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I have tried to reference external vocabulary using MIREOT Protégé Plugin. The external ontology is located in this link : http://purl.allotrope.org/voc/afo/REC/2018/07/afo (TTL File : http://purl.allotrope.org/voc/afo/REC/2018/07/afo.ttl).

The problem is that the plugin cannot get any results from this ontology when I try to look for a term. The MIREOT Plugin return only superclasses (BFO terms in this case) See screen 1 Screen 1.

When I tried to look for the term "sample processing" (which is a specialized class), I didn't get any results while the term exist in the ontology (see screen 2). Screen 2

Thank you for help.

Zakariae Aloulen
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    It seems that MIREOT doesn't search in `skos:prefLabel`s and `skos:definition`s. At least, by default. – Stanislav Kralin Sep 24 '18 at 17:14
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    https://github.com/UAMS-DBMI/MIREOT-plugin/blob/master/src/main/java/edu/uams/dbmi/protege/plugin/mireot/search/AdditionalOntologySearcher.java#L303 or https://github.com/UAMS-DBMI/MIREOT-plugin/blob/master/src/main/java/edu/uams/dbmi/protege/plugin/mireot/search/AdditionalOntologySearcher.java#L347. – Stanislav Kralin Sep 24 '18 at 17:27
  • Thank you, is there any alternative solution ? – Zakariae Aloulen Sep 24 '18 at 17:53
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    Fork the project and add code such that it is configurable. Then, in best case create a pull request. Finally, build the plugin and replace the existing plugin – UninformedUser Sep 25 '18 at 05:37
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    BTW, the authors [said](http://ceur-ws.org/Vol-914/paper_48.pdf) that the plugin *"pulls every annotation of the source component, not just `rdfs:label` and `iao:definition`*, so perhaps you could contact them via e. g. GitHub. – Stanislav Kralin Sep 25 '18 at 08:41
  • @AKSW can you help me in editing the plugin files please, I ve tried in eclipse, but I can't generate the new jar file – Zakariae Aloulen Sep 25 '18 at 12:34
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    *"is there any alternative solution"* — to be honest, I was not able modify the plugin in the way you need after 2 or 3 hours of work... I hope your [pull request](https://github.com/UAMS-DBMI/MIREOT-plugin/pull/2) does that. BTW, Protege has search capabilities (Ctrl+F). Possibly you could also use *Refactor > Copy/move/delete axioms* (see also [this question](https://stackoverflow.com/a/44266590/7879193)). – Stanislav Kralin Oct 03 '18 at 09:21
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    Thank so much, yes my pull request did the job, I will respond my question with all details as soon as possible – Zakariae Aloulen Oct 04 '18 at 10:07

1 Answers1

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The authors said in the research paper that the plugin :

pulls every annotation of the source component, not just rdfs:label and iao:definition (Simplifying MIREOT: a MIREOT Protégé Plugin).

This fact is not correct, the plugin is able to search only using rdfs:label, rdfs:comment, and iao:definition (you can test that).

So, if you want to use other annotation vocabulary (SKOS for example) you have to edit the source code of the plugin.

To do so, you have to :

  1. Clone the project in eclipse using git.
  2. Import the project to your work space.
  3. Transform the project to Plugin using Plug-in Development Environment (PDE)
  4. Import the project into your workspace.
  5. Edit the project and deploy it using maven install (to generate the jar file).
  6. To finish you can send a pull request to github or install the plugin in Protégé using the generated jar file (Step 5).

I have already did the modifications for the plugin to support SKOS annotations (skos:prefLabel, skos:definition and skos:altLabel). Please check my pull request Here.

To test plugin (my pull request), you can download the jar from HERE and past the file in the Protégé plugins' folder. Please keep a copy of the original jar file.

What is new in this pull request :

  1. Correct the problem of search by iao:definition (don't work in the actual version).
  2. Add SKOS Annotations support (see the picture).MIREOT with SKOS Annotations support

Important EDIT I added a new version with that supports search of datatype properties.

In this new edit :

  • I added datatype search option (see screen below).
  • I added datatype tab. I have replaced the jar file in my github account, you can download the new version by using the same link.

I have also sent a new pull request.

enter image description here

This version have been tested with Protégé version Protege-5.5.0-beta-3

Zakariae Aloulen
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