biointerchange 1.0.1 → 1.0.2

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Files changed (54) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +2 -4
  3. data/Gemfile +2 -3
  4. data/README.md +36 -22
  5. data/VERSION +1 -1
  6. data/examples/Felis_catus.gvf.gz +0 -0
  7. data/examples/Felis_catus_incl_consequences.vcf.gz +0 -0
  8. data/generators/rdfxml.rb +1 -1
  9. data/generators/tsv2rubyclass.rb +31 -0
  10. data/lib/biointerchange/core.rb +17 -5
  11. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +591 -137
  12. data/lib/biointerchange/genomics/gff3_reader.rb +16 -3
  13. data/lib/biointerchange/genomics/gvf_reader.rb +1 -1
  14. data/lib/biointerchange/genomics/vcf_feature.rb +46 -0
  15. data/lib/biointerchange/genomics/vcf_feature_set.rb +14 -0
  16. data/lib/biointerchange/genomics/vcf_reader.rb +238 -0
  17. data/lib/biointerchange/gfvo.rb +689 -553
  18. data/lib/biointerchange/life_science_registry.rb +3595 -0
  19. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +33 -35
  20. data/lib/biointerchange/writer.rb +11 -16
  21. data/make.sh +4 -0
  22. data/spec/exceptions_spec.rb +1 -7
  23. data/spec/gff3_rdfwriter_spec.rb +2 -16
  24. data/spec/gvf_rdfwriter_spec.rb +2 -19
  25. data/spec/phylogenetics_spec.rb +1 -13
  26. data/spec/text_mining_pdfx_xml_reader_spec.rb +1 -13
  27. data/spec/text_mining_pubannos_json_reader_spec.rb +1 -14
  28. data/spec/text_mining_rdfwriter_spec.rb +8 -19
  29. data/test.sh +4 -0
  30. data/web/about.html +10 -14
  31. data/web/api.html +11 -13
  32. data/web/bootstrap/css/bootstrap-theme.css +347 -0
  33. data/web/bootstrap/css/bootstrap-theme.css.map +1 -0
  34. data/web/bootstrap/css/bootstrap-theme.min.css +7 -0
  35. data/web/bootstrap/css/bootstrap.css +4764 -4603
  36. data/web/bootstrap/css/bootstrap.css.map +1 -0
  37. data/web/bootstrap/css/bootstrap.min.css +6 -8
  38. data/web/bootstrap/fonts/glyphicons-halflings-regular.eot +0 -0
  39. data/web/bootstrap/fonts/glyphicons-halflings-regular.svg +229 -0
  40. data/web/bootstrap/fonts/glyphicons-halflings-regular.ttf +0 -0
  41. data/web/bootstrap/fonts/glyphicons-halflings-regular.woff +0 -0
  42. data/web/bootstrap/js/bootstrap.js +1372 -1448
  43. data/web/bootstrap/js/bootstrap.min.js +5 -5
  44. data/web/cli.html +14 -28
  45. data/web/index.html +15 -33
  46. data/web/ontologies.html +1089 -945
  47. data/web/webservices.html +12 -14
  48. metadata +24 -27
  49. data/lib/biointerchange/gff3o.rb +0 -525
  50. data/lib/biointerchange/gvf1o.rb +0 -1354
  51. data/web/bootstrap/css/bootstrap-responsive.css +0 -1040
  52. data/web/bootstrap/css/bootstrap-responsive.min.css +0 -9
  53. data/web/bootstrap/img/glyphicons-halflings-white.png +0 -0
  54. data/web/bootstrap/img/glyphicons-halflings.png +0 -0
data/web/webservices.html CHANGED
@@ -9,13 +9,13 @@
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  <!-- Le styles -->
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  <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
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+ <link href="bootstrap/css/bootstrapi-theme.min.css" rel="stylesheet">
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  <style type="text/css">
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  body {
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  padding-top: 60px;
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  padding-bottom: 40px;
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  }
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  </style>
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- <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
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  <script src="bootstrap/js/jquery-1.8.1.min.js"></script>
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  <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
@@ -29,26 +29,24 @@
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  <body>
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  <a href="https://github.com/BioInterchange/BioInterchange"><img style="z-index: 5000; position: fixed; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_gray_6d6d6d.png" alt="Fork me on GitHub"></a>
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+
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  <div class="navbar navbar-inverse navbar-fixed-top">
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- <div class="navbar-inner">
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- <div class="container">
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- <a class="brand" href="index.html">BioInterchange</a>
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- <ul class="nav">
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- <li><a href="cli.html">Shell Tool</a></li>
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- <li class="active"><a href="webservices.html">Web-Services</a></li>
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- <li><a href="api.html">API</a></li>
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- <li><a href="ontologies.html">Ontologies</a></li>
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- <li><a href="about.html">About</a></li>
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- </ul>
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- </div>
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+ <div class="container-fluid">
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+ <a class="navbar-brand" href="index.html">BioInterchange</a>
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+ <ul class="nav navbar-nav">
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+ <li><a href="cli.html">Shell Tool</a></li>
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+ <li class="active"><a href="webservices.html">Web-Services</a></li>
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+ <li><a href="api.html">API</a></li>
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+ <li><a href="ontologies.html">Ontologies</a></li>
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+ <li><a href="about.html">About</a></li>
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+ </ul>
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  </div>
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  </div>
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-
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  <div class="container">
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  <!-- Example row of columns -->
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  <div class="row">
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- <div class="span12">
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+ <div class="col-md-12">
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  <h1>Web-Services</h1>
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  <p>Two query points to access BioInterchange are provided on the internet:
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  <ol>
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: biointerchange
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.1
4
+ version: 1.0.2
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  platform: ruby
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  authors:
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  - Joachim Baran
@@ -12,7 +12,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-08-19 00:00:00.000000000 Z
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+ date: 2014-10-27 00:00:00.000000000 Z
16
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rdf
@@ -20,14 +20,14 @@ dependencies:
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  requirements:
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  - - '>='
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  - !ruby/object:Gem::Version
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- version: 0.3.4.1
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+ version: 1.1.4.3
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - '>='
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  - !ruby/object:Gem::Version
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- version: 0.3.4.1
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+ version: 1.1.4.3
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  - !ruby/object:Gem::Dependency
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  name: json
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  requirement: !ruby/object:Gem::Requirement
@@ -62,14 +62,14 @@ dependencies:
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  requirements:
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  - - '>='
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  - !ruby/object:Gem::Version
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- version: 2.3.2
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+ version: 2.3.6
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - '>='
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  - !ruby/object:Gem::Version
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- version: 2.3.2
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+ version: 2.3.6
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !ruby/object:Gem::Requirement
@@ -126,20 +126,6 @@ dependencies:
126
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  - - ~>
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  - !ruby/object:Gem::Version
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  version: 1.8.4
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- - !ruby/object:Gem::Dependency
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- name: bio
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- requirement: !ruby/object:Gem::Requirement
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- requirements:
133
- - - '>='
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- - !ruby/object:Gem::Version
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- version: 1.4.2
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- type: :development
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- prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - '>='
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- - !ruby/object:Gem::Version
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- version: 1.4.2
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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  requirement: !ruby/object:Gem::Requirement
@@ -174,6 +160,8 @@ files:
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  - VERSION
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  - bin/biointerchange
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  - examples/BovineGenomeChrX.gff3.gz
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+ - examples/Felis_catus.gvf.gz
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+ - examples/Felis_catus_incl_consequences.vcf.gz
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  - examples/ReaderModelWriterSequenceDiagram.graffle
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  - examples/ReaderModelWriterSequenceDiagram.png
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  - examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz
@@ -194,6 +182,7 @@ files:
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  - generators/make_supplement_releases.rb
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  - generators/pythonify.rb
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  - generators/rdfxml.rb
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+ - generators/tsv2rubyclass.rb
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  - lib/biointerchange.rb
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  - lib/biointerchange/cdao.rb
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  - lib/biointerchange/core.rb
@@ -210,10 +199,12 @@ files:
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  - lib/biointerchange/genomics/gvf_pragmas.rb
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  - lib/biointerchange/genomics/gvf_reader.rb
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  - lib/biointerchange/genomics/locations.rb
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- - lib/biointerchange/gff3o.rb
202
+ - lib/biointerchange/genomics/vcf_feature.rb
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+ - lib/biointerchange/genomics/vcf_feature_set.rb
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+ - lib/biointerchange/genomics/vcf_reader.rb
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  - lib/biointerchange/gfvo.rb
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  - lib/biointerchange/goxref.rb
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- - lib/biointerchange/gvf1o.rb
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+ - lib/biointerchange/life_science_registry.rb
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  - lib/biointerchange/model.rb
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  - lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb
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  - lib/biointerchange/phylogenetics/newick_reader.rb
@@ -232,6 +223,7 @@ files:
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  - lib/biointerchange/textmining/text_mining_rdf_ntriples.rb
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  - lib/biointerchange/textmining/text_mining_reader.rb
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  - lib/biointerchange/writer.rb
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+ - make.sh
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  - spec/exceptions_spec.rb
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  - spec/gff3_rdfwriter_spec.rb
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  - spec/gvf_rdfwriter_spec.rb
@@ -262,15 +254,20 @@ files:
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  - supplemental/python/biointerchange/sofa.py
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  - supplemental/python/example.py
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  - supplemental/python/setup.py
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+ - test.sh
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  - web/about.html
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  - web/api.html
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  - web/biointerchange.js
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- - web/bootstrap/css/bootstrap-responsive.css
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- - web/bootstrap/css/bootstrap-responsive.min.css
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+ - web/bootstrap/css/bootstrap-theme.css
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+ - web/bootstrap/css/bootstrap-theme.css.map
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+ - web/bootstrap/css/bootstrap-theme.min.css
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  - web/bootstrap/css/bootstrap.css
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+ - web/bootstrap/css/bootstrap.css.map
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  - web/bootstrap/css/bootstrap.min.css
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- - web/bootstrap/img/glyphicons-halflings-white.png
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- - web/bootstrap/img/glyphicons-halflings.png
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+ - web/bootstrap/fonts/glyphicons-halflings-regular.eot
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+ - web/bootstrap/fonts/glyphicons-halflings-regular.svg
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+ - web/bootstrap/fonts/glyphicons-halflings-regular.ttf
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+ - web/bootstrap/fonts/glyphicons-halflings-regular.woff
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  - web/bootstrap/js/bootstrap.js
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  - web/bootstrap/js/bootstrap.min.js
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  - web/bootstrap/js/jquery-1.8.1.min.js
@@ -307,7 +304,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.0.5
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+ rubygems_version: 2.0.3
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  signing_key:
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  specification_version: 4
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  summary: An open source framework for transforming heterogeneous data formats into
data/lib/biointerchange/gff3o.rb DELETED
@@ -1,525 +0,0 @@
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- require 'rdf'
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- module BioInterchange
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-
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- class GFF3O
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-
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- # Establishes the landmark (e.g. a chromosome) on which a feature is located.
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- # (http://www.biointerchange.org/gff3o#GFF3_0004)
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- def self.seqid
9
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004')
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- end
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-
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- # Either:
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- # Strand of the feature.
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- # (http://www.biointerchange.org/gff3o#GFF3_0010)
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- # Or:
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- # Strand of a target -- if applicable.
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- # (http://www.biointerchange.org/gff3o#GFF3_0045)
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- def self.strand
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- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0045') ]
20
- end
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-
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- # Tag name/value pair attributes of a feature that are not covered by object-/data-properties of the ontology. Tags that are represented as object-/data-properties are: ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular
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- # (http://www.biointerchange.org/gff3o#GFF3_0012)
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- def self.attributes
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0012')
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- end
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-
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- # Link out to the parent feature.
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- # (http://www.biointerchange.org/gff3o#GFF3_0014)
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- def self.parent
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0014')
32
- end
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-
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- # Relationship that describes which features belong to a feature set.
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- # (http://www.biointerchange.org/gff3o#GFF3_0015)
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- def self.contains
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0015')
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- end
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-
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- # Either:
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- # FALDO "Region" instance replacement for a feature's start, stop, strand properties.
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- # (http://www.biointerchange.org/gff3o#GFF3_0021)
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- # Or:
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- # FALDO "Region" instance replacement for a target's start, stop, strand properties.
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- # (http://www.biointerchange.org/gff3o#GFF3_0050)
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- def self.region
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- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0021'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0050') ]
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- end
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-
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- # NCBI Taxonomy Ontology "NCBITaxon_1" (or sub-classes) instance that denotes the species for a feature set.
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- # (http://www.biointerchange.org/gff3o#GFF3_0023)
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- def self.species
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0023')
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- end
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-
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- # Either:
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- # Properties that are directly associated with Set class instances.
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- # (http://www.biointerchange.org/gff3o#GFF3_0025)
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- # Or:
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- # Properties that are directly associated with Set class instances.
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- # (http://www.biointerchange.org/gff3o#GFF3_0027)
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- def self.set_properties
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- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') ]
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- end
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-
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- # Either:
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- # Properties that are directly associated with Feature class instances.
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- # (http://www.biointerchange.org/gff3o#GFF3_0026)
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- # Or:
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- # Properties that are directly associated with Feature class instances.
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- # (http://www.biointerchange.org/gff3o#GFF3_0028)
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- def self.feature_properties
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- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') ]
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- end
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-
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- # Identifies the target that the features aligns to.
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- # (http://www.biointerchange.org/gff3o#GFF3_0039)
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- def self.target
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039')
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- end
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-
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- # Either:
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- # Properties that are directly associated with Target class instances.
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- # (http://www.biointerchange.org/gff3o#GFF3_0044)
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- # Or:
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- # Properties that are directly associated with Target class instances.
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- # (http://www.biointerchange.org/gff3o#GFF3_0040)
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- def self.target_properties
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- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') ]
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- end
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-
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- # Describes a temporal relationship between two features, where the object denotes the subjects origin.
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- # (http://www.biointerchange.org/gff3o#GFF3_0047)
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- def self.derives_from
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0047')
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- end
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-
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- # Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
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- # (http://www.biointerchange.org/gff3o#GFF3_0056)
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- def self.feature_ontology
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0056')
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- end
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-
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- # A free text qualifier that describes the algorithm or operating procedure that generated this feature. For example, the name of the software that generated this feature or a database name.
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- # (http://www.biointerchange.org/gff3o#GFF3_0005)
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- def self.source
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005')
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- end
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-
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- # Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
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- # (http://www.biointerchange.org/gff3o#GFF3_0006)
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- def self.type
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006')
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- end
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-
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- # Either:
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- # Start coordinate of the feature on the seqid landmark.
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- # (http://www.biointerchange.org/gff3o#GFF3_0007)
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- # Or:
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- # Start coordinate of the target.
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- # (http://www.biointerchange.org/gff3o#GFF3_0042)
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- # Or:
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- # Genomic start coordinate of the landmark.
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- # (http://www.biointerchange.org/gff3o#GFF3_0054)
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- def self.start
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- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0054') ]
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- end
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-
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- # Either:
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- # End coordinate of the feature on the seqid landmark.
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- # (http://www.biointerchange.org/gff3o#GFF3_0008)
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- # Or:
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- # End coordinate of the target.
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- # (http://www.biointerchange.org/gff3o#GFF3_0043)
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- # Or:
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- # Genomic end coordinate of the landmark.
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- # (http://www.biointerchange.org/gff3o#GFF3_0055)
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- def self.end
139
- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') ]
140
- end
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-
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- # Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
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- # (http://www.biointerchange.org/gff3o#GFF3_0009)
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- def self.score
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0009')
146
- end
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-
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- # Phase for "CDS" features. It indicates where the feature begins with reference to the reading frame. For forward strand features, phase is counted from the start field, whilst for reverse strand features, phase is counted from the end field.
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- # (http://www.biointerchange.org/gff3o#GFF3_0011)
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- def self.phase
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0011')
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- end
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-
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- # Tag name of a feature attribute.
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- # (http://www.biointerchange.org/gff3o#GFF3_0013)
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- def self.tag
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0013')
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- end
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-
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- # Version of the GFF3 specification that defines the feature set contents.
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- # (http://www.biointerchange.org/gff3o#GFF3_0022)
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- def self.version
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- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0022')
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- end
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-
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- # Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'.
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- # (http://www.biointerchange.org/gff3o#GFF3_0024)
168
- def self.build
169
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0024')
170
- end
171
-
172
- # Properties that are directly associated with Attribute class instances.
173
- # (http://www.biointerchange.org/gff3o#GFF3_0029)
174
- def self.attribute_properties
175
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029')
176
- end
177
-
178
- # A database cross-reference to associate a sequence alteration to its representation in another database.
179
- # (http://www.biointerchange.org/gff3o#GFF3_0034)
180
- def self.dbxref
181
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034')
182
- end
183
-
184
- # A cross-reference to an ontology term that is associated with a feature.
185
- # (http://www.biointerchange.org/gff3o#GFF3_0035)
186
- def self.ontology_term
187
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035')
188
- end
189
-
190
- # Name of a feature, which can be used for display purposes. The name is not a unique property among features.
191
- # (http://www.biointerchange.org/gff3o#GFF3_0036)
192
- def self.name
193
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036')
194
- end
195
-
196
- # An alternative name for a feature. This can be another descriptive name of a feature, such as a locus name or accession number.
197
- # (http://www.biointerchange.org/gff3o#GFF3_0037)
198
- def self.alias
199
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0037')
200
- end
201
-
202
- # ID or accession of the target alignment.
203
- # (http://www.biointerchange.org/gff3o#GFF3_0041)
204
- def self.target_id
205
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0041')
206
- end
207
-
208
- # Gap describing the feature/target alignment if the sequences are not collinear. The formal description of this property has been lost due to a dead link in the GFF3 specification.
209
- # (http://www.biointerchange.org/gff3o#GFF3_0046)
210
- def self.gap
211
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0046')
212
- end
213
-
214
- # A free text note.
215
- # (http://www.biointerchange.org/gff3o#GFF3_0048)
216
- def self.note
217
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0048')
218
- end
219
-
220
- # Describes whether a feature is circular or not.
221
- # (http://www.biointerchange.org/gff3o#GFF3_0049)
222
- def self.is_circular
223
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049')
224
- end
225
-
226
- # Properties that are directly associated with Landmark class instances.
227
- # (http://www.biointerchange.org/gff3o#GFF3_0052)
228
- def self.landmark_properties
229
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052')
230
- end
231
-
232
- # ID that uniquely establishes the Landmark's identity within a Set.
233
- # (http://www.biointerchange.org/gff3o#GFF3_0053)
234
- def self.id
235
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053')
236
- end
237
-
238
- # Either:
239
- # Sequence associated with this feature, if it has been specified using a FASTA string.
240
- # (http://www.biointerchange.org/gff3o#GFF3_0057)
241
- # Or:
242
- # Sequence associated with this feature, if it has been specified using a FASTA string.
243
- # (http://www.biointerchange.org/gff3o#GFF3_0058)
244
- def self.sequence
245
- return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') ]
246
- end
247
-
248
- # Set of genomic sequence features, whose identifiers are unique within the set.
249
- # (http://www.biointerchange.org/gff3o#GFF3_0001)
250
- def self.Set
251
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0001')
252
- end
253
-
254
- # A genomic sequence feature.
255
- # (http://www.biointerchange.org/gff3o#GFF3_0002)
256
- def self.Feature
257
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0002')
258
- end
259
-
260
- # Describes additional feature attributes besides ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular.
261
- # (http://www.biointerchange.org/gff3o#GFF3_0003)
262
- def self.Attribute
263
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0003')
264
- end
265
-
266
- # Class describing a genomic strand. Instances of the class (individuals) are used to denote forward-/reverse-strands, etc.
267
- # (http://www.biointerchange.org/gff3o#GFF3_0016)
268
- def self.Strand
269
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0016')
270
- end
271
-
272
- # Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
273
- # (http://www.biointerchange.org/gff3o#GFF3_0038)
274
- def self.Target
275
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0038')
276
- end
277
-
278
- # A landmark that establishes the coordinate system for features.
279
- # (http://www.biointerchange.org/gff3o#GFF3_0051)
280
- def self.Landmark
281
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0051')
282
- end
283
-
284
- # Location on the positive (forward) strand.
285
- # (http://www.biointerchange.org/gff3o#GFF3_0017)
286
- def self.Positive
287
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0017')
288
- end
289
-
290
- # Location on the negative (reverse) strand.
291
- # (http://www.biointerchange.org/gff3o#GFF3_0018)
292
- def self.Negative
293
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0018')
294
- end
295
-
296
- # Strand was not determined, which leaves it open whether the location is on the positive (forward) or negative (reverse) strand.
297
- # (http://www.biointerchange.org/gff3o#GFF3_0019)
298
- def self.UnknownStrand
299
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0019')
300
- end
301
-
302
- # Strand is not applicable.
303
- # (http://www.biointerchange.org/gff3o#GFF3_0020)
304
- def self.NotStranded
305
- return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0020')
306
- end
307
-
308
- # Determines whether the given URI is an object property.
309
- #
310
- # +uri+:: URI that is tested for being an object property
311
- def self.is_object_property?(uri)
312
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') then
313
- return true
314
- end
315
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010') then
316
- return true
317
- end
318
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0012') then
319
- return true
320
- end
321
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0014') then
322
- return true
323
- end
324
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0015') then
325
- return true
326
- end
327
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0021') then
328
- return true
329
- end
330
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0023') then
331
- return true
332
- end
333
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') then
334
- return true
335
- end
336
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') then
337
- return true
338
- end
339
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039') then
340
- return true
341
- end
342
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') then
343
- return true
344
- end
345
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0045') then
346
- return true
347
- end
348
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0047') then
349
- return true
350
- end
351
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0050') then
352
- return true
353
- end
354
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0056') then
355
- return true
356
- end
357
- return false
358
- end
359
-
360
- # Determines whether the given URI is a datatype property.
361
- #
362
- # +uri+:: URI that is tested for being a datatype property
363
- def self.is_datatype_property?(uri)
364
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005') then
365
- return true
366
- end
367
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') then
368
- return true
369
- end
370
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007') then
371
- return true
372
- end
373
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008') then
374
- return true
375
- end
376
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0009') then
377
- return true
378
- end
379
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0011') then
380
- return true
381
- end
382
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0013') then
383
- return true
384
- end
385
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0022') then
386
- return true
387
- end
388
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0024') then
389
- return true
390
- end
391
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') then
392
- return true
393
- end
394
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') then
395
- return true
396
- end
397
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029') then
398
- return true
399
- end
400
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') then
401
- return true
402
- end
403
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') then
404
- return true
405
- end
406
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') then
407
- return true
408
- end
409
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0037') then
410
- return true
411
- end
412
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') then
413
- return true
414
- end
415
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0041') then
416
- return true
417
- end
418
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042') then
419
- return true
420
- end
421
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043') then
422
- return true
423
- end
424
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0046') then
425
- return true
426
- end
427
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0048') then
428
- return true
429
- end
430
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049') then
431
- return true
432
- end
433
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') then
434
- return true
435
- end
436
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053') then
437
- return true
438
- end
439
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0054') then
440
- return true
441
- end
442
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') then
443
- return true
444
- end
445
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057') then
446
- return true
447
- end
448
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') then
449
- return true
450
- end
451
- return false
452
- end
453
-
454
- # Determines whether the given URI is a class.
455
- #
456
- # +uri+:: URI that is tested for being a class
457
- def self.is_class?(uri)
458
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0001') then
459
- return true
460
- end
461
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0002') then
462
- return true
463
- end
464
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0003') then
465
- return true
466
- end
467
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0016') then
468
- return true
469
- end
470
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0038') then
471
- return true
472
- end
473
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0051') then
474
- return true
475
- end
476
- return false
477
- end
478
-
479
- # Determines whether the given URI is a named individual.
480
- #
481
- # +uri+:: URI that is tested for being a named individual
482
- def self.is_named_individual?(uri)
483
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0017') then
484
- return true
485
- end
486
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0018') then
487
- return true
488
- end
489
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0019') then
490
- return true
491
- end
492
- if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0020') then
493
- return true
494
- end
495
- return false
496
- end
497
-
498
- # Returns only those URIs that fall under a designated parent URI.
499
- #
500
- # +uris+:: Set of URIs that are tested whether they have the given parent URI.
501
- # +parent+:: Parent URI.
502
- def self.with_parent(uris, parent)
503
- return uris.select { |uri| has_parent?(uri, parent) }
504
- end
505
-
506
- # Recursively tries to determine the parent for a given URI.
507
- #
508
- # +uri+:: URI that is tested for whether it has the given parent URI.
509
- # +parent+:: Parent URI.
510
- def self.has_parent?(uri, parent)
511
- if @@parent_properties.has_key?(uri) then
512
- if @@parent_properties[uri] == parent then
513
- return true
514
- end
515
- return has_parent?(@@parent_properties[uri], parent)
516
- end
517
- return false
518
- end
519
-
520
- private
521
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522
-
523
- end
524
-
525
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