loftsetr.blogg.se - Protege synonym

#Protege synonym how to
#Protege synonym full

We also provide the NCIt in a tab-delimited format that some users prefer over XML for simple purposes.

You should repeat this process to ensure that your synonym slot also displays the preferred name.The NCIt is developed in OWL using NCI-developed plug-ins for the Protege editor, hence OWL is the primary distribution format and we provide asserted and inferred versions.

Then choose Set Display Slot and select the slot that you want to display as browser text (in most cases this will be rdfs:label). Now, in the individual browser, select the downward-pointing arrow (menu button) near the top. Select owl:Class from the class hierarchy browser.

In the main screen, go to the individuals tab.

Under the visibility tab, put a check by owl:Class.

#Protege synonym how to

How to configure your protege project so concepts have preferred name as browser text: We strongly advise allocating additional virtual memory with the command -Xmx1500m (or however memory you choose to allocate).

LOOM makes use of thread synchronization and so its speed is significantly improved with additional memory allocation.

Your project should be configured so that the preferred name of the concepts and synonyms are set as the browser text (instructions on how to do this are below).

NOTE: LOOM can be used with ontologies in OBO format by loading the file into Protege 4 ( ).

% java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj NOTE: The designates an optional flag for allocating additional virtual memory to LOOM.įor example, if you were to try to use LOOM to map Mouse Adult Gross Anatomy to Zebrafish Anatomy and Development, you would use the following command:

These URIs are quite often annotation properties in the ontologies.

#Protege synonym full

TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology. SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names. target.pprj is the protege project file for the target ontology. In this command, source.pprj is the protege project file for the OWL source ontology to be mapped. % java -jar Loom.jar source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI LOOM can be executed with a command of the following form: LOOM can currently be obtained here Using LOOM More information about LOOM can be found in the technical report Obtaining LOOM It then uses an approximate matching technique to compare the strings, allowing for a mismatch of at most one character in strings with length greater than four and no mismatches for shorter strings. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.).

It identifies two concepts from different ontologies as similar, if and only if their preferred names or synonyms are equivalent based on a modified string-comparison function. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment.