balhoff/arachne

RDF rule engine

arachne's Issues

Integration with RDF4J

Is it possible - with limited effort - to integrate arachne with RDF4J?
I think it would be useful to have a forward chaining reasoner for RDF4J SAILs.

Option to output explanations with URIs bound to variables

From @goodb: I wonder if it would be possible to adjust your explanation code such that the variables in the rules (e.g. ?x1) were replaced by the URIs that were bound to them when the rule activated? That would make it a little easier to string together the inference chain.

Provide configurations for reasoning with TBoxes as ABoxes

Context: @deepakunni3 is building an uber kg for translator. We just want to use simple edges for existentials. See https://douroucouli.wordpress.com/2019/07/11/proposed-strategy-for-semantics-in-rdf-and-property-graphs/

We want to propagate properties down is-a hierarchies @realmarcin will take results and analyze as matrix

Here we want to ignore the OWL translation rules and instead just have rules like

?c owl:subClassOf ?d .
?d ?r ?y .
?r a owl:ObjectProperty .
==>
?c ?r ?y .

possibly also annotating triples with inference provenance.

Can we have these rules stored in this repo, and have an option to use these rather than owl ones?

Installation / usage manual available?

I would like to try out this reasoner, but I have no knowledge about Scala and the mentioned build tools (sbt). Is there an installation manual available?

If not, could you tell me what to do after building the software? Do I run it as a stand alone CLI or use some jar file?

I found a binary in the latest release (arachne-1.2.1.tgz, in bin folder). When executing it, an error is raised about missing parameters:

./arachne
Constructed reasoner from rules in 0.013s
Exception in thread "main" java.lang.IllegalArgumentException: Parameter 'directory' is not a directory: data
	at org.apache.commons.io.FileUtils.validateListFilesParameters(FileUtils.java:541)
	at org.apache.commons.io.FileUtils.listFiles(FileUtils.java:517)
	at org.apache.commons.io.FileUtils.listFiles(FileUtils.java:689)
	at org.geneontology.rules.cli.Main$.$anonfun$run$10(Main.scala:65)
	at org.geneontology.rules.cli.Main$.time(Main.scala:93)
	at org.geneontology.rules.cli.Main$.run(Main.scala:63)
	at org.geneontology.rules.cli.Main$.run(Main.scala:22)
	at org.backuity.clist.CliMain.$anonfun$runWith$1(CliMain.scala:14)
	at org.backuity.clist.Parser.$anonfun$withCommand$1(Parser.scala:156)
	at org.backuity.clist.Parser.withParsingException(Parser.scala:199)
	at org.backuity.clist.Parser.withCommand(Parser.scala:154)
	at org.backuity.clist.CliMain.runWith(CliMain.scala:14)
	at org.backuity.clist.CliMain.main(CliMain.scala:6)
	at org.geneontology.rules.cli.Main.main(Main.scala)

Thanks for any hint in advance.

Explore Cheló̱na for native RDF parsing

https://github.com/JuPfu/chelona/

Would be useful for Scala.js version of Arachne.

sbt compile fails

I tried to compile arache using using sbt compile command. Running scalaVersion=2.12, sbtVersion=1.0, on OS X 10.15 (Catalina).

Received the following errors:

[error] sbt.librarymanagement.ResolveException: unresolved dependency: com.typesafe.sbt#sbt-native-packager;1.3.19: Resolution failed several times for dependency: com.typesafe.sbt#sbt-native-packager;1.3.19 {compile=[default(compile)]}:: 
[error] 	typesafe-ivy-releases: unable to get resource for com.typesafe.sbt#sbt-native-packager;1.3.19: res=https://repo.typesafe.com/typesafe/ivy-releases/com.typesafe.sbt/sbt-native-packager/scala_2.12/sbt_1.0/1.3.19/ivys/ivy.xml: javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
[error] 	sbt-plugin-releases: unable to get resource for com.typesafe.sbt#sbt-native-packager;1.3.19: res=https://repo.scala-sbt.org/scalasbt/sbt-plugin-releases/com.typesafe.sbt/sbt-native-packager/scala_2.12/sbt_1.0/1.3.19/ivys/ivy.xml: javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target

Enable incremental updates to active RuleEngine

In some cases it would be useful to be able to modify the rules without rebuilding the whole RuleEngine object (which can be a little slow when there are large numbers of rules to process).

Use case produced by consistency checking system for BioPAX2GO .

Consider making datatype optional for Literals

See balhoff/blazegraph-runner#3

Protege plugin?

A Protege plugin for Arachne would be very useful for exploring GO use-cases.

use appropriate jena method for using prefixes when parsing rules file

property chains not working?

no inference:

inference:

inference:

This could be a minerva config issue, but I'm pretty sure all of RO is loaded, and we have the axiom MC-part part-of some MC.

Could it be that TBox property chains aren't recognized (the 3rd example shows that ABox property chains are)

MinCardinality not handled

with --ontology=uberon.owl

Exception in thread "main" scala.MatchError: ObjectMinCardinality(2 <http://purl.obolibrary.org/obo/RO_0002176> <http://purl.obolibrary.org/obo/UBERON_0003221>) (of class uk.ac.manc
hester.cs.owl.owlapi.OWLObjectMinCardinalityImpl)
        at org.geneontology.jena.OWLtoRules$.org$geneontology$jena$OWLtoRules$$translateExpression(OWLtoRules.scala:264)

oddly, I can't replicate this with a smaller test example.