ?object WHERE {
?subject ?predicate ?object.
}
(Generally not a good idea as it will pull down
the whole dataset)
Binding variables
Graph matching

51. ?
SELECT ?person WHERE {
?person b4x:has_favorite_beer b4x:karmeliet
}

52. ?

53. SPARQL Query Syntax
• Limit result size :
SELECT ?subject ?predicate ?object WHERE {
?subject ?predicate ?object.
} LIMIT 10

54. SPARQL Query Syntax
• Find all classes:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?class ?label WHERE {
?class a rdfs:Class.
?class rdfs:label ?label.
}
(This will only retrieve classes that have a label)

55. SPARQL Query Syntax
• Find all classes:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?class ?label WHERE {
?class a rdfs:Class.
OPTIONAL {
?class rdfs:label ?label.
}
}

56. SPARQL Query Syntax
• Find all classes that contain “duck” in the
label:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?class ?label WHERE {
?class a rdfs:Class.
?class rdfs:label ?label.
FILTER( CONTAINS (str(?label) , “duck” ) )
}

57. SPARQL Query Syntax
• Make it case insensitive:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?class ?label WHERE {
?class a rdfs:Class.
?class rdfs:label ?label.
FILTER( CONTAINS ( UCASE(str(?label)) , “DUCK” ) )
}

58. SPARQL Query Syntax
• Search in specific graph:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?class ?label
FROM <http://example.org/animals>
WHERE {
?class a rdfs:Class.
?class rdfs:label ?label.
FILTER( CONTAINS ( UCASE(str(?label)) , “DUCK” ) )
}

59. SPARQL Query Syntax
• Search in specific graph:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?class ?label WHERE {
GRAPH <http://example.org/animals> {
?class a rdfs:Class.
?class rdfs:label ?label.
FILTER( CONTAINS ( UCASE(str(?label)) , “DUCK” ) )
}
}

60. SPARQL Query Syntax
• Can also search for graphs :
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?g WHERE {
GRAPH ?g {
?class a rdfs:Class.
?class rdfs:label ?label.
FILTER( CONTAINS ( UCASE(str(?label)) , “DUCK” ) )
}
}

61. Summary: Querying RDF data
RDF Data
Inference
Engine
RDFS/OWL
RDF Data
Inferred
SPARQL
Endpoint

62. • Basic data element = a Triple
– A mini sentence
– Contains three Terms:
– Subject Predicate Object
• Example:
<http://xmpl/entities#martijn>
<http://xmpl/relations#has_favorite_beer>
<http://xmpl/entities#karmeliet>.
Take home Summary

63. • Combine triples to represent
knowledge

64. • Use terms from ONTOLOGIES
– COMMON VOCABULARIES
– POSSIBLE TO INFER
MEANING
• OMIABIS
• OBIB
• SNOMED/ICD
• MESH

65. ?
• SPARQL searches for patterns

66. ?

67. Interoperability between OBO and
Semantic Technologies
• Originated from two separate academic worlds
• Computing applications of OBO mainly
consistency checking and overrepresentation
analysis
• Semantic Technologies: much broader toolset
• Interoperability ?
– Direct offering in both formats
– Automated mappings
• Migration towards semantic toolkits

68. Where to find ontologies
• OBO Foundry
• Bioportal; NCBO
• Biogateway
• Bio2RDF

69. Where to find RDF data
• Google for SPARQL endpoint
• => e.g. EBI databases
• Non biological: DBpedia

70. How about Tim Berners Lee’s vision
• We’re not there yet, but for bio data we’re
getting quite close
– The explicitome
– Crowd sourcing
– Nanopublications

71. SPARQL REFERENCE
http://www.w3.org/TR/sparql11-overview/
Recap:
SPARQL in 11 minutes

72. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label

73. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label
• FIND the pattern ?x rdfs:label ?label.

74. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label
• FIND the pattern ?x rdfs:label ?label.
• BIND variables ?label, ?x

75. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label
• FIND the pattern ?x rdfs:label ?label.
• BIND variables ?label, ?x
• RETRIEVE variable ?label

76. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label
• FIND the pattern ?x rdfs:label ?label.
• BIND variables ?label, ?x
• RETRIEVE variable ?label
• PREFIX: replace rdfs:label by <http://www.w3.org/2000/01/rdf-schema#label>

77. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label
• FIND the pattern ?x rdfs:label ?label.
• BIND variables ?label, ?x
• RETRIEVE variable ?label
• PREFIX: replace rdfs:label by <http://www.w3.org/2000/01/rdf-schema#>
• FILTER results to labels containing “dimethylalinine”

78. SPARQL : Recap
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?label
FROM <http://graphName> WHERE {
?x rdfs:label ?label.
FILTER ( CONTAINS(?label, “dimethylalinine”) )
} LIMIT 10 ORDER BY ?label
• FIND the pattern ?x rdfs:label ?label.
• BIND variables ?label, ?x
• RETRIEVE variable ?label
• PREFIX: replace rdfs:label by <http://www.w3.org/2000/01/rdf-schema#>
• FILTER results to labels containing “dimethylalinine”
• LIMIT results to first 10 matches ordered by label

79. SPARQL : Recap
DESCRIBE
<http://rdf.wikipathways.org/Pathway/WP1425_r74390/WP/Interaction/e077e>
• Useful short query to get direct links from/to a
given node

80. Running SPARQL
• From a web interface

81. • From a web interface
• Using http
– HTTP GET
– HTTP POST : for larger query strings
– Headers determine response type (JSON, XML, HTML)
http://…/sparql?default-graph-uri=<http://graphName>&query=URLENCODEDQUERYSTRING
Running SPARQL

82. BIO-ONTOLOGIES

83. BioPortal

84. Access
• From the web interface !
• SPARQL endpoint: using API key; on request
• Running a local copy: download VM image; on
request

85. Exercises
• Find a term
• Find ontologies containing a term
• Browse some ontologies
• Check the NCBO annotator !

86. BIO-DATA

87. EBI RDF Resources

88. EBI RDF Resources

89. Ensembl

90. gene
transcript
exon
ordered part
sio:SIO_001261
obo:SO_0000147
obo:SO_0000234
obo:SO_transcribed_from
faldo:location
obo:SO_0001217
obo:SO_has_part
location
faldo:location
location
faldo:location
location
obo:SO_translates_to
sio:SIO_000300
rank
translation
id
id
id
id
synonym
skos:altLabelxref
Simplified

91. Exercise
• From uniprot find proteins that are annotated
with a given Gene Ontology term

92. PREFIX up:<http://purl.uniprot.org/core/>
PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo:<http://purl.obolibrary.org/obo/>
SELECT * WHERE {
?protein up:classifiedWith obo:GO_0004499.
?protein up:organism taxon:9606.
}
http://sparql.uniprot.org

93. Exercise
• From Expression Atlas find proteins that are
differentially expressed (P < 1e-12) in Crohn’s
disease

94. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>
PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX up:<http://purl.uniprot.org/core/>
PREFIX biopax3:<http://www.biopax.org/release/biopax-level3.owl#>
SELECT distinct ?protein ?expressionValue ?pvalue WHERE {
?factor rdf:type efo:EFO_0000384 .
?value atlasterms:hasFactorValue ?factor .
?value atlasterms:isMeasurementOf ?probe .
?value atlasterms:pValue ?pvalue .
?value rdfs:label ?expressionValue .
?probe atlasterms:dbXref ?protein .
FILTER ( ?pvalue < 1e-12 )
FILTER ( strstarts(str(?protein),"http://purl.uniprot.org/uniprot/") )
}ORDER BY ASC (?pvalue)
https://www.ebi.ac.uk/rdf/services/atlas/sparql

95. • Links pathways with genes, terms from
Pathway, Cell line and Disease ontology,
PubMed references
• Models individual Interactions
• Can be downloaded as RDF
• Has an experimental SPARQL endpoint
WikiPathways

96. • Define a query to find pathways linked to
TNFalpha gene
Exercise

97. PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?PathwayName where {
?geneProduct a wp:GeneProduct .
?geneProduct dc:identifier ?GeneID .
?geneProduct dcterms:isPartOf ?pathway .
?geneProduct rdfs:label ?geneName .
?pathway dc:identifier ?pathwayid .
?pathway dc:title ?PathwayName .
FILTER(str(?geneName) = "TNFalpha" )
}
http://sparql.wikipathways.org

100. • Try this, or another query
– Using web interface
– Using http get
• Define a simple describe
• Use a web tool to URLEncode the query
• Submit query as a URL parameter
Exercise

101. DisGeNet

102. Phenotype
GDA
gene
sio:SIO_001121 ncit:C7057
sio:SIO_010056
sio:SIO_000628
id
id
skos:exactMatch
Mesh
DiseaseClass
sio:SIO_000628
HPO
score
ncit:C25338
ncit:C16612
sio:SIO_000628
id
skos:exactMatch
Simplified

104. • Find diseases linked to BRCA1
Exercise

105. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT DISTINCT ?disease WHERE {
?gda a sio:SIO_000983.
?gda sio:SIO_000628 ?disease.
?disease a ncit:C7057.
?gda sio:SIO_000628 ?gene.
?gene a ncit:C16612.
?gene skos:exactMatch <http://identifiers.org/hgnc.symbol/BRCA1>}
http://rdf.disgenet.org/lodestar/sparql

106. • Yields no results
????

107. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT DISTINCT ?disease WHERE {
?gda a sio:SIO_000983.
?gda sio:SIO_000628 ?disease.
?disease a ncit:C7057.
?gda sio:SIO_000628 ?gene.
?gene a ncit:C16612.
?gene skos:exactMatch <http://identifiers.org/hgnc.symbol/BRCA1>}
http://rdf.disgenet.org/lodestar/sparql

108. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT DISTINCT ?disease WHERE {
?gda a [(rdfs:subClassOf)* sio:SIO_000983].
?gda sio:SIO_000628 ?disease.
?disease a ncit:C7057.
?gda sio:SIO_000628 ?gene.
?gene a ncit:C16612.
?gene skos:exactMatch <http://identifiers.org/hgnc.symbol/BRCA1>}
http://rdf.disgenet.org/lodestar/sparql

109. • Inference cannot be assumed on a SPARQL
endpoint => take care with defining queries
Why ?

110. • Define a query to find genes with important
link to Crohn’s disease (score > 0.35)
Exercise

111. PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT DISTINCT ?gene WHERE {
?gda sio:SIO_000628 ?gene,?disease .
?gene a ncit:C16612 .
?gene skos:exactMatch ?GeneID .
?disease a ncit:C7057 .
?disease dcterms:title ?DiseaseName .
?gda sio:SIO_000216 ?scoreIRI .
?scoreIRI sio:SIO_000300 ?score .
FILTER (?score > "0.35"^^xsd:decimal)
FILTER (contains(str(?DiseaseName),"Crohn"))
}
http://rdf.disgenet.org/lodestar/sparql

113. neXtProt

114. • Define a query to find proteins related with
Cardio diseases
• Define a query to find the genomic location of
gene “TP53”
Exercise

115. select distinct ?id where {
?entry skos:exactMatch ?id.
?entry :isoform ?isoform.
?isoform :medical ?medical_annotation.
?medical_annotation :term ?term.
?term :related ?disease.
?disease a :MeshCv.
?disease rdfs:label ?label.
FILTER(CONTAINS(?label,"Cardio")).
}
https://snorql.nextprot.org/

117. select ?chrom ?start ?end where
{
?gene rdf:type :Gene.
?gene :name ?name.
?gene :chromosome ?chrom.
?gene :begin ?start.
?gene :end ?end.
FILTER (str(?name) = "TP53")
}
https://snorql.nextprot.org/

119. • Federated querying: include data from
another endpoint using the SERVICE keyword
• Example: find pathways (from wikipathways)
involving gene linked to Crohn’s disease (from
disgenet)
SPARQL and federated queries

120. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
http://rdf.disgenet.org/lodestar

121. SELECT DISTINCT ?PathwayName WHERE {
?gda sio:SIO_000628 ?gene, ?disease .
?gene a ncit:C16612 .
?disease a ncit:C7057 .
?disease dcterms:title ?DiseaseName .
?gda sio:SIO_000216 ?scoreIRI .
?scoreIRI sio:SIO_000300 ?score .
FILTER (?score > "0.35"^^xsd:decimal)
FILTER (contains(str(?DiseaseName),"Crohn"))
SERVICE <http://sparql.wikipathways.org/> {
?geneProduct a wp:GeneProduct .
?geneProduct dc:identifier ?gene .
?geneProduct dcterms:isPartOf ?pathway .
?pathway dc:identifier ?pathwayid .
?pathway dc:title ?PathwayName .
}
}
http://rdf.disgenet.org/lodestar/sparql

123. Application: BOINQ
• Framework for managing sequencing data
using semantic technologies
• Find it here :
https://github.com/mr-tijn/boinq2

124. Functionalities
• Uploader/converter
– Upload BED/GFF/VCF files
– Automatically translated into triples
– Stored in triplestore

125. Functionalities
• Query builder
– Visually build SPARQL queries that query your data
along with public data
– Store results as new graphs or download as CSV

126. Demo: query for finding first exons of
genes related to colon cancer