Need to describe all Bio2RDF entities

[micheldumontier]

Currently there is no support for entity resolution for arbitrary entities that appear in Bio2RDF datasets. Consider the statistics page for affymetrix probesets http://download.bio2rdf.org/release/3/html/affymetrix.html

The first type http://bio2rdf.org/wormbase_vocabulary:Resource does not resolve even though WormBase is part of the Bio2RDF distribution.

The second type http://bio2rdf.org/uniprot_vocabulary:Resource does not resolve.

the web application should send out a federated query to SPARQL endpoints to gather triples to describe these terms.

@VEmonet

[vemonet]

bio2rdf.org now supporting every dataset that is part of the Bio2RDF release 2 or 3.

Actually working on bio2rdf.org resolving any arbitrary entity.

[fbelleau]

@micheldumontier @VEmonet

I have deployed a first version of Talend implementation of the queryAll service based on the statistics of the release 3.

http://queryall.rest.bio2rdf.org/

The project in beta mode is here

https://github.com/fbelleau/bio2rdf-queryall

Michel infirm Vincent of the needed modification, then he will be possible to integrate the resolution of the 400 namespace URIs into Bio2RRDF main REST service.

[vemonet]

For Uniprot you were trying to resolve http://bio2rdf.org/uniprot_vocabulary:Resource But seems like you are using UniProt URI : http://purl.uniprot.org/core/Resource http://uniprot.bio2rdf.org/describe/?url=http%3A%2F%2Fpurl.uniprot.org%2Fcore%2FResource&sid=99

I have begun to implement the "QueryAll" like service in beta.bio2rdf.org For example try to resolve some URI : curl -i -H 'Accept: application/rdf+xml' http://beta.bio2rdf.org/genbank:BC149752 curl -i -H 'Accept: application/rdf+xml' http://beta.bio2rdf.org/ec:2.7.1.1

There might be some problems with some namespaces, feel free to point it out !

And note that when asking html through content-negociation it returns only the Virtuoso fct describe page for the entity (if it exists)

[micheldumontier]

Vincent, the redirection to the uniprot endpoint is on the bio2rdf side (not mine). Still, asking for curl -i -H 'Accept: application/rdf+xml' http://bio2rdf.org/wormbase_vocabulary:Resource does not federate over the lsr endpoint, where there is an additional "owl:Class" type assertion.

[micheldumontier]

What's the status on this item?

[vemonet]

Update of the REST service : to resolve a bio2rdf URI the service send a federated query to every bio2rdf triplestore to describe this URI Deployed on bio2rdf.org

But now the service don't redirect to the virtuoso page when html is asked

[vemonet]

http://answers.semanticweb.com/questions/11990/what-html-templating-systems-exist-for-rdf

ideas for the html rendering to be done

[vemonet]

http://bio2rdf.org/hgnc:4945

Found a bug due to :

com.hp.hpl.jena.shared.BadURIException: Only well-formed absolute URIrefs can be included in RDF/XML output: <http://> Code: 57/REQUIRED_COMPONENT_MISSING in HOST: A component that is required by the scheme is missing.

This error happens only when Jena try to write the RDF in the RDF/XML format. No problem when it's the n-triple or turtle format. I think that Jena is more strict with the URI formation when it writes in RDF/XML

[vemonet]

The Jena error is triggered by this triple :

<http://bio2rdf.org/hgnc:4945> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://hgnc.bio2rdf.org> .

[vemonet]

Found out where the problem comes from : According to Jena http://hgnc.bio2rdf.org is not a valid URI http://hgnc.bio2rdf.org/ is a valid URI.

[vemonet]

It comes from uniprot endpoint Note that I was using the latest version of Jena (http://mvnrepository.com/artifact/org.apache.jena/apache-jena-libs/2.11.2) And here is the code I was using to convert the triple :

String rdfInput = "<http://bio2rdf.org/hgnc:4945> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://hgnc.bio2rdf.org/> .";
Reader reader = new StringReader(rdfInput);
Writer writer = new StringWriter();
Model model = ModelFactory.createDefaultModel();
model.read(reader,  "default", "N-TRIPLE"); 
model.write(writer, "RDF/XML"); 
System.out.println(writer.toString());