VIVO Documentation
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Here are some of the ways for accessing data models:
Attributes on Context, Session, or Request
Previously, it was common to assign a model to the ServletContext, to the HTTP Session, or to the HttpSessionRequest like this:
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It remains to be seen whether this uniformity can satisfy the various needs of the application. If not, at least the changes can all be made within a single point of access.
The DAO layer
This mechanism is pervasive through the code, and remains quite useful. In it, a WebappDaoFactory
is created, with access to particular data models. This factory then can be used to create DAO objects which satisfy interfaces like IndividualDao
, OntologyDAO
, or UserAccountsDAO
. Each of these object implements a collection of convenience methods which are used to manipulate the backing data models.
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Initially, the WebappDaoFactory
may have been used only with the full Union model. But what if you want to use these DAOs only against asserted triples? Or only against the ABox? This led to the OntModelSelector
.
OntModelSelectors
An OntModelSelector
provides a way to collect a group of Models and construct a WebappDaoFactory
. With slots for ABox, TBox, and Full model, an OntModelSelector
could provide a consistent view on assertions, or on inferences, or on the union. The OntModelSelector
also holds references to a display model, an application metadata model, and a user accounts model, but these are more for convenience than flexibility.
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Again, this is a change in the semantics of OntModelSelectors. It insures a consistent representation of OntModel
s across OntModelSelector
s, but it is certainly possible that existing code relies on an inconsistent model instead.
The RDF Service
Note |
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TBD |
Model makers and Model sources
The ModelAccess class
Note |
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TBD - Show how it represents all of these distinctions. Describe the scope searching and masking, wrt set and get. Include the OntModelSelectors and WADFs. |
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depending on the particular model.
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.
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Where are the RDF files?
In the distribution, the RDF files appear in [vivo]/rdf
and in [vitro]/webapp/rdf
. These directories are merged during the build process in the usual way, with files in VIVO preferred over files in Vitro.
During the build process, the RDF files are copied to the VIVO home directory, and at runtime VIVO will read them from there.
The "first time"
For purposes of initialization, "first time" RDF files are loaded if the relevant data model contains no statements. Content models may also load "first time" files if the RDFService detects that its SDB-based datastore has not been initialized.
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- In Vitro, there are none
- In VIVO, geopolitical.ver1.1-11-18-11.individual-labels.rdf, vocabularySource-labels.n3
Every timerestart, read the files in rdf/abox/filegraph, 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 geopolitical.abox.ver1.1-11-18-11.owl, academicDegree.rdf, continents.n3
us-states.rdf, dateTimeValuePrecision.owl, validation.n3, documentStatus.owl, vocabularySource.n3
base TBox
Name: http://vitro.mannlib.cornell.edu/default/asserted-tbox
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- 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 additionalHiding.n3 initialTBoxAnnotations.n3
Every restartEvery time, read the files in rdf/tbox/filegraph, 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-1.544 files:
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README.md education.owl personTypes.n3 agent.owl event.owl process.owl appControls-temp.n3 geo-political.owl publication.owl bfo-bridge.owl grant.owl relationship.owl bfo.owl linkSuppression.n3 relationshipAxioms.n3 classes-additional.owl location.owl research-resource-iao.owl clinical.owl object-properties.owl research-resource.owl contact-vcard.owl object-properties2.owl research.owl contact.owl object-properties3.owl role.owl data-properties.owl objectDomains.rdf sameAs.n3 dataDomains.rdf objectRanges.rdf service.owl dataset.owl ontologies.owl skos-vivo.owl date-time.owl orcid-interface.n3 teaching.owl dateTimeValuePrecision.owl other.owl vitro-0.7.owl documentStatus.owl outreach.owl vitroPublic.owl |
base Full
Source: a combination of base ABox and base TBox
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