scanning


OOPS! is scanning...

OOPS! (OntOlogy Pitfall Scanner!) helps you to detect some of the most common pitfalls appearing when developing ontologies.

To try it, enter a URI or paste an OWL document into the text field above. A list of pitfalls and the elements of your ontology where they appear will be displayed.

Scanner by URI:

Example: http://data.semanticweb.org/ns/swc/swc_2009-05-09.rdf


Scanner by direct input:

Uncheck this checkbox if you don't want us to keep a copy of your ontology.

Evaluation results

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

Results for P08: Missing annotations. 164 cases | Minor 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].

• The following elements have neither rdfs:label or rdfs:comment (nor skos:definition) defined:
http://www.biopax.org/release/biopax-level3.owl#regionType
http://www.biopax.org/release/biopax-level3.owl#component

• The following elements have no rdfs:label defined:
http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction
http://www.biopax.org/release/biopax-level3.owl#TemplateReactionRegulation
http://www.biopax.org/release/biopax-level3.owl#TemplateReaction
http://www.biopax.org/release/biopax-level3.owl#DnaRegionReference
http://www.biopax.org/release/biopax-level3.owl#SequenceSite
http://www.biopax.org/release/biopax-level3.owl#Complex
http://www.biopax.org/release/biopax-level3.owl#TissueVocabulary
http://www.biopax.org/release/biopax-level3.owl#ExperimentalForm
http://www.biopax.org/release/biopax-level3.owl#Rna
http://www.biopax.org/release/biopax-level3.owl#RnaRegion
http://www.biopax.org/release/biopax-level3.owl#SequenceInterval
http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity
http://www.biopax.org/release/biopax-level3.owl#ControlledVocabulary
http://www.biopax.org/release/biopax-level3.owl#ChemicalStructure
http://www.biopax.org/release/biopax-level3.owl#Degradation
http://www.biopax.org/release/biopax-level3.owl#BiochemicalPathwayStep
http://www.biopax.org/release/biopax-level3.owl#EntityFeature
http://www.biopax.org/release/biopax-level3.owl#UtilityClass
http://www.biopax.org/release/biopax-level3.owl#Entity
http://www.biopax.org/release/biopax-level3.owl#SmallMolecule
http://www.biopax.org/release/biopax-level3.owl#SequenceModificationVocabulary
http://www.biopax.org/release/biopax-level3.owl#PublicationXref
http://www.biopax.org/release/biopax-level3.owl#KPrime
http://www.biopax.org/release/biopax-level3.owl#PhenotypeVocabulary
http://www.biopax.org/release/biopax-level3.owl#MolecularInteraction
http://www.biopax.org/release/biopax-level3.owl#SequenceLocation
http://www.biopax.org/release/biopax-level3.owl#BindingFeature
http://www.biopax.org/release/biopax-level3.owl#ModificationFeature
http://www.biopax.org/release/biopax-level3.owl#CovalentBindingFeature
http://www.biopax.org/release/biopax-level3.owl#InteractionVocabulary
http://www.biopax.org/release/biopax-level3.owl#UnificationXref
http://www.biopax.org/release/biopax-level3.owl#Transport
http://www.biopax.org/release/biopax-level3.owl#Gene
http://www.biopax.org/release/biopax-level3.owl#DeltaG
http://www.biopax.org/release/biopax-level3.owl#RelationshipTypeVocabulary
http://www.biopax.org/release/biopax-level3.owl#Pathway
http://www.biopax.org/release/biopax-level3.owl#Score
http://www.biopax.org/release/biopax-level3.owl#ExperimentalFormVocabulary
http://www.biopax.org/release/biopax-level3.owl#SmallMoleculeReference
http://www.biopax.org/release/biopax-level3.owl#CellularLocationVocabulary
http://www.biopax.org/release/biopax-level3.owl#ProteinReference
http://www.biopax.org/release/biopax-level3.owl#Stoichiometry
http://www.biopax.org/release/biopax-level3.owl#Dna
http://www.biopax.org/release/biopax-level3.owl#Control
http://www.biopax.org/release/biopax-level3.owl#Xref
http://www.biopax.org/release/biopax-level3.owl#GeneticInteraction
http://www.biopax.org/release/biopax-level3.owl#EntityReferenceTypeVocabulary
http://www.biopax.org/release/biopax-level3.owl#Conversion
http://www.biopax.org/release/biopax-level3.owl#CellVocabulary
http://www.biopax.org/release/biopax-level3.owl#Catalysis
http://www.biopax.org/release/biopax-level3.owl#DnaRegion
http://www.biopax.org/release/biopax-level3.owl#Protein
http://www.biopax.org/release/biopax-level3.owl#DnaReference
http://www.biopax.org/release/biopax-level3.owl#Provenance
http://www.biopax.org/release/biopax-level3.owl#SequenceRegionVocabulary
http://www.biopax.org/release/biopax-level3.owl#Interaction
http://www.biopax.org/release/biopax-level3.owl#TransportWithBiochemicalReaction
http://www.biopax.org/release/biopax-level3.owl#RnaRegionReference
http://www.biopax.org/release/biopax-level3.owl#Modulation
http://www.biopax.org/release/biopax-level3.owl#BioSource
http://www.biopax.org/release/biopax-level3.owl#FragmentFeature
http://www.biopax.org/release/biopax-level3.owl#RelationshipXref
http://www.biopax.org/release/biopax-level3.owl#PathwayStep
http://www.biopax.org/release/biopax-level3.owl#EntityReference
http://www.biopax.org/release/biopax-level3.owl#ComplexAssembly
http://www.biopax.org/release/biopax-level3.owl#Evidence
http://www.biopax.org/release/biopax-level3.owl#EvidenceCodeVocabulary
http://www.biopax.org/release/biopax-level3.owl#RnaReference
http://www.biopax.org/release/biopax-level3.owl#interactionType
http://www.biopax.org/release/biopax-level3.owl#nextStep
http://www.biopax.org/release/biopax-level3.owl#cofactor
http://www.biopax.org/release/biopax-level3.owl#entityFeature
http://www.biopax.org/release/biopax-level3.owl#organism
http://www.biopax.org/release/biopax-level3.owl#xref
http://www.biopax.org/release/biopax-level3.owl#controller
http://www.biopax.org/release/biopax-level3.owl#stepConversion
http://www.biopax.org/release/biopax-level3.owl#bindsTo
http://www.biopax.org/release/biopax-level3.owl#featureLocation
http://www.biopax.org/release/biopax-level3.owl#experimentalForm
http://www.biopax.org/release/biopax-level3.owl#experimentalFormDescription
http://www.biopax.org/release/biopax-level3.owl#sequenceIntervalEnd
http://www.biopax.org/release/biopax-level3.owl#kEQ
http://www.biopax.org/release/biopax-level3.owl#relationshipType
http://www.biopax.org/release/biopax-level3.owl#cellularLocation
http://www.biopax.org/release/biopax-level3.owl#participant
http://www.biopax.org/release/biopax-level3.owl#pathwayOrder
http://www.biopax.org/release/biopax-level3.owl#notFeature
http://www.biopax.org/release/biopax-level3.owl#pathwayComponent
http://www.biopax.org/release/biopax-level3.owl#experimentalFeature
http://www.biopax.org/release/biopax-level3.owl#tissue
http://www.biopax.org/release/biopax-level3.owl#participantStoichiometry
http://www.biopax.org/release/biopax-level3.owl#evidenceCode
http://www.biopax.org/release/biopax-level3.owl#componentStoichiometry
http://www.biopax.org/release/biopax-level3.owl#featureLocationType
http://www.biopax.org/release/biopax-level3.owl#cellType
http://www.biopax.org/release/biopax-level3.owl#modificationType
http://www.biopax.org/release/biopax-level3.owl#memberFeature
http://www.biopax.org/release/biopax-level3.owl#deltaG
http://www.biopax.org/release/biopax-level3.owl#confidence
http://www.biopax.org/release/biopax-level3.owl#phenotype
http://www.biopax.org/release/biopax-level3.owl#right
http://www.biopax.org/release/biopax-level3.owl#evidence
http://www.biopax.org/release/biopax-level3.owl#interactionScore
http://www.biopax.org/release/biopax-level3.owl#stepProcess
http://www.biopax.org/release/biopax-level3.owl#feature
http://www.biopax.org/release/biopax-level3.owl#physicalEntity
http://www.biopax.org/release/biopax-level3.owl#sequenceIntervalBegin
http://www.biopax.org/release/biopax-level3.owl#controlled
http://www.biopax.org/release/biopax-level3.owl#product
http://www.biopax.org/release/biopax-level3.owl#absoluteRegion
http://www.biopax.org/release/biopax-level3.owl#entityReference
http://www.biopax.org/release/biopax-level3.owl#memberPhysicalEntity
http://www.biopax.org/release/biopax-level3.owl#subRegion
http://www.biopax.org/release/biopax-level3.owl#dataSource
http://www.biopax.org/release/biopax-level3.owl#left
http://www.biopax.org/release/biopax-level3.owl#experimentalFormEntity
http://www.biopax.org/release/biopax-level3.owl#template
http://www.biopax.org/release/biopax-level3.owl#scoreSource
http://www.biopax.org/release/biopax-level3.owl#structure
http://www.biopax.org/release/biopax-level3.owl#memberEntityReference
http://www.biopax.org/release/biopax-level3.owl#entityReferenceType
http://www.biopax.org/release/biopax-level3.owl#structureData
http://www.biopax.org/release/biopax-level3.owl#author
http://www.biopax.org/release/biopax-level3.owl#year
http://www.biopax.org/release/biopax-level3.owl#standardName
http://www.biopax.org/release/biopax-level3.owl#deltaH
http://www.biopax.org/release/biopax-level3.owl#stoichiometricCoefficient
http://www.biopax.org/release/biopax-level3.owl#dbVersion
http://www.biopax.org/release/biopax-level3.owl#chemicalFormula
http://www.biopax.org/release/biopax-level3.owl#controlType
http://www.biopax.org/release/biopax-level3.owl#pMg
http://www.biopax.org/release/biopax-level3.owl#eCNumber
http://www.biopax.org/release/biopax-level3.owl#term
http://www.biopax.org/release/biopax-level3.owl#ph
http://www.biopax.org/release/biopax-level3.owl#db
http://www.biopax.org/release/biopax-level3.owl#molecularWeight
http://www.biopax.org/release/biopax-level3.owl#sequence
http://www.biopax.org/release/biopax-level3.owl#structureFormat
http://www.biopax.org/release/biopax-level3.owl#ionicStrength
http://www.biopax.org/release/biopax-level3.owl#idVersion
http://www.biopax.org/release/biopax-level3.owl#sequencePosition
http://www.biopax.org/release/biopax-level3.owl#name
http://www.biopax.org/release/biopax-level3.owl#url
http://www.biopax.org/release/biopax-level3.owl#patoData
http://www.biopax.org/release/biopax-level3.owl#stepDirection
http://www.biopax.org/release/biopax-level3.owl#templateDirection
http://www.biopax.org/release/biopax-level3.owl#title
http://www.biopax.org/release/biopax-level3.owl#id
http://www.biopax.org/release/biopax-level3.owl#spontaneous
http://www.biopax.org/release/biopax-level3.owl#displayName
http://www.biopax.org/release/biopax-level3.owl#kPrime
http://www.biopax.org/release/biopax-level3.owl#availability
http://www.biopax.org/release/biopax-level3.owl#source
http://www.biopax.org/release/biopax-level3.owl#temperature
http://www.biopax.org/release/biopax-level3.owl#comment
http://www.biopax.org/release/biopax-level3.owl#positionStatus
http://www.biopax.org/release/biopax-level3.owl#deltaGPrime0
http://www.biopax.org/release/biopax-level3.owl#value
http://www.biopax.org/release/biopax-level3.owl#catalysisDirection
http://www.biopax.org/release/biopax-level3.owl#intraMolecular
http://www.biopax.org/release/biopax-level3.owl#deltaS
http://www.biopax.org/release/biopax-level3.owl#conversionDirection

Results for P11: Missing domain or range in properties. 2 cases | Important Important

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

• This pitfall appears in the following elements:
http://www.biopax.org/release/biopax-level3.owl#displayName
http://www.biopax.org/release/biopax-level3.owl#standardName

Tip: Solving this pitfall may lead to new results for other pitfalls and suggestions. We encourage you to solve all cases when needed and see what else you can get from OOPS!

Results for P13: Inverse relationships not explicitly declared. 54 cases | Minor 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 appears in the following elements:
http://www.biopax.org/release/biopax-level3.owl#interactionType
http://www.biopax.org/release/biopax-level3.owl#nextStep
http://www.biopax.org/release/biopax-level3.owl#cofactor
http://www.biopax.org/release/biopax-level3.owl#entityFeature
http://www.biopax.org/release/biopax-level3.owl#organism
http://www.biopax.org/release/biopax-level3.owl#xref
http://www.biopax.org/release/biopax-level3.owl#controller
http://www.biopax.org/release/biopax-level3.owl#stepConversion
http://www.biopax.org/release/biopax-level3.owl#featureLocation
http://www.biopax.org/release/biopax-level3.owl#experimentalForm
http://www.biopax.org/release/biopax-level3.owl#experimentalFormDescription
http://www.biopax.org/release/biopax-level3.owl#sequenceIntervalEnd
http://www.biopax.org/release/biopax-level3.owl#kEQ
http://www.biopax.org/release/biopax-level3.owl#relationshipType
http://www.biopax.org/release/biopax-level3.owl#cellularLocation
http://www.biopax.org/release/biopax-level3.owl#participant
http://www.biopax.org/release/biopax-level3.owl#pathwayOrder
http://www.biopax.org/release/biopax-level3.owl#notFeature
http://www.biopax.org/release/biopax-level3.owl#pathwayComponent
http://www.biopax.org/release/biopax-level3.owl#experimentalFeature
http://www.biopax.org/release/biopax-level3.owl#tissue
http://www.biopax.org/release/biopax-level3.owl#participantStoichiometry
http://www.biopax.org/release/biopax-level3.owl#evidenceCode
http://www.biopax.org/release/biopax-level3.owl#componentStoichiometry
http://www.biopax.org/release/biopax-level3.owl#regionType
http://www.biopax.org/release/biopax-level3.owl#featureLocationType
http://www.biopax.org/release/biopax-level3.owl#component
http://www.biopax.org/release/biopax-level3.owl#cellType
http://www.biopax.org/release/biopax-level3.owl#modificationType
http://www.biopax.org/release/biopax-level3.owl#memberFeature
http://www.biopax.org/release/biopax-level3.owl#deltaG
http://www.biopax.org/release/biopax-level3.owl#confidence
http://www.biopax.org/release/biopax-level3.owl#phenotype
http://www.biopax.org/release/biopax-level3.owl#right
http://www.biopax.org/release/biopax-level3.owl#evidence
http://www.biopax.org/release/biopax-level3.owl#interactionScore
http://www.biopax.org/release/biopax-level3.owl#stepProcess
http://www.biopax.org/release/biopax-level3.owl#feature
http://www.biopax.org/release/biopax-level3.owl#physicalEntity
http://www.biopax.org/release/biopax-level3.owl#sequenceIntervalBegin
http://www.biopax.org/release/biopax-level3.owl#controlled
http://www.biopax.org/release/biopax-level3.owl#product
http://www.biopax.org/release/biopax-level3.owl#absoluteRegion
http://www.biopax.org/release/biopax-level3.owl#entityReference
http://www.biopax.org/release/biopax-level3.owl#memberPhysicalEntity
http://www.biopax.org/release/biopax-level3.owl#subRegion
http://www.biopax.org/release/biopax-level3.owl#dataSource
http://www.biopax.org/release/biopax-level3.owl#left
http://www.biopax.org/release/biopax-level3.owl#experimentalFormEntity
http://www.biopax.org/release/biopax-level3.owl#template
http://www.biopax.org/release/biopax-level3.owl#scoreSource
http://www.biopax.org/release/biopax-level3.owl#structure
http://www.biopax.org/release/biopax-level3.owl#memberEntityReference
http://www.biopax.org/release/biopax-level3.owl#entityReferenceType

Results for P24: Using recursive definitions. 14 cases | Important Important

An ontology element (a class, an object property or a datatype property) is used in its own definition. Some examples of this would be: (a) the definition of a class as the enumeration of several classes including itself; (b) the appearance of a class within its owl:equivalentClass or rdfs:subClassOf axioms; (c) the appearance of an object property in its rdfs:domain or range rdfs:range definitions; or (d) the appearance of a datatype property in its rdfs:domain definition.

• This pitfall appears in the following elements:
http://www.biopax.org/release/biopax-level3.owl#RnaReference
http://www.biopax.org/release/biopax-level3.owl#RnaRegionReference
http://www.biopax.org/release/biopax-level3.owl#DnaReference
http://www.biopax.org/release/biopax-level3.owl#Protein
http://www.biopax.org/release/biopax-level3.owl#DnaRegion
http://www.biopax.org/release/biopax-level3.owl#Dna
http://www.biopax.org/release/biopax-level3.owl#ProteinReference
http://www.biopax.org/release/biopax-level3.owl#SmallMoleculeReference
http://www.biopax.org/release/biopax-level3.owl#SmallMolecule
http://www.biopax.org/release/biopax-level3.owl#RnaRegion
http://www.biopax.org/release/biopax-level3.owl#Rna
http://www.biopax.org/release/biopax-level3.owl#Complex
http://www.biopax.org/release/biopax-level3.owl#DnaRegionReference
http://www.biopax.org/release/biopax-level3.owl#bindsTo

Results for P25: Defining a relationship as inverse to itself. 1 case | Important Important

A relationship is defined as inverse of itself. In this case, this relationship could have been defined as owl:SymmetricProperty instead.

• This pitfall appears in the following elements:
http://www.biopax.org/release/biopax-level3.owl#bindsTo

Results for P26: Defining inverse relationships for a symmetric one. 1 case | Important Important

A symmetric object property (owl:SymmetricProperty) is defined as inverse of another object property (using owl:inverseOf).

• This pitfall appears in the following elements:
http://www.biopax.org/release/biopax-level3.owl#bindsTo

Results for P36: URI contains file extension. ontology* | Minor Minor

This pitfall occurs if file extensions such as ".owl", ".rdf", ".ttl", ".n3" and ".rdfxml" are included in an ontology URI. This pitfall is related with the recommendations provided in [9].

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

Results for P41: No license declared. ontology* | Important Important

The ontology metadata omits information about the license that applies to the ontology.

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

SUGGESTION: symmetric or transitive object properties. 2 cases

The domain and range axioms are equal for each of the following object properties. Could they be symmetric or transitive?
http://www.biopax.org/release/biopax-level3.owl#nextStep
http://www.biopax.org/release/biopax-level3.owl#memberEntityReference


According to the highest importance level of pitfall found in your ontology the conformace bagde suggested is "Important pitfalls" (see below). You can use the following HTML code to insert the badge within your ontology documentation:


Important pitfalls were found
<p>
<a href="http://oops.linkeddata.es"><img
	src="http://oops.linkeddata.es/resource/image/oops_important.png"
	alt="Important pitfalls were found" height="69.6" width="100" /></a>
</p>


References:

  • [1] Aguado-De Cea, G., Montiel-Ponsoda, E., Poveda-Villalón, M., and Giraldo-Pasmin, O.X. (2015). Lexicalizing Ontologies: The issues behind the labels. In Multimodal communication in the 21st century: Professional and academic challenges. 33rd Conference of the Spanish Association of Applied Linguistics (AESLA), XXXIII AESLA.
  • [2] Noy, N. F., McGuinness, D. L., et al. (2001). Ontology development 101: A guide to creating your first ontology.
  • [3] Gómez-Pérez, A. (1999). Evaluation of Taxonomic Knowledge in Ontologies and Knowledge Bases. Proceedings of the Banff Knowledge Acquisition for Knowledge-Based Systems Workshop. Alberta, Canada.
  • [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.
  • [5] Vrandecic, D. (2010). Ontology Evaluation. PhD thesis.
  • [6] Gómez-Pérez, A. (2004). Ontology evaluation. In Handbook on ontologies, pages 251-273. Springer.
  • [7] Rector, A., Drummond, N., Horridge, M., Rogers, J., Knublauch, H., Stevens, R., Wang, H., and Wroe, C. (2004). Owl pizzas: Practical experience of teaching owl-dl: Common errors & common patterns. In Engineering Knowledge in the Age of the Semantic Web, pages 63-81. Springer.
  • [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.
  • [9] Archer, P., Goedertier, S., and Loutas, N. (2012). D7. 1.3-study on persistent URIs, with identification of best practices and recommendations on the topic for the Mss and the EC. PwC EU Services.
  • [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

Please, help us making OOPS! better. Feedback is more than welcome!
In addition, you can also suggest new pitfalls so that they can be detected in future evaluations.

Want to help?

Documentation:

Related papers:

Web services:

Developed by:

OEG logo