Site Administration

Once you are logged into VIVO, you will notice in the upper right hand portion of the page links to "Index" and "Site Admin", alongside a drop-down menu with your name on it, and containing links to "My account" and "Log out".

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There are several avenues available to acquire guidance with these advanced tools. Information sources such as the VIVO Data Ingest Guide, the W3C’s Resource Description Framework model, and the W3C’s SPARQL Query Language for RDF, to name a few. Please refer to Appendix A for links and additional resources.

Ingest tools – A suite of data management tools. See below for a detail of each tool.

Add/Remove RDF data  – This tool allows for the manipulation of RDF data in the main model through importing RDF documents for addition or removal.

Ingest tools  – A suite of data management tools. See below for a description of each tool.

RDF export  - This tool allows for the export of ontology and data in a variety of RDF formats. Options include:

• Export all instance data(Abox)
• Export a specific ontology (Tbox) such as FOAF, VIVO core, SKOS, etc.
• Export the entire ontology (Tbox) for VIVO

Note: It is recommended to select the ‘Export only asserted statements’ sub option, as the inferred statements will be generated when the data is imported into another VIVO.

SPARQL query  - This tool allows SPARQL select, construct, and describe statements against the main model to be saved in a variety of formats including: CSV, RDF/XML, N3 and more.

SPARQL query builder – A query generating interface with pre-populated drop down lists.

Ingest Menu Short Description

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Ingest tools

Manage Jena Models  – This tool allows for the management of the main webapp, as well as separate data models and datasets. The ability to attach separate models to the webapp, load RDF data to a mode, clear statements, and output models as N3 RDF is performed here.

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Convert CSV to RDF  — This tool allows for VIVO to read and convert CSV (comma-separated values) and Tab-delimited data into RDF

Load Convert XML and convert to RDF  — This tool allows for VIVO to read and convert well-formed XML into RDF

Execute SPARQL CONSTRUCT  — This tool allows for using SPARQL to produce desired RDF from one or multiple source models. This tool is commonly used to map classes and properties to VIVO namespace(s).

Generate Tbox  — Tbox statements describe the terms of controlled vocabularies, for example, a set of classes and properties that constitute the ontology. This tool allows for the creation of a Tbox from one or multiple source models.

Name Blank Nodes  — This action turns blank nodes, a node in an RDF graph which is not identified by a URI and is not a literal, into nodes with either randomly generated or pattern based URIs.

Smush Resources  — This tool allows for using a compression method to distinguish like entities and “Smush” them together based on the specified URI of a property.

Generate Tbox — Tbox statements describe the terms of controlled vocabularies, for example, a set of classes and properties that constitute the ontology. This tool allows for the creation of a Tbox from one or multiple source models.

Execute SPARQL CONSTRUCT — This tool allows for using SPARQL to produce desired RDF from one or multiple source models. This tool is commonly used to map classes and properties to VIVO namespace(s)Merge Resources — This tool allows two individuals with different URIs to be collapsed into a single URI. Any statements using the “duplicate individual URI” will be rewritten using the “primary individual URI.” If there are multiple statements for a property that can have only a single value, the extra statements will be retracted from the model and offered for download.

Process Property Value Strings  — This tool allows for an arbitrary method on a Java class available on the application class path to transform string values of a given property. The method should take a single String as a parameter and return a String.

Change Namespace of Resources  — This tool will change all resources in the supplied “old namespace” to be in the “new namespace.” Additionally, the local names will be updated to follow the established “n” + random integer naming convention.

Split Property Value Strings into Multiple Property Values  — This tool allows for parsing multiple property values from a single ingested string. This can be used to parse MeSH Terms, controlled vocabulary, and keywords associated with the ingested data.

Execute Workflow  — This tool allows for a simple way of scripting actions (specified in RDF) that would otherwise require manual interaction with the ingest tools.

Merge Individuals — This tool allows two individuals with different URIs to be collapsed into a single URI. Any statements using the “duplicate individual URI” will be rewritten using the “primary individual URI.” If there are multiple statements for a property that can have only a single value, the extra statements will be retracted from the model and offered for download.

Change Namespace of Resources — This tool will change all resources in the supplied “old namespace” to be in the “new namespace.” Additionally, the local names will be updated to follow the established “n” + random integer naming convention.

Refreshing Content

V1.3 Specific: Site Administrators can rebuild their search, class group cache, visualizations, and inferencing in the Site Admin interface. It is important to build the visualization code after ingesting publication data or it will take a long time to display the visualization to the user.

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Rebuild visualization cache

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Dump or restore the knowledge base  – dump or restore configuration models or content models

Site Maintenance

Rebuild search index  – in some situations, you may need to rebuild the SOLR search index.  See Inferences and Indexing

Rebuild visualization cache –  Large-scale visualizations like the Temporal Graph or the Map of Science involve calculating total counts of publications or of grants for some entity. Since thismeans checking also through all of its sub-entities, the underlying queries can be both memory-intensive and time-consuming. For a faster user experience, we wish to save the results of these queries for later re-use.

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 To this end we have devised a caching solution which will retain information about the hierarchy of organizations-namely, which publications are attributed to which organizations-by storing the RDF model. We're currently caching these models in memory. The cache is built (only once) on the first user request after a server restart. Because of this, the same model will be served until the next restart. This means that the data in these models may become stale depending upon when it was last created. To avoid restarting the server in order to refresh the cache, administrators can use the Rebuild visualization cache link.

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Recompute inferences  – in some cases, you may wish to recompute the inferences in VIVO.  See Inferences and Indexing

Startup status  – shows the messages that were produced during VIVO startup.

Restrict logins  – toggles user login.  When logins are restricted, only the root user may login

Activate Developer panel  – Shows the developer panel from which additional debugging information is available.  See Tips for Interface Developers