NCBO Wiki - User contributions [en]

Mapping Set

2009-06-30T15:33:17Z

Amirg: /* Data */

== Introduction ==

We created a set of mappings by applying simple lexical matching to preferred names and synonyms across all 4,021,662 concepts in 140 BioPortal ontologies and 67 vocabularies in the Uniﬁed Medical Language System (UMLS). This process resulted in 4,001,775 mappings.

By analyzing these mappings, we were able to produce data on the connectivity of ontologies.

== Data ==

The data gathered over the set of mappings can be found [[media:MappingData.xls|here]]. The data is in a .xls format spreadsheet, with several worksheets containing data. Please be sure to consult the worksheet labeled "Introduction" for explanations of the data contained in the spreadsheet.

Additionally, we created several graphs of the ontologies for different thresholds of percent-normalized links. These graphs can be found [[media:OntologyGraphs.zip | here]]. Each graph image has the filename ontoX.tiff, where x is the the similarity threshold for links included in the graph. For example, every edge in the graph onto70.tiff has at least 70% of concepts in the source ontology mapped to concepts in the target ontology.

Finally, we make avaialable the mappings we plan to upload into BioPortal. They are available [http://www.stanford.edu/~amirg/mappings.zip here]. The mappings file is a SQL dump of a table containing all mappings between BioPortal ontologies generated by our algorithm. It can be used to generate a table of mappings with the following columns:

* source_ont: the id of the source ontology
* source_version_id: the version id for the source ontology
* source_ont_name: the name of the source ontology
* source_id: the identifier for the concept from the source ontology being mapped
* source_name: the preferred name of the concept from the source ontology
* target_ont: the id of the target ontology
* target_version_id: the version id for the target ontology
* target_ont_name: the name of the target ontology
* target_id: the identifier for the concept from the target ontology being mapped
* target_name: the preferred name of the concept from the target ontology

File:MappingData.xls

2009-06-22T06:08:49Z

Amirg: uploaded a new version of "Image:MappingData.xls"

Data from a set of mappings created by simple lexical matching across several BioPortal and UMLS ontologies.

Mapping Set

2009-06-22T05:55:08Z

Amirg:

File:OntologyGraphs.zip

2009-06-22T05:54:31Z

Amirg:

Mapping Set

2009-06-22T05:53:39Z

Amirg:

Mapping Set

2009-06-17T18:14:13Z

Amirg: /* Data */

File:MappingData.xls

2009-06-17T18:04:34Z

Amirg: Data from a set of mappings created by simple lexical matching across several BioPortal and UMLS ontologies.

Data from a set of mappings created by simple lexical matching across several BioPortal and UMLS ontologies.

Mapping Set

2009-06-17T18:00:16Z

Amirg:

Mapping Set

2009-06-17T17:48:34Z

Amirg: New page: Placeholder

Placeholder

LOOM

2009-03-20T19:54:03Z

Amirg:

== 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.

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 ==

LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here]

== Using LOOM ==

LOOM can be executed with a command of the following form: 
''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.

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: 
''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:
# 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.

LOOM

2009-03-20T06:23:20Z

Amirg:

== 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 ==

LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here]

== Using LOOM ==

LOOM can be executed with a command of the following form: 
''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.

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: 
''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:
# 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.

LOOM

2009-03-20T06:22:35Z

Amirg:

== 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 ==

LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here]

== Using LOOM ==

LOOM can be executed with a command of the following form: 
''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: 
''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.

LOOM

2009-03-20T06:19:48Z

Amirg:

== 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 ==

LOOM can currently be obtained at http://www.stanford.edu/~amirg/Loom.jar.zip

== Using LOOM ==

LOOM can be executed with a command of the following form: 
''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: 
''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.

LOOM

2009-03-20T02:31:33Z

Amirg:

== 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: 
''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: 
''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.

LOOM

2009-03-19T04:37:07Z

Amirg: New page: This is a placeholder for a page about the LOOM ontology alignment tool.

This is a placeholder for a page about the LOOM ontology alignment tool.