biointerchange 0.2.2 → 1.0.0

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Files changed (55) hide show
  1. data/Gemfile +1 -0
  2. data/README.md +269 -19
  3. data/VERSION +1 -1
  4. data/examples/bininda_emonds_mammals.new +1 -0
  5. data/examples/rdfization.rb +17 -0
  6. data/examples/tree1.new +1 -0
  7. data/examples/tree2.new +1 -0
  8. data/examples/vocabulary.rb +26 -5
  9. data/generators/javaify.rb +12 -18
  10. data/generators/make_supplement_releases.rb +2 -0
  11. data/generators/pythonify.rb +21 -8
  12. data/generators/rdfxml.rb +15 -1
  13. data/lib/biointerchange/cdao.rb +2014 -0
  14. data/lib/biointerchange/core.rb +70 -77
  15. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
  16. data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
  17. data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
  18. data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
  19. data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
  20. data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
  21. data/lib/biointerchange/registry.rb +50 -8
  22. data/lib/biointerchange/so.rb +150 -0
  23. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
  24. data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
  25. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
  26. data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
  27. data/spec/phylogenetics_spec.rb +79 -0
  28. data/supplemental/java/biointerchange/pom.xml +1 -1
  29. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
  30. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
  31. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
  32. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
  33. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
  34. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
  35. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
  36. data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
  37. data/supplemental/python/biointerchange/cdao.py +2021 -0
  38. data/supplemental/python/biointerchange/faldo.py +37 -38
  39. data/supplemental/python/biointerchange/gff3o.py +156 -157
  40. data/supplemental/python/biointerchange/goxref.py +172 -172
  41. data/supplemental/python/biointerchange/gvf1o.py +428 -429
  42. data/supplemental/python/biointerchange/sio.py +3133 -3134
  43. data/supplemental/python/biointerchange/so.py +6626 -6527
  44. data/supplemental/python/biointerchange/sofa.py +790 -791
  45. data/supplemental/python/example.py +23 -5
  46. data/supplemental/python/setup.py +2 -2
  47. data/web/about.html +1 -0
  48. data/web/api.html +223 -15
  49. data/web/biointerchange.js +27 -6
  50. data/web/cli.html +8 -3
  51. data/web/index.html +6 -2
  52. data/web/ontologies.html +3 -0
  53. data/web/service/rdfizer.fcgi +7 -15
  54. data/web/webservices.html +6 -2
  55. metadata +30 -3
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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2
  name: biointerchange
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3
  version: !ruby/object:Gem::Version
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- version: 0.2.2
4
+ version: 1.0.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -13,7 +13,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-05-10 00:00:00.000000000 Z
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+ date: 2013-06-08 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rdf
@@ -79,6 +79,22 @@ dependencies:
79
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 2.3.2
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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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+ none: false
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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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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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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: rspec
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  requirement: !ruby/object:Gem::Requirement
@@ -180,12 +196,16 @@ files:
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  - bin/biointerchange
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  - examples/BovineGenomeChrX.gff3.gz
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  - examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz
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+ - examples/bininda_emonds_mammals.new
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  - examples/chromosome_BF.gff
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  - examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
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  - examples/gb-2007-8-3-R40.xml
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  - examples/pubannotation.10096561.json
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  - examples/pubannotation.10096561.json.old
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  - examples/pubannotation.2626671.json
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+ - examples/rdfization.rb
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+ - examples/tree1.new
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+ - examples/tree2.new
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  - examples/vocabulary.rb
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  - examples/webservice_example.json
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  - generators/GOxrefify.rb
@@ -194,6 +214,7 @@ files:
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  - generators/pythonify.rb
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  - generators/rdfxml.rb
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  - lib/biointerchange.rb
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+ - lib/biointerchange/cdao.rb
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  - lib/biointerchange/core.rb
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  - lib/biointerchange/exceptions.rb
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  - lib/biointerchange/faldo.rb
@@ -210,6 +231,9 @@ files:
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  - lib/biointerchange/goxref.rb
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  - lib/biointerchange/gvf1o.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
236
+ - lib/biointerchange/phylogenetics/tree_set.rb
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  - lib/biointerchange/reader.rb
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  - lib/biointerchange/registry.rb
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  - lib/biointerchange/sio.rb
@@ -227,12 +251,14 @@ files:
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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
254
+ - spec/phylogenetics_spec.rb
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  - spec/text_mining_pdfx_xml_reader_spec.rb
231
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  - spec/text_mining_pubannos_json_reader_spec.rb
232
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  - spec/text_mining_rdfwriter_spec.rb
233
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  - supplemental/java/biointerchange/pom.xml
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  - supplemental/java/biointerchange/src/main/java/org/biointerchange/App.java
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  - supplemental/java/biointerchange/src/main/java/org/biointerchange/AppSIO.java
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+ - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java
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  - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java
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  - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
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  - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java
@@ -242,6 +268,7 @@ files:
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  - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java
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  - supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java
244
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  - supplemental/python/biointerchange/__init__.py
271
+ - supplemental/python/biointerchange/cdao.py
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  - supplemental/python/biointerchange/faldo.py
246
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  - supplemental/python/biointerchange/gff3o.py
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  - supplemental/python/biointerchange/goxref.py
@@ -286,7 +313,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -3312965476220723123
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+ hash: 3715660603784796436
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: