Some RDF imported classes and properties are not available in autocomplete search in EDG

[Fan Li]

After importing an existing ontology (e.g. BFO) into my ontology in EDG, I see the imported classes won't appear in the autocomplete search box (for example, sh:class). Similarly imported object properties are not available when adding a new property shape (see below). Meanwhile I can verify their existence in the graph via SPARQL. So I guess perhaps the imported triples were not added into the autocomplete index? Thanks!

[Irene Polikoff]

I could not reproduce this issue.

Did you physically imported BFO using Import -> Import RDF or did you include it using Settings -> Includes.

In either case, the autocomplete index will be updated automatically.

One difference is that if you use Import -> Import RDF, EDG will insert missing rdfs:subclassOf relationships for any class that has no parent. With this, classes from BFO will appear in the class tree.

I did not find ‘has member’ property in the BFO 2.0 downloaded from https://github.com/bfo-ontology/BFO/wiki

It has some declarations for dc:member property, but there is no label:

dc:member

  rdf:type owl:AnnotationProperty ;

.

On Jul 28, 2019, at 12:15 AM, Fan Li <lifa...@gmail.com> wrote:

After importing an existing ontology (e.g. BFO) into my ontology in EDG, I see the imported classes won't appear in the autocomplete search box (for example, sh:class). Similarly imported object properties are not available when adding a new property shape (see below). Meanwhile I can verify their existence in the graph via SPARQL. So I guess perhaps the imported triples were not added into the autocomplete index? Thanks!

<shape.jpg>

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<shape.jpg>

[Fan Li]

Hi Irene, my understanding is that relations are not removed in BFO 2.0. Instead they form a separator ontology called Relation Ontology. Anyway I actually imported the "has member" relation through the Information Artifact Ontology, which is built on BFO.

https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2019-06-07/iao.owl

It contains the following triples:

<!-- http://purl.obolibrary.org/obo/RO_0002351 --> 
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002351"> 
  <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/> 
  <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#IrreflexiveProperty"/> 
  <obo:IAO_0000115>has member is a mereological relation between a collection and an item.</obo:IAO_0000115> 
  <obo:IAO_0000119>SIO</obo:IAO_0000119> 
  <obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/> 
  <rdfs:label xml:lang="en">has member</rdfs:label> 
</owl:ObjectProperty>

I just created a new ontology in EDG and imported the above mentioned iao.owl file (Import RDF with RDF/XML format). The import was successful but unfortunately I am still not able to add a property shape for "has member".

On Sunday, July 28, 2019 at 4:17:00 PM UTC-4, Irene Polikoff wrote:

I could not reproduce this issue.

Did you physically imported BFO using Import -> Import RDF or did you include it using Settings -> Includes.

In either case, the autocomplete index will be updated automatically.

One difference is that if you use Import -> Import RDF, EDG will insert missing rdfs:subclassOf relationships for any class that has no parent. With this, classes from BFO will appear in the class tree.

I did not find ‘has member’ property in the BFO 2.0 downloaded from https://github.com/bfo-ontology/BFO/wiki

It has some declarations for dc:member property, but there is no label:

dc:member

  rdf:type owl:AnnotationProperty ;

.

On Jul 28, 2019, at 12:15 AM, Fan Li <lifa...@gmail.com> wrote:

After importing an existing ontology (e.g. BFO) into my ontology in EDG, I see the imported classes won't appear in the autocomplete search box (for example, sh:class). Similarly imported object properties are not available when adding a new property shape (see below). Meanwhile I can verify their existence in the graph via SPARQL. So I guess perhaps the imported triples were not added into the autocomplete index? Thanks!

<shape.jpg>

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[Holger Knublauch]

Hi Fan Li,

it seems that the auto-complete index is not always refreshed after such file imports. I am still investigating details and know how to improve this for the next release, yet I wanted to give you this work-around if it blocks your progress:

After you imported the OWL file, please go to Server Administration > Auto-Complete Management and click Rebuild for the Graph that you imported into. The direct link to that page from a TBC-ME installation is http://localhost:4500/tbl/swp?_viewClass=tbladmin:AutoCompletePage. The problem would also be resolved by a server restart.

Thanks,
Holger

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[Fan Li]

Thanks, Holger. The manual reindex works for me! 

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