This page describes how the data models were initialized before release 1.6. The principal changes are these:

• RDF initialization files were in several different locations of the distribution
• There was no consistent naming structure - no way to tell whether a file was loaded every time VIVO started, or only the first time that VIVO started.
• In some cases, a particular hard-coded filename was loaded, instead of reading any files in the appropriate directory.

Compare to the Initialization section in the parent page.

Initializing the Models

When VIVO starts up, OntModel objects are created to represent the various data models. The configuration models are created from the datasource connection, usually to a MySQL database. The content models are created using the new RDFService layer. By default this also uses the datasource connection, but it can be configured to use any SPARQL endpoint for its data.

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.

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: http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts

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

If this model is empty, read the files in /WEB-INF/ontologies/auth (without subdirectories). 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: http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata

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

If this model is empty, read the files in /WEB-INF/ontologies/app/ (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/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-displayMetadataTBOX

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

Every time, read /WEB-INF/ontologies/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-displayMetadata-displayModel

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

Every time, read /WEB-INF/ontologies/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: named graph from the RDFService

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

• In 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 ABox. 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

base TBox

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

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

inference Full

Source: a combination of inference ABox and inference TBox

union ABox

Source: a combination of base ABox and inference ABox

union TBox

Source: a combination of base TBox and inference TBox

union Full

Source: a combination of union ABox and union TBox