*Vocabulary*
Resource = a record of a "thing" in eagle-i. A resource is an instance of a class defined in the eagle-i ontology (e.g. "My nifty DNA Microarray" is an instance of the class "DNA MicroArray", which is a subclass of "Instrument")\\
*Configuration*
\# General
\# What general type of resources we are dealing with\\
baseType=[http://purl.obolibrary.org/obo/ERO_0000071|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)\\
virtualOrganization=http://harvard.eagle-i.net/i/xyz\\
\# What properties to show in the overview record
\# Literal properties (i.e. properties whose value is a simple string)\\
lp1=[http://purl.obolibrary.org/obo/ERO_0000480|http://purl.obolibrary.org/obo/ERO_0000480]
\# Object properties (i.e. properties whose value is a link to another resource or ontology term)\\
op1=[http://purl.obolibrary.org/obo/ERO_0001719|http://purl.obolibrary.org/obo/ERO_0001719]
op2=[http://purl.obolibrary.org/obo/ERO_0000078|http://purl.obolibrary.org/obo/ERO_0000078]\\ \\
========= More advanced version with open-ended lists, potentially using yaml (but need to get the syntax right \;-)
\# 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|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|http://purl.obolibrary.org/obo/ERO_0001719]
propertyUri: [http://purl.obolibrary.org/obo/ERO_0000078|http://purl.obolibrary.org/obo/ERO_0000078]\\
\# What properties to show on the left nav
\# What properties to filter on
\# => TBD with Richard\\ \\
*Queries*
* *
*Query for 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\\
*Option 1 one query*
PREFIX ei: <[http://purl.obolibrary.org/obo/|http://purl.obolibrary.org/obo/ERO_0000070]>
PREFIX eiapp: <[http://eagle-i.org/ont/app/1.0/|http://eagle-i.org/ont/app/1.0/]>
PREFIX rdfs: <[http://www.w3.org/2000/01/rdf-schema#|http://www.w3.org/2000/01/rdf-schema]>\\
SELECT
?resourceUri
?resourceLabel
?resourceDescription
?lp1Label
?lp1Value
?op1Label
?op1ValueLabel
?op1ValueUri
?op2Label
?op2ValueLabel
?op2ValueUri\\
WHERE {
?resourceUri a <${baseType}> .
?resourceUri ei:ERO_0000070 <${virtualOrganization}> .
?resourceUri rdfs:label ?resourceLabel .
OPTIONAL {
?resourceUri eiapp:resource_description ?resourceDescription .
?resourceUri <${lp1}> ?lp1Value . <${lp1}> eiapp:preferredLabel ?lp1Label .
?resourceUri <${op1}> ?op1ValueUri . ?op1ValueUri rdfs:label ?op1ValueLabel . <${op1}> eiapp:preferredLabel ?op1Label .
?resourceUri <${op2}> ?op2ValueUri . ?op2ValueUri rdfs:label ?op2ValueLabel . <${op2}> eiapp:preferredLabel ?op2Label .
}
}\\ \\
*Option 2 split in two queries (one for Ontology labels, one for instances) = > this may be preferable*
*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)*
* *
PREFIX eiapp: <[http://eagle-i.org/ont/app/1.0/|http://eagle-i.org/ont/app/1.0/]>
SELECT \\
?lp1Label
?op1Label
?op2Label\\
WHERE {
OPTIONAL {
<${lp1}> eiapp:preferredLabel ?lp1Label .
<${op1}> eiapp:preferredLabel ?op1Label .
<${op2}> eiapp:preferredLabel ?op2Label .
}
}\\ \\
*Query 2*
* *
PREFIX ei: <[http://purl.obolibrary.org/obo/|http://purl.obolibrary.org/obo/ERO_0000070]>
PREFIX eiapp: <[http://eagle-i.org/ont/app/1.0/|http://eagle-i.org/ont/app/1.0/]>
PREFIX rdfs: <[http://www.w3.org/2000/01/rdf-schema#|http://www.w3.org/2000/01/rdf-schema]>\\
SELECT
?resourceUri
?resourceLabel
?resourceDescription
?lp1Value
?op1ValueLabel
?op1ValueUri
?op2ValueLabel
?op2ValueUri\\
WHERE {
?resourceUri a <${baseType}> .
?resourceUri ei:ERO_0000070 <${virtualOrganization}> .
?resourceUri rdfs:label ?resourceLabel .
OPTIONAL {
?resourceUri eiapp:resource_description ?resourceDescription .
?resourceUri <${lp1}> ?lp1Value .
?resourceUri <${op1}> ?op1ValueUri . ?op1ValueUri rdfs:label ?op1ValueLabel .
?resourceUri <${op2}> ?op2ValueUri . ?op2ValueUri rdfs:label ?op2ValueLabel .
}
}\\ \\ \\ \\
*Example with substituted values (option 1)*
PREFIX ei: <[http://purl.obolibrary.org/obo/|http://purl.obolibrary.org/obo/ERO_0000070]>
PREFIX eiapp: <[http://eagle-i.org/ont/app/1.0/|http://eagle-i.org/ont/app/1.0/]>
PREFIX rdfs: <[http://www.w3.org/2000/01/rdf-schema#|http://www.w3.org/2000/01/rdf-schema]>\\
SELECT
?resourceUri
?resourceLabel
?resourceDescription
?lp1Label
?lp1Value
?op1Label
?op1ValueLabel
?op1ValueUri
?op2Label
?op2ValueLabel
?op2ValueUri\\
WHERE {
?resourceUri a <[http://purl.obolibrary.org/obo/ERO_0000071|http://purl.obolibrary.org/obo/ERO_0000071]> .
?resourceUri rdfs:label ?resourceLabel .
OPTIONAL {
?resourceUri eiapp:resource_description ?resourceDescription .
?resourceUri <[http://purl.obolibrary.org/obo/ERO_0000480|http://purl.obolibrary.org/obo/ERO_0000480]> ?lp1Value . <[http://purl.obolibrary.org/obo/ERO_0000480|http://purl.obolibrary.org/obo/ERO_0000480]> eiapp:preferredLabel ?lp1Label .
?resourceUri <[http://purl.obolibrary.org/obo/ERO_0001719|http://purl.obolibrary.org/obo/ERO_0001719]> ?op1ValueUri . ?op1ValueUri rdfs:label ?op1ValueLabel . <[http://purl.obolibrary.org/obo/ERO_0001719|http://purl.obolibrary.org/obo/ERO_0001719]> eiapp:preferredLabel ?op1Label .
?resourceUri <[http://purl.obolibrary.org/obo/ERO_0000078|http://purl.obolibrary.org/obo/ERO_0000078]> ?op2ValueUri . ?op2ValueUri rdfs:label ?op2ValueLabel . <[http://purl.obolibrary.org/obo/ERO_0000078|http://purl.obolibrary.org/obo/ERO_0000078]> eiapp:preferredLabel ?op2Label .
}
} |