*Deprecated* See https://wiki.duraspace.org/display/VIVODOC/All+Documentation for current documentation

If you know the id of the blank node go to

http://vivo.ufl.edu/admin/conceptRepair.jsp

Ticking "describe" shows the statements that use the blank node. Ticking "remove" will attempt to remove the statements from the database.

Plug the object name value into the form (example: -4d009451:1289c793af1:-7cb5)
Check "describe concept" noting:

prefix xsd: . @prefix afn: . @prefix swrlb: . @prefix rdfs: . @prefix owl: .
@prefix vivo: . @prefix swrl: . @prefix dc: . @prefix vitro: .
@prefix rdf: . rdf:type [] .

Where "rdf:type [] ." is an issue.

Click "remove". If the removal was successful, you should then be able to run the describe again and just get N3 namespace declarations with no accompanying triple data.

After that, make an edit through the GUI to trigger Pellet to retry reasoning. (Just creating an individual and immediately deleting it again does the trick.)

Here's a sparql query that can sometimes identify blank nodes:

SELECT ?type
WHERE {
?individual rdf:type ?type .
OPTIONAL {
?type ?predicate ?something
}
FILTER (isBlank(?type))
FILTER (!bound(?something))
}

If you do not know the id of the blank node, perform the following steps.

  • Log in to VIVO
  • Select Site Admin
  • Select Class Hierarchy
  • Select All Classes
  • Search for 'Thing'
  • Select the 'Thing' class
  • Select 'Show Individuals Asserted To Be in This Class
  • The instances with the structure similar to '-5d2968f2:12a361caea3:-7ba0' are highly correlated to be blank nodes.

*Deprecated* See https://wiki.duraspace.org/display/VIVODOC/All+Documentation for current documentation