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Make nanopublications trusty

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tkuhn committed Oct 31, 2018
1 parent d041e6f commit 620249243cf25d47eb1676a6479ea0c23f037717
Showing with 1,678 additions and 644 deletions.
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  30. +20 −0 make-trusty.sh
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/nanopub.jar
88 FM_A1.1
@@ -1,70 +1,60 @@
@prefix this: <https://purl.org/fair-metrics/FM_A1.1> . # canonical URI for the metric
@prefix sub: <https://purl.org/fair-metrics/FM_A1.1#> .
@prefix this: <https://purl.org/fair-metrics/FM_A1.1#nanopub.RA6ETcEOEBQ2cP7rxPHcdf5h2RXHZZpdPvehohpiWABAQ> .
@prefix sub: <https://purl.org/fair-metrics/FM_A1.1#nanopub.RA6ETcEOEBQ2cP7rxPHcdf5h2RXHZZpdPvehohpiWABAQ.> .
@prefix metrics: <https://purl.org/fair-metrics/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix dcelem: <http://purl.org/dc/elements/1.1/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix nx: <http://www.nextprot.org/db/search#> .
@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix prv: <http://purl.org/net/provenance/ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ro: <http://purl.org/obo/owl/OBO_REL#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix fair: <http://purl.org/fair-ontology#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix fm: <https://purl.org/fair-metrics/terms/> .

sub:Head {
sub:nanopub np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}

sub:assertion {
this: a fair:FAIR-Metric ;
foaf:primaryTopic fair:A1.1 .

}
metrics:FM_A1.1 a fair:FAIR-Metric ;
foaf:primaryTopic fair:A1.1 .
}

sub:provenance {
sub:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Access Protocol"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle A1.1"^^xsd:string ;

fm:measuring "The nature and use limitations of the access protocol"^^xsd:string ;
fm:rationale "Access to a resource may be limited by the specified communication protocol. In particular, we are worried about access to technical specifications and any costs associated with implementing the protocol. Protocols that are closed source or that have royalties associated with them could prevent users from being able to obtain the resource"^^xsd:string ;
fm:requirements "i) A URL to the description of the protocol\nii) true/false as to whether the protocol is open source\niii) true/false as to whether the protocol is (royalty) free"^^xsd:string ;
fm:procedure "Do an HTTP get on the URL to see if it returns a valid document. Ideally, we would have a universal database of communication protocols from which we can check this URL. We also check whether questions 2 and 3 are true or false."^^xsd:string ;
fm:validation "The HTTP GET on the URL should return a 200,202,203 or 206 HTTP response after resolving all and any prior redirects. e.g. 301 -> 302 -> 200 OK. The other two should be true/false."^^xsd:string ;
fm:relevance "All"^^xsd:string ;
fm:examples "None"^^xsd:string ;
fm:comments "None"^^xsd:string ;

dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
prov:wasGeneratedBy "FAIR Metrics Working Group" .


_:dist1 dcelem:format "application/x-texinfo" ;
rdf:type <http://rdfs.org/ns/void#Dataset> ;
rdf:type <http://www.w3.org/ns/dcat#Distribution> ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.1.tex> .

_:dist2 dcelem:format "application/pdf" ;
rdf:type <http://rdfs.org/ns/void#Dataset> ;
rdf:type <http://www.w3.org/ns/dcat#Distribution> ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.1.pdf> .

sub:_1 dcelem:format "application/x-texinfo" ;
a <http://rdfs.org/ns/void#Dataset> , dcat:Distribution ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.1.tex> .

sub:_2 dcelem:format "application/pdf" ;
a <http://rdfs.org/ns/void#Dataset> , dcat:Distribution ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.1.pdf> .

sub:assertion dcterms:author "Erik Schultes" , "Luiz Bonino" , "Mark Wilkinson" , "Michel Dumontier" , "Peter Doorn" , "Susanna Sansone" ;
dcterms:title "Access Protocol" ;
rdfs:comment "FAIR Metric for Fair Principle A1.1" ;
dcat:distribution sub:_1 , sub:_2 ;
prov:wasGeneratedBy "FAIR Metrics Working Group" ;
fm:comments "None" ;
fm:examples "None" ;
fm:measuring "The nature and use limitations of the access protocol" ;
fm:procedure "Do an HTTP get on the URL to see if it returns a valid document. Ideally, we would have a universal database of communication protocols from which we can check this URL. We also check whether questions 2 and 3 are true or false." ;
fm:rationale "Access to a resource may be limited by the specified communication protocol. In particular, we are worried about access to technical specifications and any costs associated with implementing the protocol. Protocols that are closed source or that have royalties associated with them could prevent users from being able to obtain the resource" ;
fm:relevance "All" ;
fm:requirements """i) A URL to the description of the protocol
ii) true/false as to whether the protocol is open source
iii) true/false as to whether the protocol is (royalty) free""" ;
fm:validation "The HTTP GET on the URL should return a 200,202,203 or 206 HTTP response after resolving all and any prior redirects. e.g. 301 -> 302 -> 200 OK. The other two should be true/false." .
}


sub:pubinfo {
this: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
dcterms:rightsHolder <http://go-fair.org> ;
pav:authoredBy "Mark Wilkinson" , <https://orcid.org/0000-0001-6960-357X> ;
pav:versionNumber "1" ;
this: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
dcterms:rightsHolder <http://go-fair.org> ;
pav:authoredBy "Mark Wilkinson" , <https://orcid.org/0000-0001-6960-357X> ;
pav:versionNumber "1" .
}
@@ -0,0 +1,74 @@
# Use this file (with '.pre' extension) for editing. The respective files
# without that extension are automatically generated from the '.pre' files by
# running make-trusty.sh.

@prefix : <https://purl.org/fair-metrics/FM_A1.1#nanopub> .
@prefix metrics: <https://purl.org/fair-metrics/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix dcelem: <http://purl.org/dc/elements/1.1/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix nx: <http://www.nextprot.org/db/search#> .
@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix prv: <http://purl.org/net/provenance/ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ro: <http://purl.org/obo/owl/OBO_REL#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix fair: <http://purl.org/fair-ontology#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix fm: <https://purl.org/fair-metrics/terms/> .

:Head {
: np:hasAssertion :assertion ;
np:hasProvenance :provenance ;
np:hasPublicationInfo :pubinfo ;
a np:Nanopublication .
}

:assertion {
metrics:FM_A1.1 a fair:FAIR-Metric ;
foaf:primaryTopic fair:A1.1 .

}

:provenance {
:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Access Protocol"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle A1.1"^^xsd:string ;

fm:measuring "The nature and use limitations of the access protocol"^^xsd:string ;
fm:rationale "Access to a resource may be limited by the specified communication protocol. In particular, we are worried about access to technical specifications and any costs associated with implementing the protocol. Protocols that are closed source or that have royalties associated with them could prevent users from being able to obtain the resource"^^xsd:string ;
fm:requirements "i) A URL to the description of the protocol\nii) true/false as to whether the protocol is open source\niii) true/false as to whether the protocol is (royalty) free"^^xsd:string ;
fm:procedure "Do an HTTP get on the URL to see if it returns a valid document. Ideally, we would have a universal database of communication protocols from which we can check this URL. We also check whether questions 2 and 3 are true or false."^^xsd:string ;
fm:validation "The HTTP GET on the URL should return a 200,202,203 or 206 HTTP response after resolving all and any prior redirects. e.g. 301 -> 302 -> 200 OK. The other two should be true/false."^^xsd:string ;
fm:relevance "All"^^xsd:string ;
fm:examples "None"^^xsd:string ;
fm:comments "None"^^xsd:string ;

dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
prov:wasGeneratedBy "FAIR Metrics Working Group" .


_:dist1 dcelem:format "application/x-texinfo" ;
rdf:type <http://rdfs.org/ns/void#Dataset> ;
rdf:type <http://www.w3.org/ns/dcat#Distribution> ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.1.tex> .

_:dist2 dcelem:format "application/pdf" ;
rdf:type <http://rdfs.org/ns/void#Dataset> ;
rdf:type <http://www.w3.org/ns/dcat#Distribution> ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.1.pdf> .

}


:pubinfo {
: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
dcterms:rightsHolder <http://go-fair.org> ;
pav:authoredBy "Mark Wilkinson" , <https://orcid.org/0000-0001-6960-357X> ;
pav:versionNumber "1" ;
}
85 FM_A1.2
@@ -1,67 +1,60 @@
@prefix this: <https://purl.org/fair-metrics/FM_A1.2> . # canonical URI for the metric
@prefix sub: <https://purl.org/fair-metrics/FM_A1.2#> .
@prefix this: <https://purl.org/fair-metrics/FM_A1.2#nanopub.RA0cAAP6m2jtyXUjXEoB4DzGydzSi7QUyaQUYP4-78JjA> .
@prefix sub: <https://purl.org/fair-metrics/FM_A1.2#nanopub.RA0cAAP6m2jtyXUjXEoB4DzGydzSi7QUyaQUYP4-78JjA.> .
@prefix metrics: <https://purl.org/fair-metrics/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix dcelem: <http://purl.org/dc/elements/1.1/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix nx: <http://www.nextprot.org/db/search#> .
@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix prv: <http://purl.org/net/provenance/ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ro: <http://purl.org/obo/owl/OBO_REL#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix fair: <http://purl.org/fair-ontology#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix fm: <https://purl.org/fair-metrics/terms/> .

sub:Head {
sub:nanopub np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}

sub:assertion {
this: a fair:FAIR-Metric ;
foaf:primaryTopic fair:A1.2 .

}
metrics:FM_A1.2 a fair:FAIR-Metric ;
foaf:primaryTopic fair:A1.2 .
}

sub:provenance {
sub:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Access authorization"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle A1.2"^^xsd:string ;
fm:measuring "Specification of a protocol to access restricted content."^^xsd:string ;
fm:rationale "Not all content can be made available without restriction. For instance, access and distribution of personal health data may be restricted by law or by organizational policy. In such cases, it is important that the protocol by which such content can be accessed is fully specified. Ideally, electronic content can be obtained first by applying for access. Once the requester is formally authorized to access the content, they may receive it in some electronic means, for instance by obtaining an download URL, or through a more sophisticated transaction mechanism (e.g. authenticate, authorize), or by any other means. The goal should be to reduce the time it takes for valid requests to be fulfilled."^^xsd:string ;
fm:requirements "i) true/false concerning whether authorization is needed\nii) a URL that resolves to a description of the process to obtain access to restricted content.\n"^^xsd:string ;
fm:procedure "Computational validation of the data provided"^^xsd:string ;
fm:validation "A valid answer contains a true or false for the first question. if true, an HTTP GET on the URL provided should return a 200, 202, 203, or 206 HTTP Response after resolving all redirects."^^xsd:string ;
fm:relevance "All"^^xsd:string ;
fm:examples "None"^^xsd:string ;
fm:comments "None"^^xsd:string ;
dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
prov:wasGeneratedBy "FAIR Metrics Working Group" .

_:dist1 dcelem:format "application/x-texinfo" ;
rdf:type <http://rdfs.org/ns/void#Dataset> ;
rdf:type <http://www.w3.org/ns/dcat#Distribution> ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.2.tex> .

_:dist2 dcelem:format "application/pdf" ;
rdf:type <http://rdfs.org/ns/void#Dataset> ;
rdf:type <http://www.w3.org/ns/dcat#Distribution> ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.2.pdf> .

sub:_1 dcelem:format "application/x-texinfo" ;
a <http://rdfs.org/ns/void#Dataset> , dcat:Distribution ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.2.tex> .

sub:_2 dcelem:format "application/pdf" ;
a <http://rdfs.org/ns/void#Dataset> , dcat:Distribution ;
dcat:downloadURL <https://raw.githubusercontent.com/FAIRMetrics/Metrics/master/Distributions/FM_A1.2.pdf> .

sub:assertion dcterms:author "Erik Schultes" , "Luiz Bonino" , "Mark Wilkinson" , "Michel Dumontier" , "Peter Doorn" , "Susanna Sansone" ;
dcterms:title "Access authorization" ;
rdfs:comment "FAIR Metric for Fair Principle A1.2" ;
dcat:distribution sub:_1 , sub:_2 ;
prov:wasGeneratedBy "FAIR Metrics Working Group" ;
fm:comments "None" ;
fm:examples "None" ;
fm:measuring "Specification of a protocol to access restricted content." ;
fm:procedure "Computational validation of the data provided" ;
fm:rationale "Not all content can be made available without restriction. For instance, access and distribution of personal health data may be restricted by law or by organizational policy. In such cases, it is important that the protocol by which such content can be accessed is fully specified. Ideally, electronic content can be obtained first by applying for access. Once the requester is formally authorized to access the content, they may receive it in some electronic means, for instance by obtaining an download URL, or through a more sophisticated transaction mechanism (e.g. authenticate, authorize), or by any other means. The goal should be to reduce the time it takes for valid requests to be fulfilled." ;
fm:relevance "All" ;
fm:requirements """i) true/false concerning whether authorization is needed
ii) a URL that resolves to a description of the process to obtain access to restricted content.
""" ;
fm:validation "A valid answer contains a true or false for the first question. if true, an HTTP GET on the URL provided should return a 200, 202, 203, or 206 HTTP Response after resolving all redirects." .
}


sub:pubinfo {
this: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
dcterms:rightsHolder <http://go-fair.org> ;
pav:authoredBy "Mark Wilkinson" , <https://orcid.org/0000-0001-6960-357X> ;
pav:versionNumber "1" ;
this: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
dcterms:rightsHolder <http://go-fair.org> ;
pav:authoredBy "Mark Wilkinson" , <https://orcid.org/0000-0001-6960-357X> ;
pav:versionNumber "1" .
}

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