embrc_prov_example.ttl

@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix schema: <http://schema.org/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix ssn: <http://www.w3.org/ns/ssn/#> .
@prefix sosa: <http://www.w3.org/ns/ssn/#> .
@prefix dwc: <	http://rs.tdwg.org/dwc/terms/#> .
@prefix dct: <http://purl.org/dc/terms/> .

#### ACTIVITIES ####
## A TRANSPORT ACTIVITY
<http://example.org/Transport/transportExample>
    a prov:Activity ; 
    dct:type "Transport" ; 
    
    prov:used [
    	a prov:Entity ; 
    	dct:title "Storage conditions of the transport activity" ; 
    	dct:description {A description of the storage conditions} ; 
    	] ;     
    prov:used <http://example.org/Permit/2> ; 
    
    prov:startedAtTime {datetime} ; 
    prov:endedAtTime {datetime} ; 

    prov:wasAssociatedWith <http://example.org/Person/1> ; 

    prov:used <http://example.org/Protocol/1> ; 
.

## A PROCESSING ACTIVITY
<http://example.org/Storage/storageExample1>
    a prov:Activity ; 
    dct:type "Processing" ; 
    
    prov:used [
    	a prov:Entity ; 
    	dct:title "Materials/Chemicals used during the processing activity" ; 
    	dct:desciption {description of the materials/chemicals used} ; 
    ] ; 
    prov:used <http://example.org/Instrument/1> ; 
    
    prov:atLocation <http://example.org/location-type2> ; 
    
    prov:startedAtTime {datetime} ; 
    prov:endedAtTime {datetime} ; 

    prov:wasAssociatedWith <http://example.org/Person/2> ; 

    prov:used <http://example.org/Protocol/...> ; 
.


## A STORAGE ACTIVITY
<http://example.org/Storage/storageExample2>
    a prov:Activity ; 
    dct:type "Storage" ; 
    
    prov:atLocation <http://example.org/location-type1> ; 
    
    #Case of Bio-banking --> Agent associated with this activity is the bio-banking facility
    prov:wasAssociatedWith <http://example.org/BiobankInstitute> ; 
    
    prov:startedAtTime {datetime} ; 
    prov:endedAtTime {datetime} ; 
    
    prov:used [
        a prov:Entity ; 
        dct:title "Storage conditions during the storage activity" ; 
        dct:description {a short description of the storage conditions} ;  
    ] ; 
    prov:used <http://example.org/StorageDevice/1> ; 
.


## AN ORDERING ACTIVITY
<http://example.org/Order/1>
    a prov:Activity ;
    dct:type "Ordering - {to specify the kind of ordering}" ; 
    
    #bio-bank name can go into the description of the agent, a bit unclear in the UML diagram
    prov:wasAssociatedWith <http://example.org/BioBank/instituteName> ;  
    
    prov:startedAtTime {datetime} ; 
    prov:endedAtTime {datetime} ; 
    
    #location doesn't make sense to have here
.


## SAMPLING ACTIVITY
<http://example.org/Sampling/1>
    a ssn:Sampling, prov:Activity;
    dct:type "Sampling" ; 
    
    prov:used <http://example.org/Sampler/a> ;
    #or alternatively
    sosa:madebySampler <http://example.org/Sampler/a> ;
     
    prov:used <http://example.org/Permit/1> ; 

    prov:atLocation <http://example.org/location-type1>,  <http://example.org/location-type2>, <http://example.org/location-type3> ; 
    
    prov:startedAtTime {datetime} ;
    prov:endedAtTime {datetime} ;

    prov:wasAssociatedWith <http://example.org/person/examplePerson> ; 

    prov:used <http://example.org/SamplingProtocol/1> ; 
.


## QUALITY CONTROL ACTIVITY
<http://example.org/QualityControl/qualitycontrolExample>
    a prov:Activity ; 
    dct:type "Quality Control activity" ; 
    
    dct:description {the scope of the quality control} ; 
    prov:used <http://example.org/SoftWareProcessing/2> ; 
.


## SOFTWARE PROCESSING ACTIVITY
<http://example.org/SoftwareProcessingActivity/1>
    a prov:Activity ; 
    dct:type "Software Processing activity" ;
     
    prov:used <http://example.org/SoftwareProcessing/1> ; 
.

## DATA RETRIEVAL ACTIVITY
<http://example.org/DataRetrieval/1>
    a prov:Activity ; 
    dct:type "Data retrieval" ; 

    #need definitions of properties in the UML diagram; e.g. what does 'role' entail?
    prov:used [
        a prov:Entity ; 
        dct:title "The metadata associated with data retrieval" ; 
        schema:url <...> ; 
    ] ; 
    prov:used [
        a prov:Entity ; 
        dct:title "The data associated with data retrieval" ; 
        schema:url <...> ; 
    ] ; 
.
    

#### LOCATION ####
<http://example.org/location-type1>
    a prov:Location, schema:PostalAddress; 
        
    schema:addressCountry {} ; 
    schema:postalCode {} ; 
    schema:streetAddress {} ; 
.

<http://example.org/location-type2>
    a prov:Location, schema:Place ;
     
    schema:name {ISO country name} ; 
    schema:latitude {} ;
    schema:longitude {} ; 
    owl:sameAs {MRGID url} ;  
.

<http://example.org/location-type3>
    a prov:Location, dct:Location ;  
    
    locn:geometry {geometry could be encoded as WKT (geosparql:asWKT)} ; 
    dcat:bbox {} ; 
    dcat:centroid {} ;     
.


#### AGENT ####
<http://example.org/Person/1>
        a prov:Person, schema:Person ; 

        schema:giveName {} ;
        schema:surName {} ; 
        schema:email {} ; 
        owl:sameAs {orcID} ; #Katrina will dig through homework to check how orcID is referenced 
        prov:hadRole [
            a prov:Role ; 
            dct:type {} ;
        ] ; 
.

<http://example.org/BioBank/instituteName>
     a prov:Agent, schema:Organization ;
     
     schema:name {} ; 
     schema:email {} ; 
     schema:address {} ; 
.


#### ENTITIES ####
# PROTOCOL ENTITY
<http://example.org/SamplingProtocol/1> 
     a prov:Entity, schema:CreativeWork, dwc:samplingProtocol ; #specify the latter in case of a sampling activity
     
     schema:name {protocol of sampling 1} ; 
     schema:description {this is the description of the procotol used during sampling-1} ; 
     schema:identifier {url of the protocol - should be same as subject} ; 
     
     #need definition of 'distribution', not 100% clear what it entails, some possibilities: 
     schema:usageInfo {} ; 
     schema:accessMode {} ; 
     schema:accessibilitySummary {} ; 
.

<http://example.org/Protocol/1> 
     a prov:Entity, schema:CreativeWork ; 
     
     schema:name {protocol 1} ; 
     schema:description {this is the description of the procotol used during the transport activity ... } ; 
     schema:identifier {url of the protocol - should be same as subject} ; 
     
     #not 100% clear what the definition of 'distribution' will be, but some possibilities: 
     schema:usageInfo {} ; 
     schema:accessMode {} ; 
     schema:accessibilitySummary {} ; 
.


# INSTRUMENT ENTITY
<http://example.org/Instrument/1>
    a prov:Entity ;    
    dct:type {type of instrument} ; 
    dct:title {name of the instrument} ; 
    
    prov:wasInfluencedBy [
        a prov:Entity ;
        dct:title "Configuration/settings of the instrument during the Processing activity" ; 
        dct:description {the description/listing of the configuration settings} ; 
    ] ;  
    prov:wasInfluencedBy <http://example.org/SoftWareProcessing/1> ; 
.

<http://example.org/StorageDevice/1>
    a prov:Entity ; 
    dct:type {type of instrument} ; 
    dct:title {name of the instrument} ; 
    
    prov:wasInfluencedBy [
        a prov:Entity ;
        dct:title "Configuration/settings of the storage device during the Storage activity" ; 
        dct:description {the description/listing of the configuration settings} ; 
    ] ;   
    prov:wasInfluencedBy <http://example.org/SoftWareProcessing/1> ; 
.

<http://example.org/Sampler/a>
    a prov:Entity, sosa:Sampler ;     
    dct:type {the type of sampler} ;
    dct:title {name of the sampler} ; 
    
    prov:wasInfluencedBy [
        a prov:Entity ;
        dct:title "Configuration/settings of the Sampler during the Sampling activity" ; 
        dct:description {the description/listing of the configuration settings} ; 
    ] ; 
    prov:wasInfluencedBy <http://example.org/SoftWareProcessing/1> ;
    
    #Case when instrument is hosted on a platform:
    sosa:isHostedBy <http://example.org/Platform/A> ;
. 


# PLATFORM ENTITY
<http://example.org/Platform/A> 
    a prov:Entity, sosa:Platform ; 
    dct:type {name of the platform} ; 
.


## SOFTWAREPROCESSING ENTITY
<http://example.org/SoftWareProcessing/1>
    a prov:Entity, schema:softwareApplication ; 
    
    schema:name {name of the software processing} ; 
    schema:softwareVersion {version of the software processing} ; 
    #depending on the definition of "endpoint"
    schema:installUrl {endpoint url} ; 
    schema:downloadUrl {endpoint url} ; 
    schema:softwareRequirements {parameters} ; 
    
    #note schema:softwareApplication has some other properties that might be interesting. 
.


<http://example.org/SoftWareProcessing/2>
    a prov:Entity, schema:softwareApplication ; 
    
    schema:name {name of the software processing} ; 
    schema:softwareVersion {version of the software processing} ; 
    #depending on the definition of "endpoint"
    schema:installUrl {endpoint url} ; 
    schema:downloadUrl {endpoint url} ; 
    schema:softwareRequirements {parameters} ; 
.


------- still working on ---------
# PERMIT ENTITY
<http://example.org/Permit/1>
    
    ##MTA permit info
    a prov:Entity, pproc:SuppliesContract ; 
    
    ##ABS permit info
    a prov:Entity, pproc:SharedResultAgreementContract ; 

    ##GENERAL permit info
    schema:identifier {url of the permit | should be the same as the subject} ; 
    schema:contentReferenceTime {datetime to indicate the validity of the permit} ; 
    schema:dateCreated {datetime when the permit was issued} ;
    
    pproc:actualDuration {datetime to indicate the validity of the permit} ;
    pproc:noticeDate {datetime when the permit was issued} ; 
  
    pproc:additionalDocumentReference {url of the permit itself} ; 
.