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maxLevel	5

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")

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:

...

The same URI can be used in the dev environment, by changing the hostname as in the config property below.

...

Config File

No Format

# 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
fp4=http://purl.obolibrary.org/obo/ERO_0000076
#data type
ip4=http://www.w3.org/1999/02/22-rdf-syntax-ns#type
#has data input
fp5=http://purl.obolibrary.org/obo/ERO_0000076
#has measurement scale
ip5=http://eagle-i.org/ont/app/1.0/has_measurement_scale

...

No Format

# 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

...

Base queries

Get base, unfiltered dataset

Find all instances of baseType affiliated with virtualOrganization organization, returns a table with a column per query variable defined in property configuration above

...

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
GET [http://harvard.qa.eagle-i.net/i/0000012e-5480-32e6-55da-381e80000000?forceXML]

Getting info about After getting the main resource, the embedded resources:Assume need to be processed. Assume main resource has uri http://harvard.eagle-i.net/123

This query will return embedded resources:

No Format

PREFIX eiapp: <[http<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 .
}

Iterate To obtain the embedded resource's details, iterate over this list and do a GET as with the main resource.

...

No Format

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 .
}

Do this for each indirect filter property, e.g. ep1 ep4 and ip1ip4

No Format

PREFIX ei: <[http<http://purl.obolibrary.org/obo/]>
PREFIX rdfs: <[http<http://www.w3.org/2000/01/rdf-schema#]>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).

noformat

No Format

PREFIX ei: <[http<http://purl.obolibrary.org/obo/]>
PREFIX eiapp: <[http<http://eagle-i.org/ont/app/1.0/]>
PREFIX rdfs: <[http<http://www.w3.org/2000/01/rdf-schema#]>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}> .
}

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Old Version 11

New Version Current

Key

Vocabulary

A note of formats

Configuration

Organization Identifier

Config File

Base queries

Get base, unfiltered dataset

Get the filtered dataset