Example using OWL ontology?

[theyaa]

Hi, Do you have an example/demo using OWL ontology please? what would be the value of the efo_uri field in the documents to be indexed? @mattflax @tburdett @tomjon Thanks

[mattflax]

Hi,

The spot-ontology directory has an example set-up using an OWL ontology. See the solrconfig.xml in https://github.com/flaxsearch/BioSolr/blob/master/spot/spot-ontology/solr-conf/documents/conf/solrconfig.xml, line 586, to see how it is configured. The properties file referred to in the config can be found at https://github.com/flaxsearch/BioSolr/blob/master/spot/spot-ontology/solr-conf/documents/conf/ontology/efo.properties

Unfortunately there is no demo for that part of the project (the data source is an internal database), but you should be able to modify the swat4ls_demo material to work using an OWL ontology instead of calling OLS.

The efo_uri field in the example data contains the annotation IRI - eg. http://www.ebi.ac.uk/efo/EFO_0000180 is equivalent to the document being annotated with the EFO entry for "HIV-1 Infection". (The field is named that because the data I was working with was annotated against the EFO ontology.)

Hope that helps!

[theyaa]

Thank you for the quick reply. What I am trying to get to is, what if I use a local OWL file, how do I define the value for the efo_uri?

Is there also a way for the plugin to use a text field in the document, parse its content, and then assign the right ontology to it?

For example, I have a text field with content " This is a document related to lung cancer". Then the plugin would annotate the document with [lung, lung cancer, cancer], according to the OWL ontology I provided it with. @mattflax @tburdett @tomjon

Thanks