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Table 1 Requirements for a naming convention and metadata verification tool

From: OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4

Requirement

Aspects met and Implementation

OntoCheck Panel

Easy installation, usage and intuitive navigation.

Protégé plugin, structured into 3 self-explaining tabs. Tooltips providing on-the-spot guidance.

All

Generation and display of numeric counts for selectable ontology metrices.

Making use of the Protégé and Java API, diverse metrices are available, amending the already present 'Ontology Metrics'.

All

Selection of an 'entry class node' from where on - leaf-wards - a check should be done.

Allows to test for a certain postfix e.g. '_Disposition' only within a selected 'Disposition' entry node sub-tree. Allows checking for metadata availability in selectable subtrees.

All

Display of classes failing a specified test and export as list.

Found classes can be sorted according to different criteria and exported for later curation.

All

Display of quantitative results on detected issues in terms of absolute and percentage counts in a given subtree.

A statistical data pane verbalizes the numerical results in a copyable natural language sentence.

All

Storage and reload capabilities for created checks allowing for later re-use and propagation.

An xml file is generated storing all checks in a reproducible way.

All

Detection for 'presence' and 'required cardinality' of labels and metadata.

Checks are available on OWL elements capturing lexical information, i.e. rdf:ID, rdfs:label, own annotation properties and standard annotation properties e.g. from Dublin Core or SKOS.

Check

Check for syntactical and typographical patterns and label length i.e. to discover too short or too long names within string values of selectable entities.

Allows checking naming conventions via simple string matches and full regular expressions. Checks the length of labels. A significant fraction of the OBO Foundry naming conventions can be checked, i.e. case, separator but also morphemic conventions.

Check

Detection and counts of redundant class labels.

Label repetition can be checked for via the ComparePanel.

Compare

Comparison of values between pairs of entities to detect similarities and avoid redundancies.

Operators like equals, contains or starts with can be used to compare selectable entities.

Compare

Quantification of ontology measures useful for ontology evaluation, progress monitoring and complexity analysis.

Displays the percentage or absolute number of entities having 'exactly', 'at least' or 'at most' a certain number of annotation properties, direct sub-/superclasses, or 'usages', i.e. indicating 'hub nodes'.

Count

  1. The high level requirements are listed in the first column followed by their specific implementations, indicating the extend of requirement fulfilment in our tool. The last column indicates in which tab the function is implemented.