bel_parser 1.0.0.alpha.50 → 1.0.0.alpha.51
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/bel_parser/resources.rb +201 -0
- data/lib/bel_parser.rb +3 -0
- metadata +2 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 6b7ed1e38515df703152be71136d20446d344d9f
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data.tar.gz: 3d98624b6c65fa781a23020ec81680429a876809
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 339a699110491f75d3e664fbfa003f22317fc6c04206376306d8e180a505b66214ac265eb77c4b4ae3956f077843d5f0d3cd68c8613acc3a861cc159011b2cc8
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data.tar.gz: 65009fbf18a0751b1754d5338335e022f8194796e34ffa7f0e6de119e5be342cf8734a58cc60844fb2cfcdf6599b593f612b01f2888460bf56c4179233d7df6c
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
1.0.0.alpha.
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+
1.0.0.alpha.51
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@@ -0,0 +1,201 @@
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require_relative 'expression/model/namespace'
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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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10
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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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12
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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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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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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
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data/lib/bel_parser.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: bel_parser
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3
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version: !ruby/object:Gem::Version
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4
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-
version: 1.0.0.alpha.
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version: 1.0.0.alpha.51
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platform: ruby
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6
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authors:
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7
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- Anthony Bargnesi
|
@@ -349,6 +349,7 @@ files:
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349
349
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- lib/bel_parser/resource/resource_url_reader.rb
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350
350
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- lib/bel_parser/resource/sparql_reader.rb
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351
351
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- lib/bel_parser/resource/value.rb
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352
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+
- lib/bel_parser/resources.rb
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352
353
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- lib/bel_parser/script.rb
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353
354
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- lib/bel_parser/script/apply_resource_uri.rb
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354
355
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- lib/bel_parser/script/filter.rb
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