Version 0.7.0

Fixed

RDF translation allows for RDF prefixes to be used. Default RDF prefixes are provided (Issue #69).

URI prefixes can now be configured when translating BEL to RDF.

The expected format uses YAML mappings. For example by default the following mapping is used:

belr: 'http://www.openbel.org/bel/'
belv: 'http://www.openbel.org/vocabulary/'
bele: 'http://www.openbel.org/evidence/'
pubmed: 'http://bio2rdf.org/pubmed:'
rdfs: 'http://www.w3.org/2000/01/rdf-schema#'
rdf: 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'

You can provide your own RDF prefix file by providing options to bel2rdf.rb and bel translate. Keep in mind that RDF formats like NTriples and NQuads always write the full URIs.

bel2rdf.rb --bel file.bel --rdf-prefix-file prefix_file.yml --format turtle

bel translate --input-file file.bel --to-option rdf_prefix_file=prefix_file.yml bel turtle

Added

Annotation and Namespace definitions can now be remapped using a YAML file (Issue #92).

Annotation and Namespace definitions can now be remapped during translation to RDF. This is most useful when converting OpenBEL resource URIs to something more well-known (e.g. identifiers.org).

A remap file uses YAML for its format. You can generate an example using the command:

bel remapfile

Then provide the remap file when translating to RDF:

bel2rdf.rb --bel file.bel --remap-file remap_file.yml --format turtle

bel translate --input-file file.bel --to-option remap_file=remap_file.yml bel turtle

The following is an example remap file providing both annotation and namespace remaps:

namespaces:
  - remap:
      from:
        prefix:  "EGID"
        url:     "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns"
      to:
        prefix:  "EGID"
        url:     "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns"
        rdf_uri: "http://identifiers.org/ncbigene/"
  - remap:
      from:
        prefix:  "MESHD"
        url:     "http://resource.belframework.org/belframework/20131211/namespace/mesh-diseases.belns"
      to:
        prefix:  "MESHD"
        url:     "http://resource.belframework.org/belframework/20131211/namespace/mesh-diseases.belns"
        rdf_uri: "http://identifiers.org/meshd/"
annotations:
  - remap:
      from:
        keyword:  "Anatomy"
        type:     "url"
        domain:   "http://resource.belframework.org/belframework/20131211/annotation/anatomy.belanno"
      to:
        keyword:  "Anatomy"
        type:     "url"
        domain:   "http://resource.belframework.org/belframework/20131211/annotation/anatomy.belanno"
        rdf_uri:  "http://identifiers.org/anatomy/"
  - remap:
      from:
        keyword:  "TextLocation"
        type:     "list"
        domain:
          - Abstract
          - Results
          - Legend
          - Review
      to:
        keyword: "TextLocation"
        type:    "pattern"
        domain:  "Value[0-9]+"
        rdf_uri:  "http://identifiers.org/text-location/"

Contributors

• Alexandr Isaenco
• Rumil Baybikov
• Julia Kozlovsky