Issue92: map annotation/namespace definitions from external yml file

[rumilbaybikov]

No description provided.

[abargnesi]

It looks like we have duplicate options between --resource-override and --rdf-prefix-file.

Maybe a better name is --resource-mapping-file?

[rumilbaybikov]

then to avoid duplicates we could define 1 common yml file with structure below:

prefixes:
belr: 'http://www.openbel.org/bel/'
belv: 'http://www.openbel.org/vocabulary/'
...
namespaces:
remap:
from:
to:
...
annotations:
remap:
from:
keyword: "Anatomy"
type: "url"
domain: "http://example.com/anatomy.belanno"
to:
keyword: "Anatomy"
type: "url"
domain: "http://example.com/anatomy.belanno/anatomy.belanno"
rdf_uri: "http://identifiers.org/anatomy/"

[abargnesi]

This is looking good. Nice work! 🎉

The tests all pass, but I noticed one issue when I try to translate BEL Script to Turtle when using an RDF prefix file.

I ran this test from the root of the project using the BEL Script file ./test/resources/small_corpus.bel and the rdf prefix file examples/resource-mapping.yml.

# Using bel2rdf.rb
bin/bel2rdf.rb --bel ./test/resources/small_corpus.bel --format turtle --rdf-prefix-file examples/resource-mapping.yml

# Using "bel translate"
bel translate --input-file ./test/resources/small_corpus.bel --to-option rdf_prefix_file=examples/resource-mapping.yml bel turtle

The turtle includes @prefix directives with what looks like Ruby code:

@prefix annotations: <[{"remap"=>{"from"=>{"keyword"=>"Anatomy", "type"=>"url", "domain"=>"http://resource.belframework.org/belframework/20150611/annotation/anatomy.belanno"}, "to"=>{"keyword"=>"Anatomy", "type"=>"url", "domain"=>"http://resource.belframework.org/belframework/20150611/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/"}}}]> .
@prefix namespaces: <[{"remap"=>{"from"=>{"prefix"=>"HGNC", "url"=>"http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns"}, "to"=>{"prefix"=>"HGNC", "url"=>"http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns", "rdf_uri"=>"http://identifiers.org/hgnc/"}}}, {"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/20150611/namespace/mesh-diseases.belns"}, "to"=>{"prefix"=>"MESHD", "url"=>"http://resource.belframework.org/belframework/20150611/namespace/mesh-diseases.belns", "rdf_uri"=>"http://identifiers.org/meshd/"}}}]> .

This error looks like the wrong object type is being set as an RDF prefix.

[abargnesi]

Actually, I was sending a resource override file and not an RDF prefix file. I think that is why I got this behavior.

When I run the following bel translate it looks correct:

bin/bel translate --input-file test/resources/small_corpus.bel -t rdf_prefix_file=test/resources/prefix_file.yml bel turtle

[abargnesi]

It looks like we are missing a resource_override option in the bel translate help information. That's a minor point we can update after.