bel_parser 1.0.0.alpha.50-java → 1.0.0.alpha.51-java

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Files changed (5) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/lib/bel_parser.rb +3 -0
  4. data/lib/bel_parser/resources.rb +201 -0
  5. metadata +2 -1
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data/VERSION CHANGED
@@ -1 +1 @@
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- 1.0.0.alpha.50
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+ 1.0.0.alpha.51
data/lib/bel_parser.rb CHANGED
@@ -16,6 +16,9 @@ require 'bel_parser/ast_filter'
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  # Language; version-independent classes
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  require 'bel_parser/language'
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+ # BEL Resource support
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+ require 'bel_parser/resources'
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+
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  # BEL Expression support
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  require 'bel_parser/expression'
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data/lib/bel_parser/resources.rb ADDED
@@ -0,0 +1,201 @@
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+ require_relative 'expression/model/namespace'
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+
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+ module BELParser
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+ module Resources
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+ BASE_URL = 'http://resource.belframework.org/belframework/latest-release'
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+ DEFAULT_NAMESPACES = {
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+ 'AFFX' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'AFFX',
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+ 'http://www.openbel.org/bel/namespace/affy-probeset',
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+ "#{BASE_URL}/namespace/affy-probeset-ids.belns"),
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+ 'CHEBI' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'CHEBI',
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+ 'http://www.openbel.org/bel/namespace/chebi',
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+ "#{BASE_URL}/namespace/chebi.belns"),
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+ 'CHEBIID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'CHEBIID',
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+ 'http://www.openbel.org/bel/namespace/chebi',
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+ "#{BASE_URL}/namespace/chebi-ids.belns"),
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+ 'DEFAULT' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'DEFAULT',
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+ 'http://www.openbel.org/bel/namespace/default',
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+ "#{BASE_URL}/namespace/default-bel-namespace.belns"),
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+ 'DO' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'DO',
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+ 'http://www.openbel.org/bel/namespace/disease-ontology',
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+ "#{BASE_URL}/namespace/disease-ontology.belns"),
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+ 'DOID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'DOID',
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+ 'http://www.openbel.org/bel/namespace/disease-ontology',
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+ "#{BASE_URL}/namespace/disease-ontology-ids.belns"),
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+ 'EGID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'EGID',
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+ 'http://www.openbel.org/bel/namespace/entrez-gene',
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+ "#{BASE_URL}/namespace/entrez-gene-ids.belns"),
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+ 'GOBP' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'GOBP',
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+ 'http://www.openbel.org/bel/namespace/go-biological-process',
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+ "#{BASE_URL}/namespace/go-biological-process.belns"),
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+ 'GOBPID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'GOBPID',
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+ 'http://www.openbel.org/bel/namespace/go-biological-process',
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+ "#{BASE_URL}/namespace/go-biological-process-ids.belns"),
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+ 'GOCC' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'GOCC',
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+ 'http://www.openbel.org/bel/namespace/go-cellular-component',
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+ "#{BASE_URL}/namespace/go-cellular-component.belns"),
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+ 'GOCCID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'GOCCID',
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+ 'http://www.openbel.org/bel/namespace/go-cellular-component',
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+ "#{BASE_URL}/namespace/go-cellular-component-ids.belns"),
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+ 'HGNC' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'HGNC',
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+ 'http://www.openbel.org/bel/namespace/hgnc-human-genes',
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+ "#{BASE_URL}/namespace/hgnc-human-genes.belns"),
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+ 'MESHCS' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHCS',
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+ 'http://www.openbel.org/bel/namespace/mesh-cellular-structures',
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+ "#{BASE_URL}/namespace/mesh-cellular-structures.belns"),
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+ 'MESHCSID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHCSID',
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+ 'http://www.openbel.org/bel/namespace/mesh-cellular-structures',
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+ "#{BASE_URL}/namespace/mesh-cellular-structures-ids.belns"),
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+ 'MESHC' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHC',
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+ 'http://www.openbel.org/bel/namespace/mesh-chemicals',
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+ "#{BASE_URL}/namespace/mesh-chemicals.belns"),
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+ 'MESHCID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHCID',
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+ 'http://www.openbel.org/bel/namespace/mesh-chemicals',
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+ "#{BASE_URL}/namespace/mesh-chemicals-ids.belns"),
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+ 'MESHD' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHD',
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+ 'http://www.openbel.org/bel/namespace/mesh-diseases',
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+ "#{BASE_URL}/namespace/mesh-diseases.belns"),
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+ 'MESHDID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHDID',
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+ 'http://www.openbel.org/bel/namespace/mesh-diseases',
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+ "#{BASE_URL}/namespace/mesh-diseases-ids.belns"),
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+ 'MESHPP' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHPP',
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+ 'http://www.openbel.org/bel/namespace/mesh-processes',
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+ "#{BASE_URL}/namespace/mesh-processes.belns"),
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+ 'MESHPPID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MESHPPID',
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+ 'http://www.openbel.org/bel/namespace/mesh-processes',
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+ "#{BASE_URL}/namespace/mesh-processes-ids.belns"),
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+ 'MGI' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MGI',
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+ 'http://www.openbel.org/bel/namespace/mgi-mouse-genes',
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+ "#{BASE_URL}/namespace/mgi-mouse-genes.belns"),
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+ 'RGD' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'RGD',
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+ 'http://www.openbel.org/bel/namespace/rgd-rat-genes',
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+ "#{BASE_URL}/namespace/rgd-rat-genes.belns"),
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+ 'SCHEM' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'SCHEM',
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+ 'http://www.openbel.org/bel/namespace/selventa-legacy-chemicals',
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+ "#{BASE_URL}/namespace/selventa-legacy-chemicals.belns"),
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+ 'SCOMP' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'SCOMP',
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+ 'http://www.openbel.org/bel/namespace/selventa-named-complexes',
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+ "#{BASE_URL}/namespace/selventa-named-complexes.belns"),
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+ 'SDIS' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'SDIS',
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+ 'http://www.openbel.org/bel/namespace/selventa-legacy-diseases',
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+ "#{BASE_URL}/namespace/selventa-legacy-diseases"),
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+ 'SFAM' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'SFAM',
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+ 'http://www.openbel.org/bel/namespace/selventa-protein-families',
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+ "#{BASE_URL}/namespace/selventa-protein-families.belns"),
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+ 'SP' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'SP',
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+ 'http://www.openbel.org/bel/namespace/swissprot',
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+ "#{BASE_URL}/namespace/swissprot.belns"),
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+ 'SPID' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'SPID',
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+ 'http://www.openbel.org/bel/namespace/swissprot',
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+ "#{BASE_URL}/namespace/swissprot-ids.belns"),
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+ }
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+
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+ DEFAULT_ANNOTATIONS = {
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+ 'Anatomy' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'Anatomy',
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+ 'http://www.openbel.org/bel/namespace/uberon',
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+ "#{BASE_URL}/annotation/anatomy.belanno"),
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+ 'Cell' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'Cell',
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+ 'http://www.openbel.org/bel/namespace/cell-ontology',
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+ "#{BASE_URL}/annotation/cell.belanno"),
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+ 'CellLine' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'CellLine',
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+ 'http://www.openbel.org/bel/namespace/cell-line-ontology',
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+ "#{BASE_URL}/annotation/cell-line.belanno"),
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+ 'Disease' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'Disease',
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+ 'http://www.openbel.org/bel/namespace/disease-ontology',
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+ "#{BASE_URL}/annotation/disease.belanno"),
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+ 'ExperimentalFactor' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'ExperimentalFactor',
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+ 'http://www.openbel.org/bel/namespace/experimental-factor-ontology',
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+ "#{BASE_URL}/annotation/disease.belanno"),
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+ 'MeSHAnatomy' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MeSHAnatomy',
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+ 'http://www.openbel.org/bel/namespace/mesh-anatomy',
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+ "#{BASE_URL}/annotation/mesh-anatomy.belanno"),
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+ 'MeSHDisease' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'MeSHDisease',
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+ 'http://www.openbel.org/bel/namespace/mesh-diseases',
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+ "#{BASE_URL}/annotation/mesh-diseases.belanno"),
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+ 'Species' =>
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+ BELParser::Expression::Model::Namespace.new(
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+ 'Species',
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+ 'http://www.openbel.org/bel/namespace/ncbi-taxonomy',
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+ "#{BASE_URL}/annotation/species-taxonomy-id.belanno")
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+ }
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+
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+ def self.included(another_class)
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+ DEFAULT_ANNOTATIONS.each do |keyword, annotation|
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+ another_class.const_set(keyword.to_sym, annotation)
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+ end
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+ DEFAULT_NAMESPACES.each do |keyword, namespace|
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+ another_class.const_set(keyword.to_sym, namespace)
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+ end
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+ end
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+ end
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+ end
metadata CHANGED
@@ -1,7 +1,7 @@
1
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  --- !ruby/object:Gem::Specification
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  name: bel_parser
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  version: !ruby/object:Gem::Version
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- version: 1.0.0.alpha.50
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+ version: 1.0.0.alpha.51
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  platform: java
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  authors:
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  - Anthony Bargnesi
@@ -363,6 +363,7 @@ files:
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  - lib/bel_parser/resource/resource_url_reader.rb
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  - lib/bel_parser/resource/sparql_reader.rb
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  - lib/bel_parser/resource/value.rb
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+ - lib/bel_parser/resources.rb
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  - lib/bel_parser/script.rb
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  - lib/bel_parser/script/apply_resource_uri.rb
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  - lib/bel_parser/script/filter.rb