biointerchange 0.2.1 → 0.2.2

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Files changed (49) hide show
  1. data/README.md +61 -18
  2. data/VERSION +1 -1
  3. data/examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz +0 -0
  4. data/examples/webservice_example.json +7 -0
  5. data/generators/GOxrefify.rb +36 -28
  6. data/generators/javaify.rb +131 -112
  7. data/generators/make_supplement_releases.rb +57 -0
  8. data/generators/pythonify.rb +68 -53
  9. data/lib/biointerchange/core.rb +4 -2
  10. data/lib/biointerchange/faldo.rb +160 -0
  11. data/lib/biointerchange/genomics/gff3_feature_set.rb +1 -1
  12. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +1 -1
  13. data/lib/biointerchange/genomics/gff3_reader.rb +1 -1
  14. data/lib/biointerchange/model.rb +21 -0
  15. data/lib/biointerchange/registry.rb +1 -1
  16. data/lib/biointerchange/sio.rb +2035 -57
  17. data/lib/biointerchange/textmining/document.rb +1 -1
  18. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +1 -15
  19. data/lib/biointerchange/textmining/pubannos_json_reader.rb +1 -3
  20. data/spec/gff3_rdfwriter_spec.rb +1 -0
  21. data/spec/gvf_rdfwriter_spec.rb +1 -0
  22. data/spec/text_mining_pdfx_xml_reader_spec.rb +4 -3
  23. data/spec/text_mining_pubannos_json_reader_spec.rb +6 -5
  24. data/spec/text_mining_rdfwriter_spec.rb +2 -1
  25. data/supplemental/java/biointerchange/pom.xml +1 -1
  26. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +219 -0
  27. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +2 -1
  28. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java +1221 -0
  29. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +2 -1
  30. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +2283 -15
  31. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +2 -1
  32. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +5 -4
  33. data/supplemental/python/biointerchange/faldo.py +168 -0
  34. data/supplemental/python/biointerchange/gff3o.py +6 -4
  35. data/supplemental/python/biointerchange/goxref.py +1040 -0
  36. data/supplemental/python/biointerchange/gvf1o.py +6 -4
  37. data/supplemental/python/biointerchange/sio.py +1740 -21
  38. data/supplemental/python/biointerchange/so.py +6527 -6525
  39. data/supplemental/python/biointerchange/sofa.py +792 -790
  40. data/supplemental/python/setup.py +2 -2
  41. data/web/about.html +9 -29
  42. data/web/api.html +10 -30
  43. data/web/biointerchange.js +78 -27
  44. data/web/cli.html +137 -0
  45. data/web/index.html +19 -34
  46. data/web/ontologies.html +9 -29
  47. data/web/service/rdfizer.fcgi +19 -2
  48. data/web/webservices.html +70 -35
  49. metadata +13 -3

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