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Adding metrics metadata to generate descriptions from rdf

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c-martinez committed Jul 9, 2018
1 parent 095ee8e commit 2798ee1f5f9cc0902fa932bf20fbfe7863224621
Showing with 286 additions and 158 deletions.
  1. +1 −2 FM_A1.1
  2. +16 −6 FM_A1.2
  3. +16 −6 FM_A2
  4. +16 −6 FM_F1A
  5. +16 −6 FM_F1B
  6. +16 −6 FM_F2
  7. +16 −6 FM_F3
  8. +16 −6 FM_F4
  9. +16 −6 FM_I1
  10. +16 −6 FM_I2
  11. +16 −6 FM_I3
  12. +16 −6 FM_R1.1
  13. +16 −6 FM_R1.2
  14. +16 −6 FM_R1.3
  15. +75 −76 script.py
  16. +2 −2 template.tex
@@ -14,7 +14,6 @@
@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 {
@@ -36,7 +35,7 @@ sub:provenance {
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:reason "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: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 ;
22 FM_A1.2
@@ -10,31 +10,41 @@
@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 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 .
}

sub:assertion {
this: 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 ;
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> ;
@@ -47,7 +57,7 @@ sub:provenance {

}


sub:pubinfo {
this: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
22 FM_A2
@@ -10,31 +10,41 @@
@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 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 .
}

sub:assertion {
this: a fair:FAIR-Metric ;
foaf:primaryTopic fair:A2 .

}

sub:provenance {
sub:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Metadata Longevity"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle A2"^^xsd:string ;
fm:measuring "The existence of metadata even in the absence/removal of data"^^xsd:string ;
fm:rationale "Cross-references to data from third-party's FAIR data and metadata will naturally degrade over time, and become 'stale links'. In such cases, it is important for FAIR providers to continue to provide descriptors of what the data was to assist in the continued interpretation of those third-party data. As per FAIR Principle F3, this metadata remains discoverable, even in the absence of the data, because it contains an explicit reference to the IRI of the data."^^xsd:string ;
fm:requirements "URL to a formal metadata longevity plan"^^xsd:string ;
fm:procedure "Resolve the URL"^^xsd:string ;
fm:validation "- Successful resolution\n - Returns a document that represents a plan or policy of some kind\n - Preferably certified (e.g. DSA)\n"^^xsd:string ;
fm:relevance "All metadata"^^xsd:string ;
fm:examples "None"^^xsd:string ;
fm:comments "None"^^xsd:string ;
dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
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> ;
@@ -47,7 +57,7 @@ sub:provenance {

}


sub:pubinfo {
this: dcterms:created "2017-11-21T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
22 FM_F1A
@@ -10,31 +10,41 @@
@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 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 .
}

sub:assertion {
this: a fair:FAIR-Metric ;
foaf:primaryTopic fair:F1 .

}

sub:provenance {
sub:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Identifier Uniqueness"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle F1"^^xsd:string ;
fm:measuring "Whether there is a scheme to uniquely identify the digital resource."^^xsd:string ;
fm:rationale "The uniqueness of an identifier is a necessary condition to unambiguously refer that resource, and that resource alone. Otherwise, an identifier shared by multiple resources will confound efforts to describe that resource, or to use the identifier to retrieve it. Examples of identifier schemes include, but are not limited to URN, IRI, DOI, Handle, trustyURI, LSID, etc. For an in-depth understanding of the issues around identifiers, please see http://dx.plos.org/10.1371/journal.pbio.2001414"^^xsd:string ;
fm:requirements "URL to a registered identifier scheme."^^xsd:string ;
fm:procedure "An identifier scheme is valid if and only if it is described in a repository that can register and present such identifier schemes (e.g. fairsharing.org).\n\nInformation about the identifier scheme must be presented with a machine-readable document containing the FM1 attribute with the URL to where the scheme is described. see specification for implementation."^^xsd:string ;
fm:validation "Present or Absent"^^xsd:string ;
fm:relevance "All"^^xsd:string ;
fm:examples "Ontology \n - Gene Ontology: http://www.ebi.ac.uk/miriam/main/ datatypes/MIR:00000022 \n - HISCO: [link]\n This resource has not described or registered their identifier scheme. A recommended course of action would be to XXX. \n Model/format - RDFS: https://fairsharing.org/bsg-s000283 \n Repository \n - JWS Online: https://www.ebi.ac.uk/miriam/main\n /collections/MIR:00000130 \n - DANS EASY: \n \n Database \n - ArrayExpress: https://fairsharing.org/biodbcore-000305 \n -> FAIRsharing will implement the FAIR Metric specification to provide a machine-readable link to the MIRIAM repository (for life science content) \n API \n - smartAPI's API\n https://raw.githubusercontent.com/WebsmartAPI\n /smartAPI/master/docs/iodocs/smartapi.json \n --> the smartAPI repository will provide accessible specification of the identifier scheme that is embedded in that metadata document. \n Journal\n http://www.nature.com/developers/documentation/\n metadata-resources/doi \n --> the web site will have to provide a machine-readable pointer to the official DOI specification. \n"^^xsd:string ;
fm:comments "A first version of this metric would focus on just checking a URL that resolves to a document. We can't verify that document. \n A second version would indicate how to structure the data policy document with a particular section (similar to how the CC licenses now have a formal structure in RDF).\n A third version would insist that that document and section is signed by an approved organization and made available in an appropriate repository."^^xsd:string ;
dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
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> ;
@@ -47,7 +57,7 @@ sub:provenance {

}


sub:pubinfo {
this: dcterms:created "2017-11-20T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
22 FM_F1B
@@ -10,31 +10,41 @@
@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 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 .
}

sub:assertion {
this: a fair:FAIR-Metric ;
foaf:primaryTopic fair:F1 .

}

sub:provenance {
sub:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Identifier persistence"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle F1"^^xsd:string ;
fm:measuring "Whether there is a policy that describes what the provider will do in the event an identifier scheme becomes deprecated."^^xsd:string ;
fm:rationale "The change to an identifier scheme will have widespread implications for resource lookup, linking, and data sharing. Providers of digital resources must ensure that they have a policy to manage changes in their identifier scheme, with a specific emphasis on maintaining/redirecting previously generated identifiers."^^xsd:string ;
fm:requirements "A URL that resolves to a document containing the relevant policy."^^xsd:string ;
fm:procedure "Use an HTTP GET on URL provided."^^xsd:string ;
fm:validation "Present (a 200,202,203 or 206 HTTP response after resolving all and any prior redirects. e.g. 301 -> 302 -> 200 OK) or Absent (any other HTTP code)"^^xsd:string ;
fm:relevance "All"^^xsd:string ;
fm:examples "for each of the 'canonical' data types, examples, if available. \n @todo \n \n FAIR principles (scholarly publication in Nature Scientific Data)\n \\verb|https://www.doi.org/overview/DOI_article_ELIS3.pdf| \n http://www.nature.com/developers/\n documentation/metadata-resources/doi/ \n \n FAIR Principles (computable representation): \n https://github.com/FAIRDataInitiative/\n \\verb|FAIR-principles#fair-principles| \n For DSA-certified repositories (example below of 3TU-Datacentre at Delft) the identifier persistence policy is described in the self assessment:\n https://assessment.datasealofapproval.org/\n \\verb|assessment_187/seal/pdf/| \n \nDOI Handbook - ensuring persistence:\n \\verb|http://www.doi.org/doi_handbook/| \n\\verb|6_Policies.html#6.5}|"^^xsd:string ;
fm:comments "A first version of this metric would focus on just checking a URL that resolves to a document. We can't verify that document. \nA second version would indicate how to structure the data policy document with a particular section (similar to how the CC licenses now have a formal structure in RDF).\nA third version would insist that that document and section is signed by an approved organization and made available in an appropriate repository."^^xsd:string ;
dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
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> ;
@@ -47,7 +57,7 @@ sub:provenance {

}


sub:pubinfo {
this: dcterms:created "2017-11-20T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;
22 FM_F2
@@ -10,31 +10,41 @@
@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 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 .
}

sub:assertion {
this: a fair:FAIR-Metric ;
foaf:primaryTopic fair:F2 .

}

sub:provenance {
sub:assertion dcterms:author "Michel Dumontier", "Mark Wilkinson" , "Susanna Sansone", "Peter Doorn", "Luiz Bonino", "Erik Schultes" ;
dcterms:title "Machine-readability of metadata"^^xsd:string ;
rdfs:comment "FAIR Metric for Fair Principle F2"^^xsd:string ;
fm:measuring "The availability of machine-readable metadata that describes a digital resource."^^xsd:string ;
fm:rationale "This metric \textit{does not} attempt to measure (or even define) 'Richness' - this will be defined in a future Metric. This metric is intended to test the format of the metadata - machine readability of metadata makes it possible to optimize discovery. For instance, Web search engines suggest the use of particular structured metadata elements to optimize search. Thus, the machine-readability aspect can help people and machines find a digital resource of interest."^^xsd:string ;
fm:requirements "A URL to a document that contains machine-readable metadata for the digital resource. Furthermore, the file format must be specified."^^xsd:string ;
fm:procedure "HTTP GET on the metadata URL. A response of [a 200,202,203 or 206 HTTP response after resolving all and any prior redirects. e.g. 301 -> 302 -> 200 OK] indicates that there is indeed a document. The second URL should resolve to the record of a registered file format (e.g. DCAT, DICOM, schema.org etc.) in a registry like FAIRsharing. Future ehnancements to FAIRSharing may include tags that indicate whether or not a given file format is generally-agreed to be machine-readable"^^xsd:string ;
fm:validation "Machine-readable or Machine-not-readable"^^xsd:string ;
fm:relevance "All"^^xsd:string ;
fm:examples "This URL can resolve to:\n - A record in a metadata registry relevant to your digital object (e.g. FAIRsharing.org, FAIR Data Point, smartAPI editor)\n - Your metadata on an HTML web page using schema.org\n - A FAIR Accessor...\n \n Semanticscience Integrated Ontology : http://semanticscience.org/ontology/sio.owl https://biosharing.org/bsg-s002686 \n Example of a DANS metadata-record of an archived dataset: https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:67859/tab/1 \n smartAPI's API metadata: https://raw.githubusercontent.com/WebsmartAPI/smartAPI/master/docs/iodocs/smartapi.json \n Metadata record of a database: - GEO https://fairsharing.org/biodbcore-000441 \n Metadata record of a standard: - RDF https://fairsharing.org/bsg-s000559 \n Non-article Published Work\n - my Zenodo Deposit for polyA (https://doi.org/10.5281/zenodo.47641)\n - myExperiment Workflow (http://www.myexperiment.org/workflows/2999.html)\n - Jupyter notebook on GitHub (https://github.com/VidhyasreeRamu/GlobalClimateChange/blob/master/GlobalWarmingAnalysis.ipynb)"^^xsd:string ;
fm:comments "None"^^xsd:string ;
dcat:distribution _:dist1 ;
dcat:distribution _:dist2 ;
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> ;
@@ -47,7 +57,7 @@ sub:provenance {

}


sub:pubinfo {
this: dcterms:created "2017-11-20T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <https://creativecommons.org/publicdomain/zero/1.0> ;

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