Table 2 Example quality issues to be identified by metrics. * denotes that these are parts of the metrics divided to provide clear examples. For example, the metric “misplaced classes and properties” is divided into “misplaced classes” and “misplaced properties”. The examples without ‘Resource’ are synthetic and used for demonstrating the usage of metrics

Non-resolvable URIs

Resource: http://semanticscience.org/ontology/sio.owl Example triple: http://semanticscience.org/resource/SIO_001238http://semanticscience.org/resource/similarTohttp://purl.obolibrary.org/obo/OBI_0000052.

The URI http://semanticscience.org/resource/similarTo is expected to provide more information about the property but returns “404 NOT Found”. So the URI is non-resolvable.

Non-parsable URIs

Resource: https://raw.githubusercontent.com/ejp-rd-vp/resource-metadata-schema-ontology/main/ejprd_resource_metadata_ontology.owl Example triple: http://www.andrea-perego.name/foaf/#mehttp://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://www.w3.org/2002/07/owl#NamedIndividual.

The subject URI http://www.andrea-perego.name/foaf/#me returns structured text with the content-type “application/rdf+xml”, which is one of the content-types that supports RDF format. However, this URI cannot be parsed to RDF triples, and therefore is categorized as non-parsable. In this case, the failure is attributed to the misuse of “rdf:ID” as invalid non-colonized name (NCName) to cause a parse error.

Undefined URIs

Resource: https://obofoundry.org/registry/ontologies.ttl Example triple: http://purl.obolibrary.org/obo/bfohttp://purl.org/dc/terms/1.1/theme ’upper’.

The property http://purl.org/dc/terms/1.1/theme is resolvable and parsable, returning RDF triples of the entire DCT ontology. However, the property itself does not exist within the parsed RDF and hence is undefined.

Misplaced classes*

Resource: https://ceur-ws.org/Vol-1312/ldop2014_paper3.pdf Example triple: http://m-culture.in.th/48081http://purl.org/dc/dcmitype/Imagehttp://m-culture.in.th/media/big/%20201945.jpeg.

The URI, http://purl.org/dc/dcmitype/Image, is defined as a class, so it should not be used in the example triple as a predicate and is recognized as a misplaced class.

Misplaced properties*

Example triple: https://creativecommons.org/licenses/by/4.0/http://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://purl.org/dc/terms/license.

The URI, http://purl.org/dc/terms/license, is defined as an “rdfs:Property”. So it should not be used as the object of an “rdf:type” triple, and recognized as a misplaced property.

Misuse of owl:ObjectProperty*

Resource: http://purl.obolibrary.org/obo/cido.owl Example triple: http://purl.obolibrary.org/obo/OAE_0001045http://www.w3.org/2000/01/rdf-schema#seeAlso “NCIt:C78345”.

As an owl:ObjectProperty, the object of the property http://www.w3.org/2000/01/rdf-schema#seeAlso should be a linked resource rather than the string “NCIt:C78345”. So in this example, this property is misused.

Misuse of owl:DatatypeProperty*

Resource: https://github.com/ejp-rd-vp/CDE-semantic-model/wiki/Personal-information Example triple: http://purl.org/ejp-rd/cde/v010/example-rdf/gender1http://semanticscience.org/resource/SIO_000300http://purl.bioontology.org/ontology/SNOMEDCT/703118005.

As an owl:DatatypeProperty, the object of the property http://semanticscience.org/resource/SIO_000300 should be literal (e.g., integer or string) rather than a linked resource concerning SNOMED CT. So in this example, the property is misused.

Use of deprecated classes or properties*

Example triple: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C50680http://www.w3.org/2004/02/skos/core#relatedhttp://purl.obolibrary.org/obo/VSAO_0000002 .

The class, http://purl.obolibrary.org/obo/VSAO_0000002, has a deprecation-related triple: http://purl.obolibrary.org/obo/VSAO_0000002http://www.w3.org/2002/07/owl#deprecated “true”⌃⌃xsd:boolean . It indicates that this class is deprecated and any use of it is regarded as an error counted by this metric. The same applies to properties.