Introduction to RDF and the Semantic Web for
the life sciences
Simon Jupp
Sample Phenotypes and Ontologies Team
European Bioinformatics Institute
[email protected]
Day 2 practical session
•  Exploring EBI RDF platform
•  Querying EBI resources
•  Federated queries from one SPARQL endpoint to another
Exercise 17
•  Explore the EBI RDF platform at http://www.ebi.ac.uk/rdf
•  A) On the ChEMBL endpoint get ChEMBL activities, assays
and targets for the drug Clotrimazole (CHEMBL104)
•  B) On the Atlas endpoint find expression for
ENSDARG00000042641 (Cyp51)
•  B2) filter the results by property type contains “organism_part”
•  C) On the Reactome endpoint find pathways that
references Cyp51 (http://purl.uniprot.org/uniprot/Q1JPY5)
•  D) Query the UniProt endpoint to describe
http://purl.uniprot.org/uniprot/Q1JPY5
Exercise 17 solution A
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX chembl_molecule: <http://rdf.ebi.ac.uk/resource/chembl/molecule/>
SELECT ?activity ?assay ?target ?targetcmpt ?uniprot
WHERE {
?activity a cco:Activity ;
cco:hasMolecule chembl_molecule:CHEMBL104 ;
cco:hasAssay ?assay .
?assay cco:hasTarget ?target .
?target cco:hasTargetComponent ?targetcmpt .
?targetcmpt cco:targetCmptXref ?uniprot .
?uniprot a cco:UniprotRef
}
Exercise 17 solution B
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX identifiers:<http://identifiers.org/ensembl/>
SELECT distinct ?diffValue ?expUri ?propertyType ?propertyValue ?pvalue
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?diffValue .
?value atlasterms:hasFactorValue ?factor .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?value atlasterms:pValue ?pvalue .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref identifiers:ENSDARG00000042641 .
}
Exercise 17 solution B1
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX identifiers:<http://identifiers.org/ensembl/>
SELECT distinct ?diffValue ?expUri ?propertyType ?propertyValue ?pvalue
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?diffValue .
?value atlasterms:hasFactorValue ?factor .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?value atlasterms:pValue ?pvalue .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref identifiers:ENSDARG00000042641 .
FILTER regex (?propertyType, "organism_part")
}
Exercise 17 solution C
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX biopax3: <http://www.biopax.org/release/biopax-level3.owl#>
SELECT DISTINCT ?pathway ?pathwayname
WHERE
{?pathway rdf:type biopax3:Pathway .
?pathway biopax3:displayName ?pathwayname .
?pathway biopax3:pathwayComponent ?reaction .
?reaction rdf:type biopax3:BiochemicalReaction .
{
{?reaction ?rel ?protein .}
UNION
{
?reaction ?rel ?complex .
?complex rdf:type biopax3:Complex .
?complex ?comp ?protein .
}}
?protein rdf:type biopax3:Protein .
?protein biopax3:entityReference <http://purl.uniprot.org/uniprot/Q1JPY5>
}
LIMIT 100
Exercise 17 solution D
DESCRIBE <http://purl.uniprot.org/uniprot/Q1JPY5>
Federated querying
•  One of the biggest advantages of SPARQL and triples
stores is the ability to federate queries across endpoints
•  Integrating data at query time with SPARQL
GO annotation
Expression
value
GXA
Uniprot
Uniprot
Protein
Federated SPARQL
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
SELECT DISTINCT ?experiment ?description WHERE {
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?experiment a atlasterms:Experiment .
?experiment dcterms:identifier ?id .
?experiment dcterms:description ?description .
FILTER regex(?id, "E-GEOD-2852")
}
}
We can execute this query from any other endpoint using the SPARQL
SERVICE keyword
http://tinyurl.com/o9kvvzn
Exercise 19
•  Execute the following federated query on
•  1. The UniProt SPARQL endpoint
•  2. Your Sesame workbench SPARQL endpoint
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
SELECT DISTINCT ?experiment ?description WHERE {
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?experiment a atlasterms:Experiment .
?experiment dcterms:identifier ?id .
?experiment dcterms:description ?description .
FILTER regex(?id, "E-GEOD-2852")
}
}
Constructing a Federated query
•  Basic query to get genes out of our dataset
•  How can we integrate this with data from the EMBL-EBI
Gene Expression Atlas?
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX mydata:<http://www.mydomain.com/mydata#>
PREFIX efo:<http://www.ebi.ac.uk/efo/>
SELECT DISTINCT ?geneid ?label WHERE {
?result mydata:dbXref ?geneid .
?geneid rdfs:label ?label .
}
Querying the Atlas
Example query 3
(http://www.ebi.ac.uk/rdf/services/atlas/sparql)
SELECT distinct ?diffValue ?expUri ?propertyType ?propertyValue ?pvalue
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?diffValue .
Our query
?value atlasterms:hasFactorValue ?factor .
?factor atlasterms:propertyType ?propertyType .
SELECT DISTINCT ?geneid ?label WHERE {
?factor atlasterms:propertyValue ?propertyValue .
?result mydata:dbXref ?geneid .
?value atlasterms:pValue ?pvalue .
?geneid rdfs:label ?label .
?value atlasterms:isMeasurementOf ?probe .
}
?probe atlasterms:dbXref identifiers:ENSMUSG00000034450 .
}
ORDER BY ASC (?pvalue)
Integration point
Querying the Atlas
Example query 3
(http://www.ebi.ac.uk/rdf/services/atlas/sparql)
SELECT distinct ?diffValue ?expUri ?propertyType ?propertyValue ?pvalue
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?diffValue .
?value atlasterms:hasFactorValue ?factor .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?value atlasterms:pValue ?pvalue .
Our query
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref identifiers:ENSMUSG00000034450 .
}
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
ORDER BY ASC (?pvalue)
PREFIX mydata:<http://www.mydomain.com/mydata#>
PREFIX atlasterms:<http://rdf.ebi.ac.uk/terms/atlas/>
SELECT DISTINCT ?geneid ?label ?probe WHERE {
?result mydata:dbXref ?geneid .
?geneid rdfs:label ?label .
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?probe atlasterms:dbXref ?geneid
}
}
1st gotcha
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX mydata:<http://www.mydomain.com/mydata#>
PREFIX atlasterms:<http://rdf.ebi.ac.uk/terms/atlas/>
SELECT ?geneid ?label ?probe ?value WHERE {
?result mydata:dbXref ?geneid .
?geneid rdfs:label ?label .
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref ?geneid
}
}
This should work but there is an issue with querying the EBI RDF
Platform with this version of Sesame (fix coming soon!)
1st gotcha
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX mydata:<http://www.mydomain.com/mydata#>
PREFIX atlasterms:<http://rdf.ebi.ac.uk/terms/atlas/>
SELECT ?label ?probe ?value WHERE {
?result mydata:dbXref <http://identifiers.org/ensembl/ENSMUSG00000024673> .
<http://identifiers.org/ensembl/ENSMUSG00000024673> rdfs:label ?label .
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref <http://identifiers.org/ensembl/ENSMUSG00000024673>
}
}
Bind on gene <http://identifiers.org/ensembl/ENSMUSG00000024673>
Exercise 20
•  A) Using the previous query, extend it to query the Atlas
endpoint to also return the Experiment id and factors
(property values) where Ms4ai (ENSMUSG00000024673) is
expressed
•  B) Filter those results to only include experiments where the
factor contains “liver”
Exercise 20 solution A)
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX mydata:<http://www.mydomain.com/mydata#>
PREFIX atlasterms:<http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX identifiers:<http://identifiers.org/ensembl/>
SELECT ?label ?expUri ?propertyValue WHERE {
?result mydata:dbXref identifiers:ENSMUSG00000024673 .
identifiers:ENSMUSG00000024673 rdfs:label ?label .
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value atlasterms:hasFactorValue ?factor .
?factor atlasterms:propertyValue ?propertyValue .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref identifiers:ENSMUSG00000024673
}
}
Exercise 20 solution B)
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX mydata:<http://www.mydomain.com/mydata#>
PREFIX atlasterms:<http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX identifiers:<http://identifiers.org/ensembl/>
SELECT ?label ?expUri ?propertyValue WHERE {
?result mydata:dbXref identifiers:ENSMUSG00000024673 .
identifiers:ENSMUSG00000024673 rdfs:label ?label .
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value atlasterms:hasFactorValue ?factor .
?factor atlasterms:propertyValue ?propertyValue .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref identifiers:ENSMUSG00000024673
}
FILTER regex(?propertyValue, "liver", "i")
}
Alzheimer’s Use Case – EBI RDF platform
• 
• 
• 
• 
• 
EFO term for Alzheimer’s: EFO_0000249
Get Genes diff expressed for Alzheimer’s
Get proteins encoded for those genes
GO annotations from UniProt for those genes
Get pathways form Reactome in which those proteins are
involved
•  Get drugs that target proteins within those pathways
Q1. Get Ensembl genes diff expressed for Alzheimer’s
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 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/>
SELECT distinct ?expressionValue ?dbXref ?pvalue ?propertyValue
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?expressionValue .
?value atlasterms:pValue ?pvalue .
?value atlasterms:hasFactorValue ?factor .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref ?dbXref .
?dbXref rdf:type atlasterms:EnsemblDatabaseReference .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?factor rdf:type efo:EFO_0000249 .
}
Q2. Get UniProt proteins for those genes
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 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/>
SELECT distinct ?expressionValue ?dbXref ?pvalue ?propertyValue
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?expressionValue .
?value atlasterms:pValue ?pvalue .
?value atlasterms:hasFactorValue ?factor .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref ?dbXref .
?dbXref rdf:type atlasterms:UniprotDatabaseReference .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?factor rdf:type efo:EFO_0000270 .
}
Q3. Get UniProt GO Annotations for those genes
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 efo:<http://www.ebi.ac.uk/efo/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX upc:<http://purl.uniprot.org/core/>
PREFIX identifiers:<http://identifiers.org/ensembl/>
SELECT distinct ?valueLabel ?goid ?golabel
WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?expressionValue .
?value atlasterms:pValue ?pvalue .
?value atlasterms:hasFactorValue ?factor .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref ?dbXref.
?dbXref rdf:type atlasterms:EnsemblDatabaseReference .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?factor rdf:type efo:EFO_0000249 .
?value rdfs:label ?valueLabel .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref ?uniprot .
SERVICE <http://beta.sparql.uniprot.org/sparql> {
?uniprot a upc:Protein .
?uniprot upc:classifiedWith ?keyword .
?keyword rdfs:seeAlso ?goid .
?goid rdfs:label ?golabel .
}
}
Q4. get pathways from Reactome for those proteins
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 efo: <http://www.ebi.ac.uk/efo/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX biopax3:<http://www.biopax.org/release/biopax-level3.owl#>
SELECT DISTINCT ?pathway ?dbXref WHERE {
?expUri atlasterms:hasAnalysis ?analysis .
?analysis atlasterms:hasExpressionValue ?value .
?value rdfs:label ?expressionValue .
?value atlasterms:pValue ?pvalue .
?value atlasterms:hasFactorValue ?factor .
?value atlasterms:isMeasurementOf ?probe .
?probe atlasterms:dbXref ?dbXref .
?dbXref rdf:type atlasterms:UniprotDatabaseReference .
?factor atlasterms:propertyType ?propertyType .
?factor atlasterms:propertyValue ?propertyValue .
?factor rdf:type efo:EFO_0000270 .
SERVICE <http://www.ebi.ac.uk/rdf/services/reactome/sparql>
{?pathway rdf:type biopax3:Pathway .
?pathway biopax3:displayName ?pathwayname .
?pathway biopax3:pathwayComponent ?reaction .
?reaction rdf:type biopax3:BiochemicalReaction .
{
{?reaction ?rel ?protein .}
UNION
{
?reaction ?rel ?complex .
?complex rdf:type biopax3:Complex .
?complex ?comp ?protein .
}}
?protein rdf:type biopax3:Protein .
?protein biopax3:entityReference ?dbXref
}
}
Q5. Get drugs that target proteins within those pathways
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>!
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>!
PREFIX efo:<http://www.ebi.ac.uk/efo/>!
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>!
PREFIX biopax3:<http://www.biopax.org/release/biopax-level3.owl#>!
PREFIX cco:<http://rdf.ebi.ac.uk/terms/chembl#>!
SELECT distinct ?dbXrefProt ?pathwayname ?moleculeLabel ?expressionValue ?propertyValue!
WHERE {!
#Get differentially expressed genes (and proteins) where factor is asthma!
?value atlasterms:pValue ?pvalue .!
?value atlasterms:hasFactorValue ?factor .!
?value rdfs:label ?expressionValue .!
?value atlasterms:isMeasurementOf ?probe .!
?probe atlasterms:dbXref ?dbXrefProt .!
?dbXrefProt a atlasterms:UniprotDatabaseReference .!
?factor atlasterms:propertyType ?propertyType .!
?factor atlasterms:propertyValue ?propertyValue .!
?factor rdf:type efo:EFO_0000249 .!
#Compunds target them!
SERVICE <http://www.ebi.ac.uk/rdf/services/chembl/sparql> {!
?act a cco:Activity ;!
cco:hasMolecule ?molecule ;!
cco:hasAssay ?assay .!
?molecule rdfs:label ?moleculeLabel .!
?assay cco:hasTarget ?target .!
?target cco:hasTargetComponent ?targetcmpt .!
?targetcmpt cco:targetCmptXref ?dbXrefProt .!
?targetcmpt cco:taxonomy <http://identifiers.org/taxonomy/9606> .!
?dbXrefProt a cco:UniprotRef .!
}!
SERVICE <http://www.ebi.ac.uk/rdf/services/reactome/sparql> {!
!
?protein rdf:type biopax3:Protein .!
?protein biopax3:memberPhysicalEntity!
!
![biopax3:entityReference ?dbXrefProt] .!
?pathway biopax3:displayName ?pathwayname .!
?pathway biopax3:pathwayComponent ?reaction .!
?reaction ?rel ?protein!
}!
}!
Summary
•  Why there is a need for new technologies in the life
sciences
• 
• 
• 
• 
• 
• 
Why RDF is a good fit for some of the problems
The role of ontologies
Generating RDF triples from data
Working with an RDF database
How to write a SPARQL query
How the EBI is using RDF
Conclusions
•  Generating RDF triples is relatively easy
•  Extracting the schema from your data can be tricky
•  Avoid over modeling – have good use cases
•  Look for appropriate ontologies, reuse terms where possible
•  Good tooling now available
•  RDF APIs for most programming language
•  Lots of scalable triples stores
•  SPARQL is a powerful query language for RDF
•  Also very unforgiving; debugging queries is hard
•  Treat the same as you would SQL, not for your average user
Conclusions cont..
•  Lots of interest in Linked Data and RDF
•  See LOD clouds and DBpedia
•  Big name companies using/generating RDF content
(Facebook, Google, Oracle)
•  Some good examples of applications
•  Pharma industry (OpenPhacts project), Semantic publishing
(BBC), Government data (data,gov.uk)
•  Tread cautiously
•  This technology is still maturing
•  Not a panacea
•  Good solutions for some problems
Thinking beyond RDF and SPARQL
•  Selling SPARQL endpoints to biologists is hard i.e. near
impossible
•  Entry level is too high and advantages too intangible
•  Let programmers code against SPARQL
•  Let everyone else use more familiar modes through Apps
RDFApps
•  Our first RDFApp targets the existing community of R users
– an ArrayExpress R package already exists
•  Goal is to expose the power of the Atlas RDF+SPARQL
behind a conventional R interface
•  Enables those working with raw data to also use power of
Atlas
Codefest
•  Got an idea for an RDF App? Join us at Codefest 2014
•  http://www.open-bio.org/wiki/Codefest_2014
•  18th/19th September, Cambridge, UK
Interesting RDF resources for biology
• 
• 
• 
• 
• 
• 
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• 
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EBI RDF (http://www.ebi.ac.uk/rdf )
Bio2RDF (http://bio2rdf.org )
BioPortal (https://bioportal.bioontology.org )
OpenPhacts (https://www.openphacts.org )
PubChem RDF (https://pubchem.ncbi.nlm.nih.gov/rdf/ )
Identifiers.org (http://identifiers.org )
Wikipathways (http://wikipathways.org )
DisGeNet (http://ibi.imim.es/web/DisGeNET/v01/ )
W3C Healthcare and Life Sciences Working Group (HCLS http://www.w3.org/blog/hcls/ )
Acknowledgments
•  Samples Phenotypes and Ontologies Group and Functional
Genomics Production Team
•  James Malone, Robert Petryszak, Tony Burdett, Helen
Parkinson
•  EBI RDF platform
•  Andy Jenkinson, Mark Davies, Marco Brandizi, Sarala
Wimalaratne, Leyla Garcia, Jerven Bolleman
Funding
Components of the RDF platform pilot are supported by a
number of sources, including:
•  EMBL
•  European Commission:
•  BioMedBridges [284209]
•  Diachron [601043]
•  OpenPhacts (Innovative Medicines Initiative)
•  National Institutes of Health
Questions?
Sign up for our mailing list:
http://listserver.ebi.ac.uk/mailman/listinfo/rdf-announce