Are lobsters spiders? - Finding taxonomy relations using linked data

This repository is a school project for the semantic web course. The goal is to find a method for answering a question that is easy for a human, but difficult for a computer: are lobsters spiders?

Our solution and implementation is described in are_lobsters_spiders.pdf.

Prerequisites

• Docker
• The NCBI taxonomy ontology: http://purl.obolibrary.org/obo/ncbitaxon.owl (unless the SPARQL endpoint on http://134.209.17.65:3030/species/query is still running)

Creating the SPARQL endpoint

This part can be skipped if the SPARQL endpoint on http://134.209.17.65:3030/species/query is available.

If the endpoint is not available you have to either create an enpoint using the Docker image, or to build the Docker image yourself.

Using the Docker image

docker run --name ncbi_taxon_endpoint -p 3030:3030 skeggib/ncbi_taxon_endpoint

Building the Docker image

wget http://purl.obolibrary.org/obo/ncbitaxon.owl
docker run --name fuseki-data -v /fuseki busybox
docker run -d --name fuseki -p 3030:3030 --volumes-from fuseki-data stain/jena-fuseki
docker logs fuseki

• Go to http://<your_ip>:3030/
• Enter the credentials displayed in the fuseki logs
• Go to 'manage datasets'
• Click on 'add new dataset'
• Enter the name 'species' and check 'Persistent'

docker stop fuseki
docker run --volumes-from fuseki-data -v $(pwd):/staging \
    stain/jena-fuseki ./load.sh species ncbitaxon.owl

There are approximately 12 million triples to add so it may take a while.

docker start fuseki

Building and running the tool

If a SPARQL endpoint other than http://134.209.17.65:3030/species/query is used: replace the URL in AreLobstersSpiders/Program.cs:18.

cd AreLobstersSpiders

docker build . -t are_lobsters_spiders

docker run --rm are_lobsters_spiders isa DBpedia_URI_A DBpedia_URI_B

Some examples:

docker run --rm are_lobsters_spiders isa \
    http://dbpedia.org/resource/Lobster \
    http://dbpedia.org/resource/Spider

docker run --rm are_lobsters_spiders isa \
    http://dbpedia.org/resource/Philaeus \
    http://dbpedia.org/resource/Spider

docker run --rm are_lobsters_spiders isa \
    http://dbpedia.org/resource/Dog \
    http://dbpedia.org/resource/Cat

docker run --rm are_lobsters_spiders isa \
    http://dbpedia.org/resource/Dog \
    http://dbpedia.org/resource/Mammal