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VIVO-539 fixes bug related to excessive duplication of certain webpage links after migration

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This commit is contained in:
brianjlowe 2013-11-18 14:29:26 -05:00
parent bcf395732e
commit 9168e7c761
28 changed files with 83 additions and 385 deletions
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13
doc/upgrade-1.6.html
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@ -78,6 +78,13 @@
MySQL database (most people use mysqldump to create the backup)
</li>
</ul>
<p>
If you have used temporary models in the database to stage ingested data,
you will want to clear out any unneeded models that remain listed on the Manage
Jena Models page (under "Ingest tools"). This step is especially important if
these temporary models contain blank nodes, as this may cause unwanted or
duplicate data to appear following the upgrade.
</p>
<p>
The upgrade process is similar to the initial install process
with
@ -859,9 +866,9 @@
<p>
Changes to the VIVO core ontology may require corresponding
modifications to the knowledge base instance data and ontology annotations.
Each time VIVO starts up, it will initiate a process to examine the knowledge
base and apply necessary changes. This process should be very quick on subsequent
restarts if no data using the 1.5 ontology has been reintroduced.
The first time VIVO starts up following the upgrade,
it will initiate a process to examine the knowledge
base and apply necessary changes.
The knowledge base migration process for release 1.6 will make
the following types of changes:
</p>

29
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0.sparql Normal file
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@ -0,0 +1,29 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s a foaf:Person
FILTER (
EXISTS { ?s foaf:firstName ?firstName } ||
EXISTS { ?s foaf:lastName ?lastName } ||
EXISTS { ?s vivo:middleName ?middleName } ||
EXISTS { ?s vivo:email ?email } ||
EXISTS { ?s vivo:primaryEmail ?primaryEmail } ||
EXISTS { ?s vivo:phoneNumber ?phoneNumber } ||
EXISTS { ?s vivo:primaryPhoneNumber ?primaryPhoneNumber } ||
EXISTS { ?s vivo:faxNumber ?faxNumber } ||
EXISTS { ?s vivo:mailingAddress ?address } ||
EXISTS { ?s vivo:webpage ?webpage } ||
EXISTS { ?s vivo:preferredTitle ?preferredTitle } ||
EXISTS { ?s bibo:prefixName ?prefixName } ||
EXISTS { ?s bibo:suffixName ?suffixName }
)
FILTER NOT EXISTS { ?s arg:ARG_2000028 ?vcardNode }
}

15
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0a.sparql
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@ -1,15 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s foaf:firstName ?firstName
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

15
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0b.sparql
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@ -1,15 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s foaf:lastName ?lastName
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:middleName ?middleName .
?s a foaf:Person
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0d.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:email ?email .
?s a foaf:Person .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0e.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:primaryEmail ?email .
?s a foaf:Person .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0f.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:phoneNumber ?phoneNumber .
?s a foaf:Person .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0g.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:primaryPhoneNumber ?primaryPhoneNumber .
?s a foaf:Person
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0h.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:faxNumber ?faxNumber .
?s a foaf:Person
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0i.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:mailingAddress ?address .
?s a foaf:Person
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0j.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
} WHERE {
?s vivo:webpage ?webpage .
?s a foaf:Person
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

22
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1.sparql Normal file
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@ -0,0 +1,22 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s a foaf:Organization
FILTER (
EXISTS { ?s vivo:email ?email } ||
EXISTS { ?s vivo:primaryEmail ?primaryEmail } ||
EXISTS { ?s vivo:phoneNumber ?phoneNumber } ||
EXISTS { ?s vivo:primaryPhoneNumber ?primaryPhoneNumber } ||
EXISTS { ?s vivo:faxNumber ?faxNumber } ||
EXISTS { ?s vivo:mailingAddress ?address } ||
EXISTS { ?s vivo:webpage ?webpage }
)
FILTER NOT EXISTS { ?s arg:ARG_2000028 ?vcardNode }
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1d.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:email ?email .
?s a foaf:Organization .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1e.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:primaryEmail ?email .
?s a foaf:Organization .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1f.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:phoneNumber ?phoneNumber .
?s a foaf:Organization .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1g.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:primaryPhoneNumber ?primaryPhoneNumber .
?s a foaf:Organization
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1h.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:faxNumber ?faxNumber .
?s a foaf:Organization
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1i.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:mailingAddress ?address .
?s a foaf:Organization
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-1j.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Organization .
} WHERE {
?s vivo:webpage ?webpage .
?s a foaf:Organization
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

22
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2.sparql Normal file
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@ -0,0 +1,22 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s a foaf:Group
FILTER (
EXISTS { ?s vivo:email ?email } ||
EXISTS { ?s vivo:primaryEmail ?primaryEmail } ||
EXISTS { ?s vivo:phoneNumber ?phoneNumber } ||
EXISTS { ?s vivo:primaryPhoneNumber ?primaryPhoneNumber } ||
EXISTS { ?s vivo:faxNumber ?faxNumber } ||
EXISTS { ?s vivo:mailingAddress ?address } ||
EXISTS { ?s vivo:webpage ?webpage }
)
FILTER NOT EXISTS { ?s arg:ARG_2000028 ?vcardNode }
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2d.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:email ?email .
?s a foaf:Group .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2e.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:primaryEmail ?email .
?s a foaf:Group .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2f.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:phoneNumber ?phoneNumber .
?s a foaf:Group .
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2g.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:primaryPhoneNumber ?primaryPhoneNumber .
?s a foaf:Group
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2h.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:faxNumber ?faxNumber .
?s a foaf:Group
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2i.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:mailingAddress ?address .
?s a foaf:Group
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}

16
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-2j.sparql
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@ -1,16 +0,0 @@
PREFIX arg: <http://purl.obolibrary.org/obo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX v: <http://www.w3.org/2006/vcard/ns#>
PREFIX vivo: <http://vivoweb.org/ontology/core#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Group .
} WHERE {
?s vivo:webpage ?webpage .
?s a foaf:Group
FILTER NOT EXISTS {
?s arg:ARG_2000028 ?vcard .
}
}