FAIR score maximization

[carlinmack]

Tasks identified from issues

• No license property was found in the metadata
  This was an error with the FAIR checker and no fix was needed

• Unable to resolve DOI using HTTP Accept header application/json #2949
  Open PR bug: use Accept header to return other formats #2948

• Unable to resolve DOI using HTTP Accept header text/xhtml,text/xml
  Datacite is the preferred XML flavour of the four we have, but the implementation would depend on what happens to the above PR:

    "application/marcxml+xml": ResponseHandler(MARCXMLSerializer(), headers=etag_headers),
    "application/vnd.datacite.datacite+xml": ResponseHandler(DataCite43XMLSerializer(), headers=etag_headers),
    "application/x-dc+xml": ResponseHandler(DublinCoreXMLSerializer(), headers=etag_headers),
    "application/dcat+xml": ResponseHandler(DCATSerializer(), headers=etag_headers),

• Could not find dcterms:accessRights information in metadata
  I don't think this is applicable. I could imagine "Open metadata, restricted files" and variations thereof but I'm not sure if that would be expected

- I will check what other people do

• No info about file size available in given metadata for files
  Tested with ngrok from local system, adding file size to the headers did not work. The test here seems to suggest that it is picked up from the header.

  • Implement DataCite's size and format fields (and see if that's something that their code detects)

• Could not verify content type from downloaded files
  Could not find how to modify the current content type. (Will look into this further) This is only valid for datasets.

  • Implement DataCite's size and format fields (and see if that's something that their code detects)

• Formal provenance metadata is unavailable

• Predicates metadata should resolve to Linked Data data

• Persistence policy not identified

• GUID does not conform with any known permanent-URL system

• dcat: Missing discoverability oriented metadata

---

Using:

• https://doi.org/10.5281/zenodo.3723281

Issue	F-UJI	FAIR Checker	FAIR Evaluator	FAIR Enough	OpenAIRE Validator
Score (averaged)	79%	92%	64%	72%	80%
F1: Persistence of identifier			❌	❌
F2A: Structured metadata		❌
F3: Metadata identifier in metadata			❌	❌
F4: Searchable			⏺️ (no fix needed)	⏺️ (no fix needed)
A1.1 Uses an open free protocol for data retrieval, Data authentication and authoriazatio				❌
A2: Metadata persistence			❌	❌
FsF-I2-01M - Metadata uses semantic resources	❌
I1: Machine readable format		❌	❌	❌
I2: Metadata users FAIR vocabularies			❌	❌
FsF-R1-01MD - Metadata specifies the content of the data.	❌
R1.1 Metadata includes license			❌	❌
FsF-R1.2-01M - Metadata includes provenance information about data creation or generation.	❌
FsF-R1.3-02D - Data is available in a file format recommended by the target research community.	❌
Notes:

• F-UJI
  • Score: 79%
  • FAIR level: advanced (highest)
  • Test: FsF Metrics v0.5
  • F: 7/7 advanced
  • A : 3/3 advanced
  • I: 3/4 moderate
    • FsF-I2-01M-2 Namespaces of known semantic resources can be identified in metadata
      • NO known vocabulary namespace URI is found which is listed in the LOD registry
        • Check if known namespace(s) are used in structured metadata (RDF, XML) which exist(s) in a LOD registry -: ['http://www.openarchives.org/OAI/2.0/oai_dc.xsd', 'https://github.com/diwis', 'https://zenodo.org/api/records/7559361/files/articles_by_influence.csv', 'https://zenodo.org/records', 'https://pages.semanticscholar.org', 'https://zenodo.org/api/records/7559361/files/articles_by_influence_alt.csv', 'http://schema.datacite.org/oai/oai-1.1/oai.xsd', 'https://zenodo.org/record', 'https://zenodo.org/api/records/7559361/files/articles_by_popularity_alt.csv', 'http://schema.datacite.org/meta/kernel-4/metadata.xsd', 'https://creativecommons.org/licenses/by/4.0', 'https://doi.org/10.5281', 'https://zenodo.org/api/records/7559361/files/articles_by_tweets.csv', 'http://datacite.org/schema', 'https://zenodo.org/communities', 'http://schema.datacite.org/meta/kernel-4.3/metadata.xsd', 'http://datacite.org/schema', 'https://orcid.org', 'https://zenodo.org/api/records/7559361/files/articles_by_popularity.csv', 'https://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd']
  • R: 6/10 moderate
    • FsF-R1-01MD-2 Verifiable data descriptors (file info, measured variables or observation types) are specified in metadata, FsF-R1-01MD-3 Data content matches file type and size or protocol specified in metadata, FsF-R1-01MD-4 Data content matches measured variables or observation types specified in metadata
      • WARNING NO info about file size available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_tweets.csv/content
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_tweets.csv/content
      • WARNING Could not verify content type from downloaded file -: (expected: text/csv, found: via tika ['text/tsv'] or via header text/plain)
      • WARNING NO measured variables found in metadata, skip 'measured_variable' test.
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_tweets.csv/content
      • WARNING NO info about file size available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_influence_alt.csv/content
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_influence_alt.csv/content
      • WARNING Could not verify content type from downloaded file -: (expected: text/csv, found: via tika ['text/tsv'] or via header text/plain)
      • WARNING NO measured variables found in metadata, skip 'measured_variable' test.
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_influence_alt.csv/content
      • WARNING NO info about file size available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_popularity_alt.csv/content
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_popularity_alt.csv/content
      • WARNING Could not verify content type from downloaded file -: (expected: text/csv, found: via tika ['text/tsv'] or via header text/plain)
      • WARNING NO measured variables found in metadata, skip 'measured_variable' test.
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_popularity_alt.csv/content
      • WARNING NO info about file size available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_popularity.csv/content
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_popularity.csv/content
      • WARNING Could not verify content type from downloaded file -: (expected: text/csv, found: via tika ['text/tsv'] or via header text/plain)
      • WARNING NO measured variables found in metadata, skip 'measured_variable' test.
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_popularity.csv/content
      • WARNING NO info about file size available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_influence.csv/content
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_influence.csv/content
      • WARNING Could not verify content type from downloaded file -: (expected: text/csv, found: via tika ['text/tsv'] or via header text/plain)
      • WARNING NO measured variables found in metadata, skip 'measured_variable' test.
      • INFO NO info about data service endpoint available in given metadata for -: https://zenodo.org/api/records/7559361/files/articles_by_influence.csv/content
    • FsF-R1.2-01M-2 Metadata contains provenance information using formal provenance ontologies (PROV-O)
      • WARNING Formal provenance metadata is unavailable
    • FsF-R1.3-02D-1 The format of a data file given in the metadata is listed in the long term file formats, open file formats or scientific file formats controlled list. c The format of the data file is a scientific format
      • WARNING Could not perform file format checks as data content identifier(s) unavailable/inaccesible
• FAIR Checker
  • Score: 91.67%
  • F: 87.5%
    • F2A: Structured metadata
      • You should provide discoverability oriented metadata with one of the following properties: dct:title dct:description dcat:accessURL dcat:downloadURL dcat:endpointDescription dcat:endpointURL
  • A: 100%
  • I: 83.3%
    • I1: Machine readable format
      • You should provide discoverability oriented metadata with one of the following properties: dct:title dct:description dcat:accessURL dcat:downloadURL dcat:endpointDescription dcat:endpointURL
  • R: 100%
• FAIR Evaluator
  • Evaluation: https://fairsharing.github.io/FAIR-Evaluator-FrontEnd/#!/evaluations/17230
  • Score: 14/22 64%
  • F
    • Data Identifier Persistence - FAILURE: The GUID does not conform with any known permanent-URL system.
    • FAILURE: While (apparent) metadata record identifiers were found (["www.biorxiv.org/content/10.1101/2020.04.11.037093v2", "www.biorxiv.org/content/10.1101/2020.04.11.037093v2"]) none of them matched the initial GUID provided to the test (https://doi.org/10.5281/zenodo.3723281). Exact identifier match is required.
    • FAILURE: Was unable to discover the metadata record by search in Bing using any method
      • I feel like this isn't going to work as we use concept ID to test
  • A:
    • Metric to test if the metadata contains a persistence policy, explicitly identified by a persistencePolicy key (in hashed data) or a http://www.w3.org/2000/10/swap/pim/doc#persistencePolicy predicate in Linked Data.
  • I:
    • FAILURE: The url https://zenodo.org/api/records/7559361/files/articles_by_influence.csv/content failed to resolve via a HEAD call with headers {"Accept"=>"text/turtle, application/ld+json, application/rdf+xml, text/xhtml+xml, application/n3, application/rdf+n3, application/turtle, application/x-turtle, text/n3, text/turtle, text/rdf+n3, text/rdf+turtle, application/n-triples"}, therefore we cannot continue FAILURE: the data could not be found, or does not appear to be in a recognized knowledge representation language.
    • FAILURE: 0 of a total of 33 predicates discovered in the metadata resolved to Linked Data data. The minimum to pass this test is 2/3 (with a minimum of 3 predicates in total).
  • R:
    • FAILURE: No License property was found in the metadata.
• FAIR Enough
  • fair-enough-metadata, fair-evaluator-maturity-indicators, fair-enough-data
  • Score: 87.5%, 63.6%, 63.6%
  • F:
    • WARN: Unable to resolve https://doi.org/10.5281/zenodo.3723281 using HTTP Accept header {"Accept"=>"text/xhtml,text/xml"}. FAILURE: The GUID does not conform with any known permanent-URL system.
    • FAILURE: [2024-12-12T13:14:21] Could not find links to the metadata identifier None in the RDF metadata
    • WARN: HTTP error 406 Not Acceptable encountered when trying to resolve https://doi.org/10.5281/zenodo.3723281. WARN: Unable to resolve https://doi.org/10.5281/zenodo.3723281 using HTTP Accept header {"Accept"=>"text/xhtml,text/xml"}. FAILURE: While (apparent) metadata record identifiers were found (["www.biorxiv.org/content/10.1101/2020.04.11.037093v2", "www.biorxiv.org/content/10.1101/2020.04.11.037093v2"]) none of them matched the initial GUID provided to the test (https://doi.org/10.5281/zenodo.3723281). Exact identifier match is required.
    • FAILURE: Was unable to discover the metadata record by search in Bing using any method
  • A:
    • FAILURE: [2024-12-12T13:14:20] Could not find a persistence policy in the metadata. Searched for the following predicates: ['http://www.w3.org/2000/10/swap/pim/doc#persistencePolicy']
    • FAILURE: [2024-12-12T13:31:45] Could not find the data URI in the subject metadata.
    • FAILURE: [2024-12-12T13:31:45] Could not find the data URI in the subject metadata. WARN: [2024-12-12T13:31:45] Could not find dcterms:accessRights information in metadata. Make sure your metadata contains informations about access rights using one of those predicates: http://purl.org/dc/terms/accessRights
  • I:
    • WARN: Unable to resolve https://doi.org/10.5281/zenodo.3723281 using HTTP Accept header {"Accept"=>"text/xhtml,text/xml"}. FAILURE: The url https://zenodo.org/api/records/7559361/files/articles_by_influence.csv/content failed to resolve via a HEAD call with headers {"Accept"=>"text/turtle, application/ld+json, application/rdf+xml, text/xhtml+xml, application/n3, application/rdf+n3, application/turtle, application/x-turtle, text/n3, text/turtle, text/rdf+n3, text/rdf+turtle, application/n-triples"}, therefore we cannot continue. FAILURE: the data could not be found, or does not appear to be in a recognized knowledge representation language.
    • WARN: Unable to resolve https://doi.org/10.5281/zenodo.3723281 using HTTP Accept header {"Accept"=>"text/xhtml,text/xml"}. WARN: predicate http://schema.org/affiliation was not found as the SUBJECT of a triple, indicating that it did not resolve to its definition. WARN: predicate http://ogp.me/ns#description did not resolve to linked data. WARN: predicate http://ogp.me/ns#description was not found as the SUBJECT of a triple, indicating that it did not resolve to its definition. FAILURE: 0 of a total of 33 predicates discovered in the metadata resolved to Linked Data data. The minimum to pass this test is 2/3 (with a minimum of 3 predicates in total).
  • R:
    • WARN: Unable to resolve https://doi.org/10.5281/zenodo.3723281 using HTTP Accept header {"Accept"=>"text/xhtml,text/xml"}. WARN: did not find a schema:license predicate that followed the Schema.org license range structure. FAILURE: No License property was found in the metadata.
• OpenAIRE Validator
  • Score for content: 88%
    • Metadata uses knowledge representation expressed in standardised format.
    • Metadata refers to a reuse license
  • Score for usage: 72%
    • OpenAIRE expects metadata to be encoded in the OpenAIRE metadata format (metadataPrefix oai_openaire) .
    • OpenAIRE expects metadata to be encoded in the CERIF_OPENAIRE metadata format (metadataPrefix oai_cerif_openaire) .

[borsna]

Including information about the access restrictions in DataCite (already done in Dublin Core) would be great for harvesters that want to know if the resource in open / restricted.
See:
https://guidelines.openaire.eu/en/latest/data/field_rights.html#example

Invenio already does this for dublin core:
https://doi.org/10.5281/zenodo.14191104

<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  ...
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>Creative Commons Attribution 4.0 International</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  ...
</oai_dc:dc>

This should be done in DataCite XML as well:

<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.3/metadata.xsd">
  ...
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess" />
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode" rightsIdentifierScheme="spdx" rightsIdentifier="cc-by-4.0">Creative Commons Attribution 4.0 International</rights>
  </rightsList>
  ...
</resource>

[github-actions]

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