OrthoDB

Title: OrthoDB
URI: http://purl.orthodb.org/
Version: V10.1

The following evaluation results have been generated by the RESTFul web service provided by OOPS! (OntOlogy Pitfall Scanner!).

It is obvious that not all the pitfalls are equally important; their impact in the ontology will depend on multiple factors. For this reason, each pitfall has an importance level attached indicating how important it is. We have identified three levels:

Critical: It is crucial to correct the pitfall. Otherwise, it could affect the ontology consistency, reasoning, applicability, etc.
Important: Though not critical for ontology function, it is important to correct this type of pitfall.
Minor: It is not really a problem, but by correcting it we will make the ontology nicer.

Evaluation results

P08. Missing annotations51 cases detected. Minor

This pitfall consists in creating an ontology element and failing to provide human readable annotations attached to it. Consequently, ontology elements lack annotation properties that label them (e.g. rdfs:label, lemon:LexicalEntry, skos:prefLabel or skos:altLabel) or that define them (e.g. rdfs:comment or dc:description). This pitfall is related to the guidelines provided in [5].

This pitfall affects to the following ontology elements:

P10. Missing disjointness ontology *Important

The ontology lacks disjoint axioms between classes or between properties that should be defined as disjoint. This pitfall is related with the guidelines provided in [6], [2] and [7].

*This pitfall applies to the ontology in general instead of specific elements

P11. Missing domain or range in properties5 cases detected. Important

Object and/or datatype properties without domain or range (or none of them) are included in the ontology.

This pitfall affects to the following ontology elements:

P13. Inverse relationships not explicitly declared16 cases detected. Minor

This pitfall appears when any relationship (except for those that are defined as symmetric properties using owl:SymmetricProperty) does not have an inverse relationship (owl:inverseOf) defined within the ontology.

This pitfall affects to the following ontology elements:

P19. Defining multiple domains or ranges in properties4 cases detected. Critical

The domain or range (or both) of a property (relationships and attributes) is defined by stating more than one rdfs:domain or rdfs:range statements. In OWL multiple rdfs:domain or rdfs:range axioms are allowed, but they are interpreted as conjunction, being, therefore, equivalent to the construct owl:intersectionOf. This pitfall is related to the common error that appears when defining domains and ranges described in [7].

This pitfall affects to the following ontology elements:

P22. Using different naming conventions in the ontology ontology *Minor

The ontology elements are not named following the same convention (for example CamelCase or use of delimiters as "-" or "_") . Some notions about naming conventions are provided in [2].

*This pitfall applies to the ontology in general instead of specific elements

P31. Defining wrong equivalent classes2 cases detected. Critical

Two classes are defined as equivalent, using owl:equivalentClass, when they are not necessarily equivalent.

This pitfall affects to the following ontology elements:

"http://purl.org/net/orth#OrthologsCluster"^^xsd:anyURI , "http://purl.orthodb.org/OrthoGroup"^^xsd:anyURI

"http://purl.orthodb.org/Gene"^^xsd:anyURI , "http://purl.org/net/orth#SequenceUnit"^^xsd:anyURI

References:

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[2] Noy, N. F., McGuinness, D. L., et al. (2001). Ontology development 101: A guide to creating your first ontology.
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[4] Montiel-Ponsoda, E., Vila Suero, D., Villazón-Terrazas, B., Dunsire, G., Escolano Rodríguez, E., Gómez-Pérez, A. (2011). Style guidelines for naming and labeling ontologies in the multilingual web.
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[8] Hogan, A., Harth, A., Passant, A., Decker, S., and Polleres, A. (2010). Weaving the pedantic web. In Proceedings of the WWW2010 Workshop on Linked Data on the Web, LDOW 2010, Raleigh, USA, April 27, 2010.
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[10] Bernes-Lee Tim. (2006). “Linked Data - Design issues”. http://www.w3.org/DesignIssues/LinkedData.html
[11] Heath, T. and Bizer, C. (2011). Linked Data: Evolving the Web into a Global Data Space. Morgan & Claypool, 1st edition.
[12] Vatant, B. (2012). Is your linked data vocabulary 5-star?. http://bvatant.blogspot.fr/2012/02/is-your-linked-data-vocabulary-5-star_9588.html