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Vocabulary
Resource = a record of a
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"thing"
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in
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eagle-i.
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A
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resource
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is
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an
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instance
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of
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a
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class
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defined
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in
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the
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eagle-i
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ontology
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(e.g.
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"My
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nifty
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DNA
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Microarray"
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is
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an
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instance
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of
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the
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class
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"DNA
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MicroArray",
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which
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is
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a
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subclass
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of
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"Instrument"
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)
A note of formats
See the MIME Type Section in the eagle-i repo API guide for the different formats that are supported by the SPARQL endpoint (all our queries are SELECT, so probably the best is SPARQL Result Set, which is XML representing a table)
Configuration
Organization Identifier
The organization to which biostats tools are attached in the eagle-i repository is:
http://harvard.eagle-i.net/i/0000012e-5946-2efe-55da-381e80000000
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The
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same
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URI
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can
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be
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used
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in
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the
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dev
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environment,
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by
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changing
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the
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hostname
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as
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in
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the
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config
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property
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below.
Config File
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h4. Configuration {noformat} # General # What general type of resources we are dealing with baseType=http://purl.obolibrary.org/obo/ERO_0000071 # What organization are the resources "attached" to (all resources in eagle-i need to belong to an organization) organization=http://harvard.eagle-i.net/i/0000012e-5946-2efe-55da-381e80000000 # What properties to show in the overview record # Literal properties (i.e. properties whose value is a simple string) # Website lp1=http://purl.obolibrary.org/obo/ERO_0000480 # Object properties (i.e. properties whose value is a link to another resource or ontology term) # Not used for Biostats # op1= # op2= ################ # Filters ################ # Filter Group titles - for UI (do not grab these labels from ontology, they're usually not what you need) fg1="Software Purpose" fg2="Study Design" fg3="Algorithm" fg4="Data Type" fg5="Measurement Scale" # Properties for creating filters # Each property corresponds to a filter group # Direct filter properties #has software purpose fp1=http://purl.obolibrary.org/obo/ERO_0000078 #has related Study Design fp2=http://eagle-i.org/ont/app/1.0/has_related_study_design #Algorithm used fp3=http://www.ebi.ac.uk/efo/swo/SWO_0000740 #Indirect filter properties (the property hangs off an embedded class) - need embedded property and indirect property #has data input ep1fp4=http://purl.obolibrary.org/obo/ERO_0000076 #data type ip1ip4=http://www.w3.org/1999/02/22-rdf-syntax-ns#type #has data input ep2fp5=http://purl.obolibrary.org/obo/ERO_0000076 #has measurement scale ip2ip5=http://eagle-i.org/ont/app/1.0/has_measurement_scale {noformat} |
More
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advanced
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version
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with
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open-ended
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lists,
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potentially
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using
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yaml
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(but
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need
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to
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get
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the
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syntax right 
, for example:
| No Format |
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right ;-)
{noformat}
# What properties to show in the overview record
# Literal properties (i.e. properties whose value is a simple string)
literalProperties:
propertyUri: http://purl.obolibrary.org/obo/ERO_0000480
# Object properties (i.e. properties whose value is a link to another resource or ontology term)
objectProperties:
propertyUri: http://purl.obolibrary.org/obo/ERO_0001719
propertyUri: http://purl.obolibrary.org/obo/ERO_0000078
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Base queries
Get base, unfiltered dataset
Find all instances of baseType affiliated with organization, returns a table with a column per query variable defined in property configuration above
Need to split in two queries (one for Ontology labels, one for instances). Note that if desired props don't have preferred label we'll need to alter query 1
Query 1 => to be executed only once (labels don't change)
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# What properties to show on the left nav # What properties to filter on # => TBD with Richard {noformat} h4. Queries h5. Get base, unfiltered dataset Find all instances of {{baseType}} affiliated with {{virtualOrganization}}, returns a table with a column per query variable defined in property configuration above Need to split in two queries (one for Ontology labels, one for instances). Note that if desired props don't have preferred label we'll need to alter query 1 Query 1 => to be executed only once (labels don't change) {noformat} PREFIX eiapp: <http://eagle-i.org/ont/app/1.0/> SELECT ?lp1Label ?op1Label ?op2Label WHERE { OPTIONAL { <${lp1}> eiapp:preferredLabel ?lp1Label . <${op1}> eiapp:preferredLabel ?op1Label . <${op2}> eiapp:preferredLabel ?op2Label . } } {noformat} |
Query
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2
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Note
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that
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if
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a
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property
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is
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not
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defined
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in
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the
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config
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file
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(e.g.
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op1),
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the
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variable
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in
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the
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SELECT
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clause,
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as
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well
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as
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the
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entire
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triple
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pattern/pattern
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group
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in
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the
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WHERE
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clause
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(i.e.
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the
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corresponding
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line)
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needs
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to
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be
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omitted.
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So
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there
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need to
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be
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some
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conditional
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logic
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in
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the
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query
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generation.
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} PREFIX ei: <http://purl.obolibrary.org/obo/> PREFIX eiapp: <http://eagle-i.org/ont/app/1.0/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?resourceUri ?resourceLabel ?resourceDescription ?lp1Value ?op1ValueLabel ?op1ValueUri ?op2ValueLabel ?op2ValueUri WHERE { ?resourceUri a <${baseType}> . ?resourceUri ei:ERO_0000070 <${virtualOrganizationorganization}> . ?resourceUri rdfs:label ?resourceLabel . OPTIONAL { ?resourceUri eiapp:resource_description ?resourceDescription . ?resourceUri <${lp1}> ?lp1Value . ?resourceUri <${op1}> ?op1ValueUri . ?op1ValueUri rdfs:label ?op1ValueLabel . ?resourceUri <${op2}> ?op2ValueUri . ?op2ValueUri rdfs:label ?op2ValueLabel . } } {noformat} *Example with substituted values* {noformat} |
Example with substituted values
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PREFIX ei: <http://purl.obolibrary.org/obo/>
PREFIX eiapp: <http://eagle-i.org/ont/app/1.0/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT
?resourceUri
?resourceLabel
?resourceDescription
?lp1Label
?lp1Value
WHERE {
?resourceUri a <http://purl.obolibrary.org/obo/ERO_0000071> .
?resourceUri ei:ERO_0000070 <http://harvard.dev.eagle-i.net/i/0000012e-5946-2efe-55da-381e80000000> .
?resourceUri rdfs:label ?resourceLabel .
OPTIONAL {
?resourceUri eiapp:resource_description ?resourceDescription .
?resourceUri <http://purl.obolibrary.org/obo/ERO_0000480> ?lp1Value .
}
}
Queries to get a detailed view of a resource
For the main resource, simply do a GET of its URI; the results can be in a variety of formats - see:
[eagle-i repo API guide | https://open.med.harvard.edu/display/eaglei/Repository+Design+Specification+and+API+Manual#RepositoryDesignSpecificationandAPIManual-FormatIdentifiersandMIMETypes]
There is an additional parameter forceXML, which returns a format that may be the most useful (it's the XML from which the HTML version is generated) - pure RDF/XML is horrible
Example:
{noformat} |
Get detailed view of a resource
For the main resource, simply do a GET of its URI; the results can be in a variety of formats - see: eagle-i repo API guide
There is an additional parameter forceXML, which returns a format that may be the most useful (it's the XML from which the HTML version is generated) - pure RDF/XML is horrible
Example:
| No Format |
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GET http://harvard.qa.eagle-i.net/i/0000012e-5480-32e6-55da-381e80000000?forceXML
{noformat}
Getting info about the embedded:
assume main resource has uri |
After getting the main resource, the embedded resources need to be processed. Assume main resource has uri http://harvard.eagle-i.net/123
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This
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query
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will
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return
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embedded
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resources:
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} PREFIX eiapp: <http://eagle-i.org/ont/app/1.0/> SELECT ?embeddedResourceUri WHERE { <http://harvard.eagle-i.net/123> ?anyProperty ?embeddedResourceUri . ?embeddedResourceUri a ?type . ?type eiapp:inClassGroup eiapp:ClassGroup_EmbeddedResourceType . } |
To obtain the embedded resource's details, iterate over this list and do a GET as with the main resource.
Queries for filters
Get actual annotation values that have been used in the dataset
Do this for each direct filter property, e.g. fp1
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{noformat} Iterate over this list and do a GET as with the main resource. Queries for filters Queries to get actual annotation values that have been used in the dataset Do this for each direct filter property, e.g. fp1 {noformat} PREFIX ei: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?filterValueUri ?filterValueLabel WHERE { ?resourceUri a <${baseType}> . ?resourceUri ei:ERO_0000070 <${virtualOrganizationorganization}> . ?resource <${fp1}> ?filterValueUri . ?filterValueUri rdfs:label ?filterValueLabel . } {noformat} |
Do
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this
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for
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each
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indirect
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filter
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property,
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e.g. ep4 and ip4
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ep1 and ip1 {noformat PREFIX ei: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?filterValueUri ?filterValueLabel WHERE { ?resourceUri a <${baseType}> . ?resourceUri ei:ERO_0000070 <${virtualOrganizationorganization}> . ?resource <${ep1ep4}> ?embeddedResource . ?embeddedResource <${ip1ip4}> ?filterValueUri . ?filterValueUri rdfs:label ?filterValueLabel . } |
Get the filtered dataset
First part is identical to unfiltered query (remember to remove unset config params, e.g. op1), then conditions are added as triple patterns;
Assume filterValueUrix is the filter value selected by the user, for each filter property, e.g. filterValueUri1 for fp1
NOTE if only one filter is selected, add only that triple pattern/triple pattern group.
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{noformat} Query to get the filtered dataset First part is identical to unfiltered query, then conditions are added as triple patterns; Assume filterValueUrix is the filter value selected by the user, for each filter property, e.g. filterValueUri1 for fp1 (if only one filter is selected, add only that triple pattern/triple pattern group) {noformat} PREFIX ei: <http://purl.obolibrary.org/obo/> PREFIX eiapp: <http://eagle-i.org/ont/app/1.0/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?resourceUri ?resourceLabel ?resourceDescription ?lp1Value ?op1ValueLabel ?op1ValueUri ?op2ValueLabel ?op2ValueUri WHERE { ?resourceUri a <${baseType}> . ?resourceUri ei:ERO_0000070 <${virtualOrganizationorganization}> . ?resourceUri rdfs:label ?resourceLabel . OPTIONAL { ?resourceUri eiapp:resource_description ?resourceDescription . ?resourceUri <${lp1}> ?lp1Value . ?resourceUri <${op1}> ?op1ValueUri . ?op1ValueUri rdfs:label ?op1ValueLabel . ?resourceUri <${op2}> ?op2ValueUri . ?op2ValueUri rdfs:label ?op2ValueLabel . } ?resourceUri <${fp1}> <${filterValueUri1}> . ?resourceUri <${fp2}> <${filterValueUri2}> . ?resourceUri <${fp3}> <${filterValueUri3}> . ?resourceUri <${ep1ep4}> ?embeddedResource1 . ?embeddedResource1 <${ip1ip4}> <${filterValueUriIndirect1filterValueUri4}> . ?resourceUri <${ep2ep5}> ?embeddedResource2 . ?embeddedResource2 <${ip2ip5}> <${filterValueUriIndirect2filterValueUri5}> . } {noformat} |
Overview
Content Tools