commonmeta-ruby 3.5.4 → 3.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (275) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +16 -5
  3. data/bin/commonmeta +1 -1
  4. data/lib/commonmeta/readers/crossref_xml_reader.rb +1 -1
  5. data/lib/commonmeta/utils.rb +6 -6
  6. data/lib/commonmeta/version.rb +1 -1
  7. data/spec/cli_spec.rb +13 -8
  8. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/default.yml +13 -13
  9. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_bibtex.yml +13 -13
  10. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_crossref_xml.yml +25 -25
  11. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_datacite.yml +13 -13
  12. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_schema_org.yml +13 -13
  13. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/default.yml +7 -7
  14. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_bibtex.yml +7 -7
  15. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_crossref_xml.yml +7 -59
  16. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_datacite.yml +7 -7
  17. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_schema_org.yml +7 -7
  18. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/default.yml +24 -24
  19. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_bibtex.yml +24 -24
  20. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_citation.yml +24 -24
  21. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_crossref_xml.yml +24 -24
  22. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_datacite.yml +24 -24
  23. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_jats.yml +24 -24
  24. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_schema_org.yml +24 -24
  25. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/default.yml +16 -16
  26. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_bibtex.yml +16 -16
  27. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_citation.yml +16 -16
  28. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_datacite.yml +16 -16
  29. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_jats.yml +16 -16
  30. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_schema_org.yml +16 -16
  31. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/default.yml +479 -946
  32. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_crossref_xml.yml +957 -1891
  33. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_datacite.yml +479 -946
  34. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_schema_org.yml +481 -950
  35. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_blog.yml +5540 -968
  36. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_blog_unknown_blog_id.yml +22 -29
  37. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id.yml +25 -39
  38. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id_unknown_uuid.yml +18 -28
  39. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/crossref.yml +7 -7
  40. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/datacite.yml +7 -7
  41. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/jalc.yml +7 -7
  42. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/kisti.yml +7 -7
  43. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/medra.yml +7 -7
  44. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/op.yml +7 -7
  45. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_blog_id.yml +46 -0
  46. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_by_blog.yml +5578 -246
  47. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_not_indexed.yml +13 -2201
  48. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_unregistered.yml +176 -72
  49. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +16 -16
  50. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/crossref.yml +6 -6
  51. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/datacite.yml +6 -6
  52. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/jalc.yml +6 -6
  53. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/kisti.yml +6 -6
  54. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/medra.yml +6 -6
  55. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/not_found.yml +6 -6
  56. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/op.yml +6 -6
  57. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref.yml +6 -6
  58. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +6 -6
  59. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite.yml +6 -6
  60. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite_doi_http.yml +6 -6
  61. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +6 -6
  62. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_blog_id_for_json_feed_item_id/by_blog_post_id.yml +27 -105
  63. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_blog_id_for_json_feed_item_id/not_found.yml +20 -27
  64. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/cff-converter-python.yml +51 -25
  65. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff.yml +12 -12
  66. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +9 -9
  67. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/maremma.yml +10 -10
  68. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/metadata_reports.yml +11 -11
  69. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +78 -78
  70. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +76 -76
  71. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +35 -35
  72. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/JaLC.yml +162 -162
  73. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/KISTI.yml +131 -131
  74. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/OP.yml +75 -75
  75. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/affiliation_is_space.yml +76 -76
  76. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book.yml +113 -113
  77. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book_chapter.yml +74 -74
  78. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/article_id_as_page_number.yml +77 -77
  79. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/author_literal.yml +84 -84
  80. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book.yml +77 -77
  81. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter.yml +75 -75
  82. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +73 -73
  83. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_oup.yml +72 -72
  84. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/component.yml +94 -94
  85. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset.yml +104 -104
  86. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset_usda.yml +136 -136
  87. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/date_in_future.yml +80 -80
  88. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dissertation.yml +103 -103
  89. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/empty_given_name.yml +75 -75
  90. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/invalid_date.yml +77 -77
  91. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article.yml +76 -76
  92. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +73 -73
  93. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with.yml +128 -210
  94. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +74 -74
  95. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_funding.yml +76 -76
  96. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_issue.yml +72 -72
  97. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/mEDRA.yml +72 -72
  98. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/markup.yml +81 -81
  99. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/missing_contributor.yml +71 -71
  100. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_issn.yml +75 -75
  101. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles.yml +71 -71
  102. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +573 -573
  103. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/not_found_error.yml +65 -65
  104. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/peer_review.yml +77 -77
  105. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content.yml +74 -74
  106. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content_copernicus.yml +76 -76
  107. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/report_osti.yml +120 -120
  108. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/vor_with_url.yml +78 -78
  109. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book.yml +74 -74
  110. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book_chapter.yml +73 -73
  111. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_raw/journal_article.yml +59 -59
  112. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/SoftwareSourceCode.yml +4 -4
  113. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/dissertation.yml +13 -13
  114. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/funding_references.yml +15 -15
  115. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/subject_scheme.yml +120 -120
  116. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_id.yml +5540 -555
  117. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id.yml +31 -42
  118. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id_specific_prefix.yml +25 -39
  119. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +5540 -247
  120. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +14 -26
  121. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +176 -72
  122. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/archived_wordpress_post.yml +27 -95
  123. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml +28 -106
  124. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +21 -65
  125. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +20 -208
  126. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +26 -97
  127. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_institutional_author.yml +24 -55
  128. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_organizational_author.yml +27 -70
  129. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers.yml +41 -143
  130. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_funding.yml +54 -132
  131. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_link_to_peer-reviewed_article.yml +304 -818
  132. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +24 -169
  133. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +24 -63
  134. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post_with_anonymous_author.yml +25 -40
  135. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +278 -591
  136. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +59 -101
  137. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +135 -331
  138. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +24 -134
  139. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_many_references.yml +578 -2967
  140. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +44 -205
  141. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_tracking_code_on_url.yml +26 -160
  142. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/affiliation_is_space.yml +21 -21
  143. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_familyName.yml +15 -15
  144. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_name_in_display-order_with_ORCID.yml +13 -13
  145. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/name_with_affiliation_crossref.yml +16 -16
  146. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/only_familyName_and_givenName.yml +66 -61
  147. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting.yml +145 -146
  148. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml +149 -150
  149. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/get_schema_org_metadata_front_matter/BlogPosting.yml +114 -115
  150. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/harvard_dataverse.yml +300 -289
  151. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/pangaea.yml +66 -61
  152. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/upstream_blog.yml +64 -57
  153. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/zenodo.yml +27 -24
  154. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml +6 -6
  155. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/unknown_DOI_prefix.yml +6 -6
  156. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_schema_errors/is_valid.yml +16 -16
  157. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/BlogPosting.yml +10 -10
  158. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/Dataset.yml +10 -10
  159. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/authors_with_affiliations.yml +16 -16
  160. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/climate_data.yml +10 -10
  161. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/from_schema_org.yml +145 -146
  162. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/keywords_subject_scheme.yml +8 -8
  163. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/maremma.yml +12 -12
  164. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/text.yml +8 -8
  165. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_data_citation.yml +16 -16
  166. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_pages.yml +16 -16
  167. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/Collection_of_Jupyter_notebooks.yml +13 -13
  168. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_Zenodo.yml +13 -13
  169. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_also_Zenodo.yml +8 -8
  170. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/ruby-cff.yml +10 -10
  171. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Dataset.yml +10 -10
  172. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article.yml +16 -16
  173. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article_vancouver_style.yml +21 -21
  174. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Missing_author.yml +15 -15
  175. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/interactive_resource_without_dates.yml +8 -8
  176. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml +8 -8
  177. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml +8 -8
  178. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml +8 -8
  179. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml +12 -12
  180. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml +32 -32
  181. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml +5 -5
  182. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_from_datacite.yml +5 -5
  183. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_plos.yml +16 -16
  184. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_anonymous_author.yml +25 -40
  185. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +24 -134
  186. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_organizational_author.yml +27 -70
  187. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_relations.yml +41 -143
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- contributor_role=\"author\">\r\n <given_name>Chad L</given_name>\r\n
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- \ <jats:sec>\r\n <jats:title>Background</jats:title>\r\n
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- \ <jats:p>Accurate evaluation of the quality of genomic
518
- or proteomic data and computational methods is vital to our ability to use
519
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520
- There is currently no standard approach to evaluation in functional genomics.
521
- Our analysis of existing approaches shows that they are inconsistent and contain
522
- substantial functional biases that render the resulting evaluations misleading
523
- both quantitatively and qualitatively. These problems make it essentially
524
- impossible to compare computational methods or large-scale experimental datasets
525
- and also result in conclusions that generalize poorly in most biological applications.</jats:p>\r\n
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- \ <jats:p>We reveal issues with current evaluation methods
528
- here and suggest new approaches to evaluation that facilitate accurate and
529
- representative characterization of genomic methods and data. Specifically,
530
- we describe a functional genomics gold standard based on curation by expert
531
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532
- genomic approaches. Our evaluation framework and gold standard are freely
533
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- \ <jats:p>Proper methods for evaluating genomic data and
536
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537
- to learn from the wealth of available data. We propose one possible solution
538
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+ evaluation of the quality of genomic or proteomic data and computational methods
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+ is vital to our ability to use them for formulating novel biological hypotheses
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+ to evaluation in functional genomics. Our analysis of existing approaches
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+ shows that they are inconsistent and contain substantial functional biases
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+ that render the resulting evaluations misleading both quantitatively and qualitatively.
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+ These problems make it essentially impossible to compare computational methods
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+ or large-scale experimental datasets and also result in conclusions that generalize
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+ to evaluation that facilitate accurate and representative characterization
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+ of genomic methods and data. Specifically, we describe a functional genomics
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+ as an effective means of evaluation of genomic approaches. Our evaluation
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+ framework and gold standard are freely available to the community through
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