I am using PROTEGE 4.4. I am trying to run a Reasoner(Pellet/Hermit) on an ontology that I have created. This ontology imports sweetAll.owl. It starts the Reasoner and it begins to classify, but does not proceed after some progress. What could be the reason?? There are no error messages thrown. How is my ontology going to work if this reasoner does not execute correctly. Please help.
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as the title suggest, i am wondering why the jena-iri module is completely absent of the javadoc in jena 4. Is the package about to be deprecated ? how does it related to the package org.apache.jena.irix ?
I mean in code we still have access to jena-iri.
Can someone be kind as to clarify the difference and purpose of both jena-iri and org.apache.jena.irix ?
There are details in the pre-release news for Jena 4.0.0, the community announcement and the IRIx javadoc.
The package is not going to be deprecated or removed.
IRIx is a wrapper abstraction to allow for multiple IRI implementations.
jena-iri is the active implementation in Jena 4.0.0.
This change allows for an additional IRI parser that is centred on the task of checking incoming data with lower overhead.
I am working with Epidemiology Ontology (EPO). I have downloaded the EPO ontology file from here. I need some limited terms from the ontology. Hence, I have deleted the terms that I do not need from the ontology file. The new file is available here. Next, I have loaded ontology file to Protege. However, still, Protege GUI is showing me the terms that I deleted. How can I get rid of the deleted terms (within the red box in the picture)? I only need terms in bold font. Thank you for your help.
Did you change the import IRI in the original ontology?
If the IRI is unchanged, Protege will not load your modified ontology, but use the original ontology from the original IRI.
If the IRI has been changed but the logical IRI of the ontology (i.e., the one mentioned in the file) is the same, it is possible that Protege is using another copy of the original ontology.
The best course of action for this scenario is to ensure the modified ontology has a new logical IRI and is accessible at a different IRI, and then to use that IRI for importing. Also ensure you save and reload your importing ontology - imports resolution is carried out on loading, not on editing an existing import.
I'm learning Cypher since yesterday and I read about the user defined functions.
There's many material on how to use the functions, but not many on how to deploy new ones.
I would like to try out but I'm having a hard time on finding a step-by-step tutorial on how to deploy new functions to my desktop app.
The ones I have found bypass some concepts as they were too obvious. And maybe they are for someone coming from a Java background or whatever the background is you're supposed to have when using Neo4J. ...But I come from a Javascript background. I'm used to npm, never heard of maven (just an example).
It would be nice you someone could help with a detailed step-by-step tutorial on how to write and deploy a new user defined function in Neo4J.
For helping a bit.
User defined functions are only writables in Java code for now. They're server extensions. You write the code with a Java editor (outside Neo4j) and publish it under a Java Archive (a file with extension .jar) into the /plugins directory of your Neo4j installation (https://neo4j.com/docs/developer-manual/current/extending-neo4j/cypher-functions/).
Many useful procedures already exist with APOC extension (https://neo4j-contrib.github.io/neo4j-apoc-procedures/) depending of your Neo4j server version.
Try them first bfeore developping yours, especially if you're starting with CYPHER. Some of them should solve your usuals demands.
All of extensions are taking effect after a restart of Neo4j.
Note : Maven is a dependency manager for Java.
There is a wizard tab for Protege 3 to add multiple instances at once, but not for Protege 5. How may I add multiple instances to a class at once, for example copy & paste them from Excel to Protege?
Try to use Cellfie plugin.
It is bundled with Protégé 5.2.0 and available from Tools > Create axioms from Excel workbook...
Mapping language for transformation rules is described here.
In fact, it is just a Manchester syntax dialect with spreadsheet references.
I've done a bit of searching around for a good RDF editor. But I'm not sure what one is the most utilised. Can anyone recommend one? I'm looking to write some simple RDF and maybe parse one or two RDF documents.
Many thanks
Are you looking to work at the raw Triples level and in a human readable/editable syntax such as Turtle? If so you can get by just with Notepad or maybe try out my rdfEditor which is an early Alpha release but gives you nice syntax highlighting, checking and auto-completion. This is designed only for editing raw RDF data and does not give you any IDE tools for creating your data.
If you want to work at the class/individual (i.e. more abstract level) and have the editor care about the underlying RDF then you probably want to try either TopBraid Composer or Protege
There's a new TextMate bundle for the Turtle RDF language which offers a bunch of cool features. https://github.com/peta/turtle.tmbundle
Judging from the screenshots, Rhodonite http://rhodonite.angelite.nl/ makes a good impression.
Unfortunately it seems to be abandonded and I could not get it to run on Windows7 (x64). But maybe it runs on your system (download is Windows only)
If you're looking for a web-based RDF / Ontology editor, have a look at Web Protege, an open source web-based project by the Protege team mentioned in the accepted answer.
If you need a more advanced RDF editor, look at RDF and SPARQL plugin for JetBrains IDEs. It supports all RDF 1.1 formats as well as SPARQL 1.1. Including the RDF-star and SPARQL-star extensions.
It features syntax highlighting and validation, prefixed name completion, SPARQL 1.1 Protocol support and much more.
You don't have to buy a JetBrains IDE, since the plugin works with the free versions too.