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Some of the smaller models are "memory-mapped" for faster access. This means that they are loaded entirely into memory at startup. Any changes made to the memory image will be replicated in the original model.

Some of the models are initialized from files if they are found to be empty. Others load data from disk every time that VIVO starts. Still others combine these methods.

Initializing Content

Application data (Display model)

The data in each model persists in the application datasource (usually a MySQL database), or in the RDFService. Also, data from disk files may be loaded into the models. This may occur:

• the first time that VIVO starts up,
• if a model is found to be empty,
• every time that VIVO starts up.

depending on the particular model.

The "first time"

For purposes of initialization, VIVO is considered to be starting for the first time if the Application metadata model contains no statements, or if the RDFService detects that its SDB-based datastore has not been initialized.

Initializing Configuration models

Application metadata

Function: Describes the configuration of VIVO at this site. Many of the configuration options are obsolete.

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata

Source: the application Datasource (MySQL database) (memory-mapped)

If this is the first startup, read the files in /WEB-INF/init-data (without subdirectories)

• In Vitro, there are none
• In VIVO, initialSiteConfig.rdf

Also if this is the first startup, read the files in /WEB-INF/ontologies/user/applicationMetadata

• In Vitro, there are none
• In VIVO, classgroups.rdf and propertygroups.rdf

User Accounts

Contains login credentials and assigned roles for VIVO users.

Name: Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadatauserAccounts

Source: the application Datasource (MySQL database) (memory-mapped)

If If this model is empty, read the files in in /WEB-INF/ontologies/app/auth (without subdirectories)

• In Vitro, application.owl, menu.n3, profilePageType.n3
• In VIVO, override menu.n3
  

Every time, read /WEB-INF/ontologies/app/loadedAtStartup

• in Vitro, displayModelListViews.rdf
• In VIVO, homePageDataGetters.n3, localeSelectionGUI.n3, vivoDepartmentQueries.n3, vivoListViewConfig.rdf, vivoSearchProhibited.n3

Display TBox

. Ordinarily there are no such files. This feature is useful when running acceptance tests.

The Display model

This is the ABox for the display model, and contains the RDF statements that define managed pages, custom short views, and other items.

Name: Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadataTBOXdisplayMetadata

Source: the application Datasource (MySQL database) (memory-mapped)

Every timeIf this model is empty, read the files in /WEB-INF/ontologies/app/menuload/displayTBOX.n3 (old statements are not cleared)

DisplayDisplay

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata-displayModel

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(without subdirectories)

• In Vitro, application.owl, menu.n3, profilePageType.n3
• VIVO contains its own copy of menu.n3, which overrides the one in Vitro
  

Every time, read the files in /WEB-INF/ontologies/app/menuload/displayDisplay.n3 (old statements are not cleared)

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loadedAtStartup

• in Vitro, displayModelListViews.rdf
• In VIVO, homePageDataGetters.n3, localeSelectionGUI.n3, vivoDepartmentQueries.n3, vivoListViewConfig.rdf, vivoSearchProhibited.n3

Display TBox

The TBox for the display model.

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccountsdisplayMetadataTBOX

Source: the application Datasource (MySQL database) (memory-mapped)

Every timeIf empty, read the files in /WEB-INF/ontologies/auth (without subdirectories). None expected, except during Selenium tests.

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/app/menuload/displayTBOX.n3 (note that existing statements are not cleared, except through the GUI)

DisplayDisplay

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadatadisplayMetadata-displayModel

Source: the application Datasource (MySQL database)

 If empty, this is first setup

If first setup, read the files in /WEB-INF/init-data (without subdirectories)

• None in Vitro
• initialSiteConfig.rdf in VIVO

(memory-mapped)

Every time, read If first setup, read the files in /WEB-INF/ontologies/user/applicationMetadata

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app/menuload/displayDisplay.n3 (note that existing statements are not cleared, except through the GUI)

Initializing Content models

base ABox

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-2

Source: startup dataset named graph from the RDFService

If first setup, read the files in /WEB-INF/ontologies/user/abox (without subdirectories)

• None in VitroIn Vitro, there are none
• In VIVO, geopolitical.ver1.1-11-18-11.individual-labels.rdf, vocabularySource-labels.n3

Every time, read the files in /WEB-INF/filegraph/abox, and create named models in the RDFService. Add them as sub-models to the base ABoxABox. If these files are changed or deleted, update the RDFService accordingly.

• In Vitro, there are none
• In Vivo, academicDegree.rdf, continents.n3, dateTimeValuePrecision.owl, documentStatus.owl, geopolitical.abox.ver1.1-11-18-11.owl, us-states.rdf, vocabularySource.n3

...

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-inf

Source: startup dataset from RDFService

base TBox

Name: http://vitro.mannlib.cornell.edu/default/asserted-tbox

Source: startup dataset named graph from the RDFService (memory-mapped)

If first setup, read the files in /WEB-INF/ontologies/user/tbox (without subdirectories)

• In Vitro, there are none
• In VIVO, geopolitical-ver1.1-11-18-11-annotations.rdf, isDefinedBy-1.5-annotations.rdf, scires-1.5-annotations.rdf, vitro-0.7-annotations.rdf, vivo-core-1.5-annotations.rdf, vivo-core-1.5-labels_es_ES.n3

Every time, read the files in /WEB-INF/filegraph/tbox, and create named models in the RDFService. Add them as sub-models to the base TBox-models to the base TBox. If these files are changed or deleted, update the RDFService accordingly.

• In Vitro, vitro-0.7.owl, vitroPublic.owl
• In VIVO, geopolitical.tbox.ver1.1-11-18-11.owl, isDefinedBy-1.5.owl, scires-1.5.owl, vivo-bibo-1.5.owl, vivo-c4o-1.5.owl, vivo-core-1.5.owl, vivo-dcelements-1.5.owl, vivo-dcterms-1.5.owl, vivo-event-1.5.owl, vivo-fabio-1.5.owl, vivo-foaf-1.5.owl, vivo-pws-1.5.owl, vivo-skos-1.5.owl1.5.owl

base Full

Source: a combination of base ABox and base TBox

inference ABox

Name: http://vitro.mannlib.cornell.edu/default/vitro-kb-inf

Source: named graph from the RDFService

inference TBox

Name: http://vitro.mannlib.cornell.edu/default/inferred-tbox

Source: startup dataset named graph from the RDFService (memory-mapped)

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inference Full

Source: union a combination of base inference ABox and inference ABoxTBox

union

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ABox

Source: union a combination of base TBox ABox and inference ABox

union TBox

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Source: union a combination of base ABox and base TBox

inference Full

Source: union of inference ABox and inference TBox

union Full

Source: union a combination of union ABox and union TBox

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