LOOM - Revision history

JenniferVendetti at 18:04, 10 July 2023

2023-07-10T18:04:46Z

JenniferVendetti: /* Obtaining LOOM */ Fixed broken link. LOOM JAR file is no longer accessible. Pointed to the archived version of the code in GitHub.

2023-07-10T18:04:27Z

Obtaining LOOM: Fixed broken link. LOOM JAR file is no longer accessible. Pointed to the archived version of the code in GitHub.

JenniferVendetti: /* About LOOM */ Fixed broken link to the LOOM technical report

2023-07-10T17:58:02Z

About LOOM: Fixed broken link to the LOOM technical report

Whetzel: /* Using LOOM */

2009-12-01T07:20:57Z

Using LOOM

Whetzel: /* Using LOOM */

2009-12-01T05:30:40Z

Using LOOM

Amirg at 19:54, 20 March 2009

2009-03-20T19:54:03Z

Amirg at 06:23, 20 March 2009

2009-03-20T06:23:20Z

Amirg at 06:22, 20 March 2009

2009-03-20T06:22:35Z

Amirg at 06:19, 20 March 2009

2009-03-20T06:19:48Z

Amirg at 02:31, 20 March 2009

2009-03-20T02:31:33Z

@@ Line 8: / Line 8: @@
 LOOM can currently be obtained [https://github.com/ncbo/bioportal_mappings here]
 <!-- Old, broken link to the LOOM JAR file -->
 <!-- LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here] -->

@@ Line 7: / Line 7: @@
 == Obtaining LOOM ==
-LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here]
+LOOM can currently be obtained [https://github.com/ncbo/bioportal_mappings here]
 == Using LOOM ==

@@ Line 3: / Line 3: @@
 Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment.  LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies.  In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies.  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. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). 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.
-More information about LOOM can be found in the [https://bmir.stanford.edu/publications/view.php/creating_mappings_for_ontologies_in_biomedicine_simple_methods_work technical report]
+More information about LOOM can be found in the [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474/ technical report]
 == Obtaining LOOM ==

@@ Line 16: / Line 16: @@
 In this command, source.pprj is the protege project file for the OWL source ontology to be mapped.  target.pprj is the protege project file for the target ontology.  SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names.  TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology.  These URIs are quite often annotation properties in the ontologies.
-Note that the [] designates an optional flag for allocating additional virtual memory to LOOM.
+NOTE: The [] designates an optional flag for allocating additional virtual memory to LOOM.
 For 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:<br>
 % java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
 A few additional important tips:

@@ Line 12: / Line 12: @@
 LOOM can be executed with a command of the following form: <br>
-''java -jar [-Xmx1500m] Loom.jar source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI''
+% java -jar [-Xmx1500m] Loom.jar source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI
 In this command, source.pprj is the protege project file for the OWL source ontology to be mapped.  target.pprj is the protege project file for the target ontology.  SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names.  TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology.  These URIs are quite often annotation properties in the ontologies.
@@ Line 19: / Line 19: @@
 For 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:<br>
-''java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
+% java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
-''
 A few additional important tips:

← Older revision		Revision as of 19:54, 20 March 2009
Line 2:		Line 2:

	Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. 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. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). 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.		Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. 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. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). 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.
		+
		+	More information about LOOM can be found in the [https://bmir.stanford.edu/publications/view.php/creating_mappings_for_ontologies_in_biomedicine_simple_methods_work technical report]

	== Obtaining LOOM ==		== Obtaining LOOM ==

@@ Line 5: / Line 5: @@
 == Obtaining LOOM ==
-*how to obtain LOOM goes here
+LOOM can currently be obtained at http://www.stanford.edu/~amirg/Loom.jar.zip
 == Using LOOM ==

← Older revision		Revision as of 02:31, 20 March 2009
Line 1:		Line 1:
−	~~This~~ is a ~~placeholder~~ for a ~~page about~~ the LOOM ontology ~~alignment tool~~.	+	== About LOOM ==
		+
		+	Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. 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. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). 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.
		+
		+	== Obtaining LOOM ==
		+
		+	*how to obtain LOOM goes here
		+
		+	== Using LOOM ==
		+
		+	LOOM can be executed with a command of the following form: <br>
		+	''java -jar [-Xmx1500m] LOOM source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI''
		+
		+	In this command, source.pprj is the protege project file for the OWL source ontology to be mapped. target.pprj is the protege project file for the target ontology. SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names. TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology. These URIs are quite often annotation properties in the ontologies.
		+
		+	Note that the [] designates an optional flag for allocating additional virtual memory to LOOM.
		+
		+	For 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:<br>
		+	''java -jar -Xmx1500m LOOM mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
		+	''
		+
		+	A few additional important tips:
		+	# You should keep the .owl and .pprj files in the same folder as LOOM.
		+	# 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).
		+	# LOOM makes use of thread synchronization and so its speed is significantly improved with additional memory allocation. We strongly advise allocating additional virtual memory with the command -Xmx1500m (or however memory you choose to allocate).
		+
		+	== Notes ==
		+
		+	How to configure your protege project so concepts have preferred name as browser text:
		+	# Go to OWL -> Preferences. Under the visibility tab, put a check by owl:Class. Close preferences.
		+	# In the main screen, go to the individuals tab. Select owl:Class from the class hierarchy browser. Now, in the individual browser, select the downward-pointing arrow (menu button) near the top. 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).
		+	# You should repeat this process to ensure that your synonym slot also displays the preferred name.