commonmeta-ruby 3.3.3 → 3.3.4

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Files changed (631) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +1 -1
  3. data/bin/commonmeta +1 -1
  4. data/lib/commonmeta/cli.rb +7 -3
  5. data/lib/commonmeta/readers/json_feed_reader.rb +1 -1
  6. data/lib/commonmeta/utils.rb +34 -0
  7. data/lib/commonmeta/version.rb +1 -1
  8. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +14 -14
  9. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/crossref.yml +5 -5
  10. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/datacite.yml +5 -5
  11. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/jalc.yml +5 -5
  12. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/kisti.yml +5 -5
  13. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/medra.yml +5 -5
  14. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/not_found.yml +5 -5
  15. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/op.yml +5 -5
  16. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref.yml +5 -5
  17. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +5 -5
  18. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite.yml +5 -5
  19. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite_doi_http.yml +5 -5
  20. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +5 -5
  21. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/cff-converter-python.yml +9 -7
  22. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff.yml +16 -14
  23. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +14 -12
  24. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/maremma.yml +10 -8
  25. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/metadata_reports.yml +9 -7
  26. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +74 -74
  27. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +73 -73
  28. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +70 -70
  29. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/JaLC.yml +159 -159
  30. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/KISTI.yml +128 -128
  31. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/OP.yml +72 -72
  32. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/affiliation_is_space.yml +73 -73
  33. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book.yml +109 -109
  34. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book_chapter.yml +71 -71
  35. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/article_id_as_page_number.yml +74 -74
  36. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/author_literal.yml +82 -82
  37. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book.yml +71 -71
  38. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter.yml +72 -72
  39. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +70 -70
  40. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_oup.yml +69 -69
  41. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/component.yml +91 -91
  42. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset.yml +101 -102
  43. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset_usda.yml +133 -133
  44. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/date_in_future.yml +78 -78
  45. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dissertation.yml +100 -100
  46. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/empty_given_name.yml +72 -72
  47. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/invalid_date.yml +73 -73
  48. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article.yml +72 -72
  49. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +70 -70
  50. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with.yml +76 -514
  51. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +70 -70
  52. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_funding.yml +73 -73
  53. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_issue.yml +69 -69
  54. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/mEDRA.yml +69 -69
  55. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/markup.yml +78 -78
  56. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/missing_creator.yml +73 -73
  57. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_issn.yml +72 -72
  58. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles.yml +71 -70
  59. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +716 -716
  60. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/not_found_error.yml +63 -63
  61. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/peer_review.yml +74 -74
  62. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content.yml +71 -71
  63. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content_copernicus.yml +73 -73
  64. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/report_osti.yml +117 -117
  65. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/vor_with_url.yml +75 -75
  66. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book.yml +69 -69
  67. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book_chapter.yml +70 -70
  68. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_raw/journal_article.yml +10 -10
  69. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/dissertation.yml +9 -9
  70. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/funding_references.yml +11 -11
  71. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/subject_scheme.yml +20 -20
  72. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_id.yml +6 -419
  73. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_uuid.yml +7 -260
  74. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_uuid_specific_prefix.yml +3 -136
  75. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +225 -1432
  76. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +1380 -2112
  77. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +6 -172
  78. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml +7 -7
  79. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +12 -12
  80. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +8 -8
  81. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +7 -7
  82. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_organizational_author.yml +3 -3
  83. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +8 -8
  84. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +8 -8
  85. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +90 -176
  86. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +25 -25
  87. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +61 -61
  88. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +8 -8
  89. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +20 -20
  90. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_familyName.yml +9 -9
  91. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_name_in_display-order_with_ORCID.yml +9 -9
  92. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/name_with_affiliation_crossref.yml +14 -14
  93. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/only_familyName_and_givenName.yml +43 -36
  94. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting.yml +158 -158
  95. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml +162 -162
  96. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/get_schema_org_metadata_front_matter/BlogPosting.yml +178 -180
  97. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/harvard_dataverse.yml +226 -230
  98. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/pangaea.yml +43 -36
  99. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/upstream_blog.yml +94 -94
  100. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/zenodo.yml +14 -14
  101. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml +5 -5
  102. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/unknown_DOI_prefix.yml +5 -5
  103. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_schema_errors/is_valid.yml +13 -13
  104. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/BlogPosting.yml +4 -4
  105. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/Dataset.yml +6 -6
  106. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/authors_with_affiliations.yml +14 -14
  107. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/climate_data.yml +6 -6
  108. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/from_schema_org.yml +159 -159
  109. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/keywords_subject_scheme.yml +6 -6
  110. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/maremma.yml +12 -10
  111. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/text.yml +4 -4
  112. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_data_citation.yml +14 -14
  113. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_pages.yml +12 -12
  114. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/Collection_of_Jupyter_notebooks.yml +9 -9
  115. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_Zenodo.yml +17 -17
  116. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_also_Zenodo.yml +12 -12
  117. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/ruby-cff.yml +16 -14
  118. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Dataset.yml +6 -6
  119. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article.yml +14 -14
  120. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article_vancouver_style.yml +19 -19
  121. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Missing_author.yml +12 -12
  122. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/interactive_resource_without_dates.yml +4 -4
  123. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml +6 -6
  124. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml +4 -4
  125. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml +4 -4
  126. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml +27 -27
  127. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml +4 -4
  128. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_from_datacite.yml +4 -4
  129. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +8 -54
  130. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_organizational_author.yml +3 -3
  131. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_upstream_blog.yml +10 -53
  132. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +62 -62
  133. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/posted_content.yml +15 -15
  134. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_another_science_blog.yml +6 -6
  135. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_front_matter.yml +29 -29
  136. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_upstream_blog.yml +4 -4
  137. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/Another_dataset.yml +28 -28
  138. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/BlogPosting.yml +4 -4
  139. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/BlogPosting_schema_org.yml +158 -158
  140. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/Dataset.yml +6 -6
  141. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/container_title.yml +11 -11
  142. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/interactive_resource_without_dates.yml +4 -4
  143. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/journal_article.yml +14 -14
  144. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/keywords_subject_scheme.yml +6 -6
  145. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/maremma.yml +9 -7
  146. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/missing_creator.yml +12 -12
  147. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/multiple_abstracts.yml +6 -6
  148. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/organization_author.yml +19 -19
  149. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/software.yml +4 -4
  150. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/software_w/version.yml +6 -6
  151. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/with_only_first_page.yml +13 -13
  152. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/with_pages.yml +12 -12
  153. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/climate_data.yml +6 -6
  154. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/maremma.yml +10 -8
  155. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/text.yml +4 -4
  156. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/with_data_citation.yml +14 -14
  157. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/with_pages.yml +12 -12
  158. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/dissertation.yml +17 -17
  159. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/from_schema_org.yml +158 -158
  160. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/journal_article.yml +18 -18
  161. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/maremma.yml +10 -8
  162. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/with_ORCID_ID.yml +12 -12
  163. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/with_data_citation.yml +14 -14
  164. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/Dataset_in_schema_4_0.yml +6 -6
  165. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/Text_pass-thru.yml +4 -4
  166. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/book_chapter.yml +15 -13
  167. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/from_schema_org.yml +158 -158
  168. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/interactive_resource_without_dates.yml +4 -4
  169. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/maremma.yml +12 -10
  170. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_ORCID_ID.yml +12 -12
  171. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_data_citation.yml +14 -14
  172. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_editor.yml +13 -13
  173. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/BlogPosting.yml +4 -4
  174. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/BlogPosting_schema_org.yml +159 -159
  175. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/Dataset.yml +6 -6
  176. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/alternate_name.yml +4 -4
  177. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/journal_article.yml +8 -8
  178. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/keywords_with_subject_scheme.yml +6 -6
  179. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/maremma.yml +9 -7
  180. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/with_pages.yml +7 -7
  181. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Another_Schema_org_JSON.yml +6 -6
  182. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Funding.yml +9 -9
  183. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Funding_OpenAIRE.yml +9 -9
  184. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Schema_org_JSON.yml +17 -17
  185. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Schema_org_JSON_Cyark.yml +33 -33
  186. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/alternate_identifiers.yml +9 -9
  187. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/data_catalog.yml +9 -9
  188. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/geo_location_box.yml +12 -12
  189. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/interactive_resource_without_dates.yml +9 -9
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- falciparum is the major human malaria agent responsible for 200 to 300 million
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- infants. The origin and evolution of this pathogen within the human lineage
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- is still unresolved. A single species, P. reichenowi, which infects chimpanzees,
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- is known to be a close sister lineage of P. falciparum. Here we report the
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- discovery of a new Plasmodium species infecting Hominids. This new species
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- has been isolated in two chimpanzees (Pan troglodytes) kept as pets by villagers
96
- in Gabon (Africa). Analysis of its complete mitochondrial genome (5529 nucleotides
97
- including Cyt b, Cox I and Cox III genes) reveals an older divergence of this
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- lineage from the clade that includes P. falciparum and P. reichenowi (approximately
99
- 21+/-9 Myrs ago using Bayesian methods and considering that the divergence
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- between P. falciparum and P. reichenowi occurred 4 to 7 million years ago
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- as generally considered in the literature). This time frame would be congruent
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- with the radiation of hominoids, suggesting that this Plasmodium lineage might
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- have been present in early hominoids and that they may both have experienced
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- a simultaneous diversification. Investigation of the nuclear genome of this
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- new species will further the understanding of the genetic adaptations of P.
106
- falciparum to humans. The risk of transfer and emergence of this new species
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- in humans must be now seriously considered given that it was found in two
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- chimpanzees living in contact with humans and its close relatedness to the
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- most virulent agent of malaria.","descriptionType":"Abstract"},{"description":"Ollomo_PLoSPathog_2009Nucleotide
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- alignment concatenation of 4 mitochondrial genes for 17 Plasmodium species
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- and one outgroup.Ollomo_PLoSPathog_2009_PHYMLMaximum likelihood tree inferred
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