biointerchange 0.1.0

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Files changed (57) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/.travis.yml +12 -0
  4. data/Gemfile +17 -0
  5. data/LICENSE.txt +8 -0
  6. data/README.md +166 -0
  7. data/Rakefile +50 -0
  8. data/VERSION +1 -0
  9. data/bin/biointerchange +6 -0
  10. data/docs/exceptions_readme.txt +13 -0
  11. data/examples/BovineGenomeChrX.gff3.gz +0 -0
  12. data/examples/gb-2007-8-3-R40.xml +243 -0
  13. data/examples/pubannotation.json +1 -0
  14. data/generators/rdfxml.rb +104 -0
  15. data/lib/biointerchange/core.rb +195 -0
  16. data/lib/biointerchange/exceptions.rb +38 -0
  17. data/lib/biointerchange/genomics/gff3_feature.rb +82 -0
  18. data/lib/biointerchange/genomics/gff3_feature_set.rb +37 -0
  19. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +107 -0
  20. data/lib/biointerchange/genomics/gff3_reader.rb +86 -0
  21. data/lib/biointerchange/gff3.rb +135 -0
  22. data/lib/biointerchange/reader.rb +25 -0
  23. data/lib/biointerchange/registry.rb +29 -0
  24. data/lib/biointerchange/sio.rb +7124 -0
  25. data/lib/biointerchange/sofa.rb +1566 -0
  26. data/lib/biointerchange/textmining/content.rb +69 -0
  27. data/lib/biointerchange/textmining/document.rb +36 -0
  28. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +161 -0
  29. data/lib/biointerchange/textmining/process.rb +57 -0
  30. data/lib/biointerchange/textmining/pubannos_json_reader.rb +72 -0
  31. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +197 -0
  32. data/lib/biointerchange/textmining/text_mining_reader.rb +41 -0
  33. data/lib/biointerchange/writer.rb +23 -0
  34. data/lib/biointerchange.rb +3 -0
  35. data/spec/exceptions_spec.rb +27 -0
  36. data/spec/gff3_rdfwriter_spec.rb +67 -0
  37. data/spec/text_mining_pdfx_xml_reader_spec.rb +89 -0
  38. data/spec/text_mining_pubannos_json_reader_spec.rb +71 -0
  39. data/spec/text_mining_rdfwriter_spec.rb +57 -0
  40. data/web/about.html +89 -0
  41. data/web/biointerchange.js +133 -0
  42. data/web/bootstrap/css/bootstrap-responsive.css +1040 -0
  43. data/web/bootstrap/css/bootstrap-responsive.min.css +9 -0
  44. data/web/bootstrap/css/bootstrap.css +5624 -0
  45. data/web/bootstrap/css/bootstrap.min.css +9 -0
  46. data/web/bootstrap/img/glyphicons-halflings-white.png +0 -0
  47. data/web/bootstrap/img/glyphicons-halflings.png +0 -0
  48. data/web/bootstrap/js/bootstrap.js +2027 -0
  49. data/web/bootstrap/js/bootstrap.min.js +6 -0
  50. data/web/bootstrap/js/jquery-1.8.1.min.js +2 -0
  51. data/web/css/rdoc-style.css +5786 -0
  52. data/web/css/rdoc.css +716 -0
  53. data/web/images/BioInterchange300.png +0 -0
  54. data/web/index.html +109 -0
  55. data/web/service/rdfizer.fcgi +68 -0
  56. data/web/webservices.html +123 -0
  57. metadata +240 -0

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