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Topic - Terminologies

BioPortal Import Plugin
The BioPortal Import Plugin allows users to import classes from external ontologies stored in the BioPortal ontology repository. The user can import entire trees of classes with a desired depth and choose which properties to import for each class. This plugin works with Protege 3.x releases, not Protege 4.x.
BioPortal Reference Plugin
The BioPortal Reference Plugin allows the user to insert into the ontology references to external ontologies and terminologies stored in BioPortal.
DISCO Word Spaces is a tab widget for retrieving semantically similar words and collocations

for a query word. The similarities have been computed on the basis of large text corpora for different languages and domains. DISCO Word Spaces helps at ontology building by suggesting similar and related words.

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The DL-Learner plugin allows learning equivalence and super class axioms based on the instance data in the ontologies loaded in Protégé.
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Mastro DL-Lite Reasoner
Mastro is an Ontology-Based Data Access (OBDA) management system. Ontologies in Mastro are specified through languages belonging to the DL-Lite family of lightweight Description Logics. The ontology is connected to external relational data management or data federation systems through a mapping establishing a semantic relation between SQL queries issued over the underlying databases and elements of the ontology. To access data, users can specify SPARQL queries over the ontology and make use of the query answering services provided by Mastro.
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The OntoCheck P4 plugin allows to define clean-up checks on a generated owl ontology - e.g. to be stored and carried out before each ontology release. Found test violations can be corrected to foster consistency in entity naming and meta-annotation. Once specified, check-constraints like name patterns can be stored and exchanged for later re-use. The plugin allows the user to specify checks on certain properties of an active ontology (OntoCheck) and allows for improvements (OntoCure) in the areas of

a) Metadata completeness, e.g. via cardinality checks on mandatory and optional annotation properties

b) Naming Conventions, e.g. via lexical analysis and labeling enforcement for representational units (RU) names and IDs.

Thereby this plugin fosters lexical harmonization as e.g. demanded by the OBO Foundry Naming Conventions at http://www.obofoundry.org/wiki/index.php/Naming

A paper describing OntoChecks functionalities in more detail can be found at


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Facilitates linguistic enrichment of ontologies and includes an interface for WordNet (from 1.6 to 2.1) and DICT dictionaries. Check the

home page for further details

Snow Owl
Snow Owl is a free SNOMED CT browser and authoring tool integrating Protégé.
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TerMine Plugin
The TerMine Plugin uses text mining tools to extract candidate terms from a corpus of text and provides an interface for rapidly bringing these terms into an OWL ontology.
Allows users to search the National Library of Medicine's Unified Medical Language System (UMLS) and annotate Protege ontologies with terms, concept IDs, synonyms, relations, and other information from the UMLS.