Transforming BEL documents into nanopublications
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README.md

BEL2nanopub

This code base transforms BEL documents into nanopublications. In contrast to the mapping to RDF defined by bel.rb (https://github.com/OpenBEL/bel.rb), we are here trying to use standard URIs of existing vocabularies and ontologies.

Execution

Maven has to be installed and the latest snapshot of nanopub-java:

$ git clone git@github.com:Nanopublication/nanopub-java.git
$ cd nanopub-java
$ mvn install

Before the transformation can be run, some resource files have to be downloaded and mapping tables have to be built:

$ scripts/download-files.sh
$ scripts/CreateIdTables.sh

Alternatively to the two commands above, pre-built tables can be downloaded from the release page (https://github.com/tkuhn/bel2nanopub/releases/) and placed in tables/generated.

Then BEL documents can be transformed as follows:

$ scripts/Bel2Nanopub.sh doc1.bel doc2.bel > output.nanopubs.trig

Run the examples:

$ scripts/run-examples.sh

Run the corpora provided by OpenBEL ("small corpus" and "large corpus"):

$ scripts/run-bel-corpora.sh

Examples

See the example directory.

Mapping

Below the mapping to RDF and the differences to the mapping by bel.rb are described.

Reification

Original BEL document:

DEFINE ANNOTATION CellStructure AS URL "http://resource.belframework.org/belframework/1.0/annotation/mesh-cell-structure.belanno"
SET CellStructure = "Cell Nucleus"
p(HGNC:XRCC5) => p(HGNC:WRN)

RDF as produced by bel.rb:

bel:p_HGNC_XRCC5_directlyIncreases_p_HGNC_WRN rdf:type belv:Statement ;
    belv:hasSubject bel:p_HGNC_XRCC5 ;
    belv:hasRelationship "directlyIncreases" ;
    belv:hasObject bel:p_HGNC_WRN ;
    rdfs:label "p(HGNC:XRCC5) -> p(HGNC:WRN)" ;
    belv:hasEvidence _:1 .
_:1 belv:hasAnnotation <http://www.openbel.org/bel/annotation/cell-structure/Cell%20Nucleus> .

In nanopubs using standard reification:

sub:_3 a rdf:Statement ;
    rdf:subject sub:_1 ;
    rdf:predicate belv:directlyIncreases ;
    rdf:object sub:_2 ;
    occursIn: mesh:D002467 .

Citation/Evidence

Original BEL document:

SET Citation = {"PubMed", "Some Journal 2004 Apr 1 234(5)","12345678"}
SET Evidence = "Some quoted evidence text."

RDF as produced by bel.rb:

bel:some_statement belv:hasEvidence _:1 .
_:1 belv:hasStatement bel:some_statement ;
    belv:hasCitation <http://bio2rdf.org/pubmed:12345678> ;
    belv:hasEvidenceText """Some quoted evidence text.""" .

In nanopubs using PROV:

sub:provenance {
    sub:_1 prov:value "Some quoted evidence text." ;
        prov:wasQuotedFrom pubmed:12345678 .
    sub:assertion prov:hadPrimarySource pubmed:12345678 ;
        prov:wasDerivedFrom sub:_1 .
}

Document Metadata

Original BEL document:

SET DOCUMENT Name = "My Document"
SET DOCUMENT Description = "This is an example"
SET DOCUMENT Version = "1.0"
SET DOCUMENT Copyright = "Copyright (c) 2014, John Doe"
SET DOCUMENT ContactInfo = "john.doe@example.org"
SET DOCUMENT Authors = "John Doe"
SET DOCUMENT Licenses = "Public Domain"

In nanopubs:

sub:provenance {
    sub:_1 dce:title "My Document" ;
        dce:description "This is an example" ;
        pav:version "1.0" ;
        dce:rights "Copyright (c) 2014, John Doe" ;
        pav:authoredBy sub:_2 ;
        dct:license "Public Domain" .

    sub:_2 rdfs:comment "john.doe@example.org" ;
        rdfs:label "John Doe" .

    sub:assertion prov:wasDerivedFrom sub:_1 .
}

Third-Party Vocabularies

The mapping to identifiers of third-party vocabularies is defined in this JSON file. The tables for the manual mappings are in the tables directory.

General BEL Relations

The general relations defined by BEL like 'directlyIncreases' are currently not mapped to other existing vocabularies or ontologies, and therefore we are using URIs in the BEL namespace (the same ones used by bel.rb, except for some cases where we had to make up new ones):

http://www.selventa.com/vocabulary/directlyIncreases

To Do

The following BEL language features are currently not yet properly mapped:

For these structures, made-up URIs in the BEL namespace are used at the moment. In the future, these should be mapped to standard ontologies and vocabularies too.

License

BEL2nanopub is free software under the MIT License. See LICENSE.txt.