commonmeta-ruby 3.5.5 → 3.6

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Files changed (274) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +16 -5
  3. data/lib/commonmeta/readers/crossref_xml_reader.rb +1 -1
  4. data/lib/commonmeta/utils.rb +6 -6
  5. data/lib/commonmeta/version.rb +1 -1
  6. data/spec/cli_spec.rb +8 -8
  7. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/default.yml +13 -13
  8. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_bibtex.yml +13 -13
  9. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_crossref_xml.yml +25 -25
  10. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_datacite.yml +13 -13
  11. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_schema_org.yml +13 -13
  12. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/default.yml +7 -7
  13. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_bibtex.yml +7 -7
  14. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_crossref_xml.yml +7 -59
  15. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_datacite.yml +7 -7
  16. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_schema_org.yml +7 -7
  17. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/default.yml +24 -24
  18. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_bibtex.yml +24 -24
  19. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_citation.yml +24 -24
  20. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_crossref_xml.yml +24 -24
  21. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_datacite.yml +24 -24
  22. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_jats.yml +24 -24
  23. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_schema_org.yml +24 -24
  24. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/default.yml +16 -16
  25. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_bibtex.yml +16 -16
  26. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_citation.yml +16 -16
  27. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_datacite.yml +16 -16
  28. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_jats.yml +16 -16
  29. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_schema_org.yml +16 -16
  30. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/default.yml +479 -946
  31. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_crossref_xml.yml +957 -1891
  32. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_datacite.yml +479 -946
  33. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_schema_org.yml +481 -950
  34. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_blog.yml +5540 -968
  35. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_blog_unknown_blog_id.yml +22 -29
  36. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id.yml +25 -39
  37. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id_unknown_uuid.yml +18 -28
  38. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/crossref.yml +7 -7
  39. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/datacite.yml +7 -7
  40. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/jalc.yml +7 -7
  41. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/kisti.yml +7 -7
  42. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/medra.yml +7 -7
  43. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/op.yml +7 -7
  44. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_blog_id.yml +19 -90
  45. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_by_blog.yml +5578 -246
  46. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_not_indexed.yml +13 -2201
  47. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_unregistered.yml +176 -72
  48. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +16 -16
  49. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/crossref.yml +6 -6
  50. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/datacite.yml +6 -6
  51. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/jalc.yml +6 -6
  52. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/kisti.yml +6 -6
  53. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/medra.yml +6 -6
  54. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/not_found.yml +6 -6
  55. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/op.yml +6 -6
  56. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref.yml +6 -6
  57. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +6 -6
  58. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite.yml +6 -6
  59. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite_doi_http.yml +6 -6
  60. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +6 -6
  61. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_blog_id_for_json_feed_item_id/by_blog_post_id.yml +27 -105
  62. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_blog_id_for_json_feed_item_id/not_found.yml +20 -27
  63. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/cff-converter-python.yml +51 -25
  64. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff.yml +12 -12
  65. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +9 -9
  66. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/maremma.yml +10 -10
  67. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/metadata_reports.yml +11 -11
  68. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +78 -78
  69. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +76 -76
  70. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +35 -35
  71. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/JaLC.yml +162 -162
  72. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/KISTI.yml +131 -131
  73. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/OP.yml +75 -75
  74. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/affiliation_is_space.yml +76 -76
  75. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book.yml +113 -113
  76. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book_chapter.yml +74 -74
  77. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/article_id_as_page_number.yml +77 -77
  78. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/author_literal.yml +84 -84
  79. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book.yml +77 -77
  80. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter.yml +75 -75
  81. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +73 -73
  82. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_oup.yml +72 -72
  83. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/component.yml +94 -94
  84. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset.yml +104 -104
  85. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset_usda.yml +136 -136
  86. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/date_in_future.yml +80 -80
  87. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dissertation.yml +103 -103
  88. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/empty_given_name.yml +75 -75
  89. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/invalid_date.yml +77 -77
  90. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article.yml +76 -76
  91. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +73 -73
  92. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with.yml +128 -210
  93. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +74 -74
  94. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_funding.yml +76 -76
  95. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_issue.yml +72 -72
  96. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/mEDRA.yml +72 -72
  97. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/markup.yml +81 -81
  98. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/missing_contributor.yml +71 -71
  99. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_issn.yml +75 -75
  100. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles.yml +71 -71
  101. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +573 -573
  102. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/not_found_error.yml +65 -65
  103. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/peer_review.yml +77 -77
  104. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content.yml +74 -74
  105. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content_copernicus.yml +76 -76
  106. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/report_osti.yml +120 -120
  107. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/vor_with_url.yml +78 -78
  108. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book.yml +74 -74
  109. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book_chapter.yml +73 -73
  110. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_raw/journal_article.yml +59 -59
  111. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/SoftwareSourceCode.yml +4 -4
  112. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/dissertation.yml +13 -13
  113. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/funding_references.yml +15 -15
  114. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/subject_scheme.yml +120 -120
  115. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_id.yml +5540 -555
  116. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id.yml +31 -42
  117. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id_specific_prefix.yml +25 -39
  118. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +5540 -247
  119. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +14 -26
  120. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +176 -72
  121. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/archived_wordpress_post.yml +27 -95
  122. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml +28 -106
  123. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +21 -65
  124. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +20 -208
  125. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +26 -97
  126. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_institutional_author.yml +24 -55
  127. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_organizational_author.yml +27 -70
  128. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers.yml +41 -143
  129. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_funding.yml +54 -132
  130. 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
  131. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +24 -169
  132. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +24 -63
  133. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post_with_anonymous_author.yml +25 -40
  134. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +278 -591
  135. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +59 -101
  136. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +135 -331
  137. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +24 -134
  138. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_many_references.yml +578 -2967
  139. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +44 -205
  140. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_tracking_code_on_url.yml +26 -160
  141. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/affiliation_is_space.yml +21 -21
  142. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_familyName.yml +15 -15
  143. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_name_in_display-order_with_ORCID.yml +13 -13
  144. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/name_with_affiliation_crossref.yml +16 -16
  145. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/only_familyName_and_givenName.yml +66 -61
  146. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting.yml +145 -146
  147. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml +149 -150
  148. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/get_schema_org_metadata_front_matter/BlogPosting.yml +114 -115
  149. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/harvard_dataverse.yml +300 -289
  150. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/pangaea.yml +66 -61
  151. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/upstream_blog.yml +64 -57
  152. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/zenodo.yml +27 -24
  153. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml +6 -6
  154. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/unknown_DOI_prefix.yml +6 -6
  155. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_schema_errors/is_valid.yml +16 -16
  156. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/BlogPosting.yml +10 -10
  157. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/Dataset.yml +10 -10
  158. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/authors_with_affiliations.yml +16 -16
  159. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/climate_data.yml +10 -10
  160. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/from_schema_org.yml +145 -146
  161. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/keywords_subject_scheme.yml +8 -8
  162. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/maremma.yml +12 -12
  163. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/text.yml +8 -8
  164. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_data_citation.yml +16 -16
  165. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_pages.yml +16 -16
  166. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/Collection_of_Jupyter_notebooks.yml +13 -13
  167. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_Zenodo.yml +13 -13
  168. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_also_Zenodo.yml +8 -8
  169. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/ruby-cff.yml +10 -10
  170. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Dataset.yml +10 -10
  171. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article.yml +16 -16
  172. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article_vancouver_style.yml +21 -21
  173. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Missing_author.yml +15 -15
  174. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/interactive_resource_without_dates.yml +8 -8
  175. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml +8 -8
  176. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml +8 -8
  177. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml +8 -8
  178. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml +12 -12
  179. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml +32 -32
  180. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml +5 -5
  181. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_from_datacite.yml +5 -5
  182. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_plos.yml +16 -16
  183. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_anonymous_author.yml +25 -40
  184. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +24 -134
  185. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_organizational_author.yml +27 -70
  186. 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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+ 7.00","home_page_url":"http://sfmatheson.blogspot.com","id":"5764g49","issn":null,"language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","modified_at":"2023-09-11T17:46:56+00:00","plan":"Team","prefix":"10.59350","relative_url":null,"slug":"sfmatheson","status":"active","title":"Quintessence
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+ of Dust","use_api":null,"use_mastodon":false,"user_id":"656f9875-3304-4056-935b-b29429e14222","version":"https://jsonfeed.org/version/1.1"},"blog_name":"Quintessence
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+ of Dust","blog_slug":"sfmatheson","doi":"https://doi.org/10.59350/63055-a8604","id":"1898d2d7-4d87-4487-96c4-3073cf99e9a5","image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s320/Jan%207.jpg","indexed_at":1689006804,"language":"en","published_at":1673233380,"reference":[],"relationships":[],"summary":"It''s
53
45
  early January 2023, a little before sunset in Tucson. Live image below, showing
54
46
  the glorious Santa Catalina mountains (the snow on the upper reaches is more
55
47
  apparent earlier in the day) and my dinner preparations (shrimp and veggies
56
- on the grill).<div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s4032/Jan%207.jpg\"><img
57
- height=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s320/Jan%207.jpg\"
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- width=\"240\" /></a></div><br /><div><div>I''ve decided to start writing here
59
- at <i>Quintessence of Dust</i>, after another long hiatus. Here are some of
60
- my reasons.</div><div><br /></div><div>1. I like to write, and I have things
61
- to say, and I self-identify as an author. For eight years, I have co-organized
62
- and taught in the <a href=\"https://meetings.cshl.edu/courses.aspx?course=C-WRITE&amp;year=23\"
63
- target=\"_blank\">Scientific Writing Retreat at Cold Spring Harbor Laboratory</a>.
64
- I''m a writer and I need to write, if only for myself.</div><div><br /></div><div>2.
65
- I have an idea for a book, along with some introductory work (but no sample
66
- chapters yet) and writing here will help me develop those thoughts. The idea
67
- is over twelve years old and has never faded away, which I take to mean that
68
- I need to get it out of my system somehow.</div><div><br /></div><div>3. I
69
- have other ideas kicking around in my head and most of them are worth writing
70
- about. I have one new intellectual passion that is totally worth writing about:
71
- <a href=\"https://skyislandalliance.org/the-sky-islands/\" target=\"_blank\">the
72
- Sky Islands</a> that nearly surround us here in Tucson.</div><div><br /></div><div>4.
73
- I have an exciting new job with great new people at <a href=\"https://plos.org/\"
74
- target=\"_blank\">an organization</a> that''s all in for <a href=\"https://plos.org/open-science/\"
75
- target=\"_blank\">open science</a>. I recently turned over the tens digit
76
- on my age-o-meter. My kids will very soon be all out of college. (One is about
77
- to start a postdoc!) All of this led, predictably, to a spasm of reflection
78
- on projects and vision. One clear result is that I''m feeling more inspired.<span><a
79
- name=\"more\"></a></span></div><div><br /></div><div>5. The demise of Twitter
80
- has led to a lot of <a href=\"https://www.theatlantic.com/technology/archive/2022/11/twitter-facebook-social-media-decline/672074/\"
81
- target=\"_blank\">useful commentary</a> about the nature of social media.
82
- I left Facebook two years ago and all but left Twitter two months ago. I''m
83
- on a <a href=\"https://fediscience.org/explore\" target=\"_blank\">good server
84
- at Mastodon</a> and I like it; maybe microblogging there can satisfy my desire
85
- for conversation and connection. But <a href=\"https://www.theverge.com/23513418/bring-back-personal-blogging\"
86
- target=\"_blank\">this recent piece</a> at <i>The Verge</i> by <a href=\"https://moniquejudge.com/\"
87
- target=\"_blank\">Monique Judge</a> convinced me that blogging could (again)
88
- have a place in the future.</div><div><br /><div>Here''s her summary, emphasis
89
- mine:</div><div><blockquote>At the end of the day, we don’t know what is going
90
- to happen next with Twitter or any of these platforms. We don’t know what
91
- changes <a href=\"https://www.techtarget.com/whatis/definition/Web-30\" target=\"_blank\">Web
92
- 3.0</a> is going to bring to the internet. We do know that <b>we will all
93
- still be here, wanting to share our thoughts, talk about anything and everything,
94
- and commune with our people</b>. Personal blogging is the simplest and fastest
95
- way to do all of that. </blockquote></div><div>That''s what I want! A place
96
- to write, and (if I''m lucky) a place to discuss and \"commune\" with people.
97
- That used to happen a lot at <i>Quintessence of Dust</i>.<span></span></div></div></div><div><br
98
- /></div><div>Okay, but why here? This blog is over 15 years old and was started
99
- when I was a Christian believer. <a href=\"https://sfmatheson.blogspot.com/2007/08/kicking-off-my-blog.html\"
100
- target=\"_blank\">Its founding themes</a> were anchored in a desire to help
101
- Christians understand and enjoy biology, to help them shake free of misinformation
102
- and dishonesty. It has twice languished through long hiatuses and was <a href=\"https://sfmatheson.blogspot.com/p/about.html\"
103
- target=\"_blank\">remodeled</a> back in 2017 a few years after I deconverted.
104
- Maybe it''s time to start anew? I think not, for many of those same reasons:
105
- I''m still a biologist who loves science, still worried about misinformation,
106
- and still rooted in the power of scientific explanation. I''m still a bardolator
107
- and a Red Sox fan. <a href=\"https://sfmatheson.blogspot.com/p/about.html\">I''m
108
- still me</a>, and <i>Quintessence of Dust</i> is still my blog. The new <a
109
- href=\"https://sfmatheson.blogspot.com/p/about.html\" target=\"_blank\">About
110
- page</a> is slightly remodeled from 2017, and hints at the next post, which
111
- will outline some new goals and ongoing projects.</div><div><br /></div><div>A
112
- final note on inspiration, from Imani Perry, writing in her newsletter (<a
113
- href=\"https://newsletters.theatlantic.com/unsettled-territory/\" target=\"_blank\">Unsettled
114
- Territory</a>) at <i>The Atlantic</i>. The piece is \"<a href=\"https://newsletters.theatlantic.com/unsettled-territory/63af3facace609003751bacc/becoming-writer-habit-journalism/\"
115
- target=\"_blank\">Writing is a Democratic Art</a>.\" It''s for subscribers
116
- only but here is her challenge:</div><div><blockquote>Thinking and writing
117
- at a faster pace stretched me and gave me greater confidence. Sometimes I
118
- changed my mind about what I’d written a day later. But that was okay; a newsletter
119
- is a moment in time. Writing it each week gave me a lovely rhythm in what
120
- has otherwise been a difficult and disorienting season in history. Feeling
121
- stuck can get you stuck. But writing can, and should, inspire deeds.</blockquote></div>","published_at":1673233380,"updated_at":1680470227,"indexed_at":1689006804,"authors":[{"url":null,"name":"Stephen
122
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124
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125
- and human nature, focusing on genetics, development, evolution, neuroscience,
126
- systems biology, and topics related to scientific literacy. I occasionally
127
- discuss intelligent design, creationism, science denial, and other political/social
128
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129
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131
- recorded_at: Wed, 06 Sep 2023 14:27:24 GMT
48
+ on the grill).I''ve decided to start writing here at <i>Quintessence of Dust</i>,
49
+ after another long hiatus.","tags":["Introduction"],"title":"Quintessence
50
+ of Dust 2023 restart: the why","updated_at":1680470227,"url":"http://sfmatheson.blogspot.com/2023/01/quintessence-of-dust-2023-restart-why.html"}
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48
- years and a million links","summary":"As trailed on a Twitter thread last
49
- week I’ve been working on a manuscript describing the efforts to map taxonomic
50
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51
- trailed on a Twitter thread last week I’ve been working on a manuscript describing
52
- the efforts to map taxonomic names to their original descriptions in the taxonomic
53
- literature.</p>\n<blockquote><p>Putting together a manuscript on linking taxonomic
54
- names to the primary literature, basically “um, what, exactly, have you been
55
- doing all these years?”. TL;DR Across fungi, plants, and animals approx 1.3
56
- million names have been linked to a persistent identifier for a publication.</p>—
57
- Roderic Page (@rdmpage) <a href=\"https://twitter.com/rdmpage/status/1661714128413573120?ref_src=twsrc%5Etfw\">May
58
- 25, 2023</a></blockquote> \n<p>The preprint is on bioRxiv <a href=\"https://doi.org/10.1101/2023.05.29.542697\">doi:10.1101/2023.05.29.542697</a></p>\n<blockquote>\n<p>A
59
- major gap in the biodiversity knowledge graph is a connection between taxonomic
60
- names and the taxonomic literature. While both names and publications often
61
- have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs)
62
- or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to
63
- DOIs for publications. This article describes efforts to make those connections
64
- across three large taxonomic databases: Index Fungorum, International Plant
65
- Names Index (IPNI), and the Index of Organism Names (ION). Over a million
66
- names have been matched to DOIs or other persistent identifiers for taxonomic
67
- publications. This represents approximately 36% of names for which publication
68
- data is available. The mappings between LSIDs and publication PIDs are made
69
- available through ChecklistBank. Applications of this mapping are discussed,
70
- including a web app to locate the citation of a taxonomic name, and a knowledge
71
- graph that uses data on researcher’s ORCID ids to connect taxonomic names
72
- and publications to authors of those names.</p>\n</blockquote>\n<p>Much of
73
- the work has been linking taxa to names, which still has huge gaps. There
74
- are also interesting differences in coverage between plants, animals, and
75
- fungi (see preprint for details).</p>\n\n<div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"><img
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- width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png\"
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- /></a></div><div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s2276/fungi-coverage.png\"><img
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- width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s320/fungi-coverage.png\"
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- /></a></div><div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"><img
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- width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s320/plants-coverage.png\"
81
- /></a></div>\n\n\nThere is also a simple app to demonstrate these links, see
82
- <a href=\"https://species-cite.herokuapp.com\">https://species-cite.herokuapp.com</a>.\n\n\n\n<blockquote>\n<p>Written
83
- with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","published_at":1685553960,"updated_at":1685554180,"indexed_at":1689933917,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
84
- Page"}],"image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png","tags":[],"language":"en","reference":[],"relationships":[],"blog_id":"tyfqw20","blog_name":"iPhylo","blog_slug":"iphylo","blog":{"id":"tyfqw20","title":"iPhylo","description":"Rants,
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85
36
  raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
86
37
  and biodiversity informatics. For more ranty and less considered opinions,
87
38
  see my <a href=\"https://twitter.com/rdmpage\">Twitter feed</a>.<br>ISSN 2051-8188.
88
39
  Written content on this site is licensed under a <a href=\"https://creativecommons.org/licenses/by/4.0/\">Creative
89
- Commons Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","home_page_url":"https://iphylo.blogspot.com","user_id":"b98bb1b6-b96b-4e8a-94d3-4285ea715f5b","created_at":"2023-02-06","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
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- recorded_at: Wed, 06 Sep 2023 14:27:23 GMT
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+ Commons Attribution 4.0 International license</a>.","favicon":null,"feed_format":"application/atom+xml","feed_url":"https://iphylo.blogspot.com/feeds/posts/default","filter":null,"funding":null,"generator":"Blogger
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42
+ trailed on a Twitter thread last week I\u2019ve been working on a manuscript
43
+ describing the efforts to map taxonomic names to their original descriptions
44
+ in the taxonomic literature.","tags":[],"title":"Ten years and a million links","updated_at":1685554180,"url":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html"}
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48
- to Build an Academic Powerhouse: Let''s Study Who''s Doing it","summary":"Students
49
- and residents aspiring for a career in academic surgery are looking for training
50
- programs that will help jumpstart their careers by exposing them to mentorship
51
- and opportunities to conduct research. While the gold standard of academic
52
- productivity (for the time being) remains peer-reviewed publications, conference
53
- posters and presentations are an important secondary metric.","content_html":"<p>Students
35
+ string: '{"archive_url":null,"authors":[{"name":"Tejas S. Sathe","url":"https://orcid.org/0000-0003-0449-4469"}],"blog":{"api":true,"archive_prefix":null,"authors":null,"backlog":0,"canonical_url":null,"category":"clinicalMedicine","created_at":"2023-01-04","current_feed_url":null,"description":"Innovation
36
+ and Design Experiments in Academic Surgery (I.D.E.A.S.)","favicon":"https://www.ideasurg.pub/favicon.png","feed_format":"application/rss+xml","feed_url":"https://www.ideasurg.pub/rss/","filter":null,"funding":null,"generator":"Ghost
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+ 5.66","home_page_url":"https://www.ideasurg.pub","id":"3cxcm20","issn":"2993-1150","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","modified_at":"2023-07-29T22:28:28+00:00","plan":"Starter","prefix":"10.59350","relative_url":null,"slug":"ideas","status":"active","title":"I.D.E.A.S.","use_api":null,"use_mastodon":false,"user_id":"4cecb4b8-58b5-49fe-9edb-6af638294ef5","version":"https://jsonfeed.org/version/1.1"},"blog_name":"I.D.E.A.S.","blog_slug":"ideas","doi":"https://doi.org/10.59350/ytvy2-59450","id":"153d65e1-f0e4-49a6-a969-33d2129800ba","image":"https://www.ideasurg.pub/content/images/2023/06/Frame-2-1.png","indexed_at":1690923223,"language":"en","published_at":1685768070,"reference":[],"relationships":[],"summary":"Students
54
38
  and residents aspiring for a career in academic surgery are looking for training
55
39
  programs that will help jumpstart their careers by exposing them to mentorship
56
40
  and opportunities to conduct research. While the gold standard of academic
57
41
  productivity (for the time being) remains peer-reviewed publications, conference
58
- posters and presentations are an important secondary metric. In addition to
59
- feeding eventual papers, conference talks allow trainees to practice presentation
60
- skills, build their networks, and learn about the work being done at peer
61
- institutions and the field more broadly. Residents pursuing professional development
62
- are encouraged to apply to and attend conferences--though in the post-COVID
63
- era the cost of conference attendance and travel are being re-evaluated. For
64
- now, academic conference participation can serve as an important albeit limited
65
- metric to evaluate an overall institution''s research power – especially as
66
- it relates to trainees.</p><p>The <a href=\"https://www.academicsurgicalcongress.org/?ref=ideasurg.pub\">Academic
67
- Surgical Congress</a> (ASC) is a joint surgical meeting co-hosted by the <a
68
- href=\"https://www.aasurg.org/?ref=ideasurg.pub\">Association for Academic
69
- Surgery</a> (AAS) and the <a href=\"https://www.susweb.org/?ref=ideasurg.pub\">Society
70
- for University Surgeons</a> (SUS) and held annually in February. Anecdotally,
71
- it is a popular conference for students and residents to attend. The ASC maintains
72
- a public archive of all abstracts dating from 2015-2020. We obtained a machine
73
- readable version of this public database through the webmaster (this version
74
- of the data spans 2016 to 2023). Using number of accepted abstracts as a surrogate
75
- for research productivity, we wanted to identify successful institutions.
76
- Conceivably, by finding institutions who achieved high abstract numbers, we
77
- could conduct interviews and focus groups among key stakeholders at these
78
- programs to understand what they did, and how these actions can be replicated.
79
- We were particularly interested in seeing which programs demonstrated a high
80
- number of absolute accepted abstracts within the study period and also which
81
- programs were able to improve their abstract performance from year to year.
82
- </p><p>For each abstract, we looked at the year and primary institution at
83
- which the work was conducted. In the dataset, all of the institutional affiliations
84
- for each author are combined in one text string. To figure out the primary
85
- institution, we searched the institution block string for the first presence
86
- of \"university\", \"hospital\", \"institute\", or \"medical center\" or the
87
- first expression to occur before a comma. This method was chosen as institutions’
88
- names are written variably (Department of Surgery, University Hospital, New
89
- York, NY vs. University Hospital, Division of Colorectal Surgery, Department
90
- of Surgery, New York, NY). Next, we found that for several abstracts belonging
91
- to the same institution in reality, the institution name was written in various
92
- ways (e.g. University of Alabama vs. University of Alabama - Birmingham or
93
- University of California - Los Angeles vs. David Geffen School of Medicine).
94
- We attempted fuzzy string matching as well as some manual corrections to improve
95
- this issue. While our efforts were not able to achieve perfect results, we
96
- were able to resolve a majority of the mismatches.</p><p>In order to do a
97
- primary survey of institutional trends in this dataset, we conducted the following
98
- analyses. First, we measured the number of abstracts accepted each year from
99
- 2016 to 2023. Second, we looked at the number of accepted abstracts by institution
100
- over the entire study period and identified the top twenty institutions. Then,
101
- we looked at the number of abstract institutions by year for each of these
102
- top twenty institutions to study changes in institutional trends over time.
103
- Finally, we did a subset analysis on post-COVID data (2021 to 2023) to look
104
- at absolute and per cent year-over-year changes in accepted abstracts to see
105
- which institutions were able to significantly increase their abstract performance
106
- in one year. </p><h3>Accepted Abstracts are increasing but down from peak</h3><p>There
107
- were a total of 10,396 unique abstracts accepted at the Academic Surgical
108
- Congress between 2016 and 2023 for which complete institutional data is available.</p><p>We
109
- plotted the total number of abstracts accepted by year. The number of accepted
110
- abstracts increased from 1125 in 2016 to an all-time high of 1742 in 2020
111
- before declining to 922 and 848 in 2021 and 2022, respectively. Accepted abstracts
112
- have since rebounded to 1469 in 2023, or roughly 84% of the maximum amount.
113
- Of note, the 2021 and 2022 meetings were held virtually due to the COVID-19
114
- pandemic. Conversely the 2020 meeting was held immediately prior to the institution
115
- of lockdowns and other social distancing policies.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-2-1.png\"
116
- loading=\"lazy\" width=\"2000\" height=\"1251\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-2-1.png
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- 600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-2-1.png
118
- 1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-2-1.png
119
- 1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-2-1.png
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- 2400w\" /><figcaption>Number of accepted abstracts at the Academic Surgical
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- Congress by year from 2016-2023</figcaption></figure><h3>Alabama, Michigan
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- lead abstract acceptances during study period</h3><p>Next, we plotted the
123
- total number of accepted abstracts by institution. The graph shows data for
124
- the twenty leading institutions. The University of Alabama and the University
125
- of Michigan lead in abstract acceptances during the study period (509 and
126
- 382, respectively). Given an eight year time-range, the top twenty institutions
127
- reflect an average annual abstract acceptance ranging from roughly seventeen
128
- to 63.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-1.png\"
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- loading=\"lazy\" width=\"2000\" height=\"1061\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-1.png
130
- 600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-1.png
131
- 1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-1.png
132
- 1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-1.png
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- 2400w\" /><figcaption>Number of accepted ASC abstracts for the top twenty
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- institutions from 2016-2023</figcaption></figure><p>We also plotted the number
135
- of accepted abstracts by year using a separate line plot for each institution.
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- The University of Alabama surged from 15 to 58 abstracts from 2016 and 2017,
137
- maintaining over 60 abstracts per year thereafter. The University of Michigan
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- maintained between 30 and 60 abstracts for each year and has ranked in the
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- top three for each year studied. Overall, there appears to be a general clustering
140
- of the remaining institutions.</p><p>Of note, there is a noticeable dip from
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- 2020 to 2022 seen at most institutions which starts to recover in 2023, consistent
142
- with the aggregated data shown in the previous figure.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-3.png\"
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- loading=\"lazy\" width=\"2000\" height=\"1359\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-3.png
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- 600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-3.png
145
- 1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-3.png
146
- 1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-3.png
147
- 2400w\" /></figure><h3>MGH, Brigham lead absolute and per cent increase in
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- abstracts in 2023</h3><p>Next, we measured the absolute and percent change
149
- between accepted abstracts in consecutive years for the top twenty institutions.
150
- We restricted our analysis to 2021, 2022, and 2023. The greatest absolute
151
- increases in accepted abstracts came from Massachusetts General Hospital in
152
- 2023 (28), The University of Pennsylvania (17), and Brigham and Women''s Hospital
153
- (15), all in 2023. The greatest percentage increases in accepted abstracts
154
- came from Brigham and Women''s Hospital (500%), Massachusetts General Hospital
155
- (400%), and Yale Univeristy (275%), also all in 2023. Interestingly, University
156
- of Alabama (+0 in 2022, +5 in 2023) and University of Michigan (+5 in 2022,
157
- +8 in 2023)  - which rank at the top in all time and yearly abstracts - experienced
158
- less extreme swings during the 2021-2023 time period. The greatest year-over-year
159
- increase in the study period was University of Alabama''s increase of 43 abstracts
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- in 2017, but as it falls outside the time range of this subset analysis, that
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- data is not shown here.</p><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-4--5-.png\"
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- loading=\"lazy\" width=\"2000\" height=\"903\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-4--5-.png
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- 600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-4--5-.png
164
- 1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-4--5-.png
165
- 1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-4--5-.png
166
- 2400w\" /><figcaption>Year-over-year absolute change in ASC accepted abstracts
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- from 2021-2023</figcaption></figure><figure><img src=\"https://www.ideasurg.pub/content/images/2023/06/Frame-5--9-.png\"
168
- loading=\"lazy\" width=\"2000\" height=\"884\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/Frame-5--9-.png
169
- 600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/Frame-5--9-.png
170
- 1000w, https://www.ideasurg.pub/content/images/size/w1600/2023/06/Frame-5--9-.png
171
- 1600w, https://www.ideasurg.pub/content/images/size/w2400/2023/06/Frame-5--9-.png
172
- 2400w\" /><figcaption>Year-over-year percent change in ASC accepted abstracts
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- from 2021-2023</figcaption></figure><h3>Conclusions</h3><p>In this data exploration,
174
- we analyzed abstract acceptance data for the Academic Surgical Congress between
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- 2016 and 2023. We showed that the number of abstracts increased from 2016
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- to 2020, dipped in 2021 and 2022, and is recovering in 2023 - likely reflecting
177
- the variability forced by COVID19 and the transition to virtual conferences
178
- in 2021 and 2022. We also showed that the University of Alabama and the University
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- of Michigan have significantly led accepted abstracts throughout the study
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- period with University of Alabama maintaining a top position following an
181
- impressive 287% percent increase in abstracts between 2016 and 2017. In 2023,
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- Massachusetts General Hospital and Brigham and Women''s Hospital rank in the
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- top three for both absolute and percent changes in year-over-year abstract
184
- acceptances in 2023. </p><h3>Limitations and Future Directions</h3><p>This
185
- data exploration has several limitations. First, our study is limited to one
186
- conference, and conferences themselves are only a limited component of academic
187
- productivity. However, the Academic Surgical Congress is an international
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- meeting that is well regarded, popular among trainees, and has consistent
189
- multi-year data. We can improve the generalizability of our findings by bringing
190
- in similar data from other large meetings – such as the American College of
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- Surgeons Clinical Congress and the Society of American Gastrointestinal and
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- Endoscopic Surgeons (SAGES). We can also use the PubMed API to perform similar
193
- analyses in top surgical journals such as JAMA Surgery or the Annals of Surgery.</p><p>Furthermore,
194
- there is renewed concern that the <a href=\"https://jamanetwork.com/journals/jamasurgery/article-abstract/2797087?ref=ideasurg.pub\">ever-increasing
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- number</a> of abstracts and papers required for trainees to progress academically
196
- is leading to an unhealthy \"research treadmill\". While these concerns are
197
- valid, research productivity remains an important component of academic development,
198
- and number of abstract acceptances can serve as a meaningful metric in guaging
199
- an institution''s research productivity and culture.</p><p>Another limitation
200
- of our study is our assumption that the first institution listed in the author
201
- block is the primary institution–a method which does not take into account
202
- multi-institutional abstracts. However, we suspect this reflects the minority
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- of the abstracts. Finally, we have not fully optimized name-matching to correctly
204
- combine terms like \"University of Alabama\" and \"University of Alabama Birmingham\".
205
- One future direction to improve this analysis would be to optimize the fuzzy
206
- string matching algorithm used in our code. Alternatively, more granular source
207
- data could also help improve the accuracy of our findings.</p><p>With regards
208
- to the data we have obtained, we can conduct survey-based studies or focus
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- groups with key stakeholders from institutions that have demonstrated strong
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- abstract performance during the study period as well as those who have shown
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- significant improvement. By talking to department chairs, program directors,
212
- and research and education leaders we can understand what steps each institution
213
- took to improve abstract acceptance (e.g. hiring a new research faculty, creating
214
- a mentorship program, providing administrative support for IRBs/stats etc.).
215
- Following this, we can map individual interventions to improvements to understand
216
- the contribution that each can have on increased academic productivity.</p><p>We
217
- have also not yet mined the abstract text itself for themes. Using natural
218
- language processing, we can understand how themes and trends of emergent research
219
- change from year to year, and even develop models to predict which topics
220
- will be of interest in future works. This will likely be the subject of a
221
- future data exploration.</p><p>Overall, we hope to demonstrate that abstract
222
- acceptance data from a single international meeting can provide interesting,
223
- meaningful data on which programs have strong research infrastructure and
224
- which programs are making strides to achieve it. By studying this data and
225
- improving the inputs, we can better understand whose example to follow and
226
- ultimately develop a playbook that all institutions can employ to maximize
227
- the academic opportunities of students and trainees.</p><h3>See the Data</h3><p>You
228
- can see the raw data as well as all of our code <a href=\"https://deepnote.com/@tejas-sathe-a73f/ASC-Data-Exploration-948ca211-bfc7-459b-9d6d-ef952a5baf32?ref=ideasurg.pub\">here</a>,
229
- and use this for your own studies with appropriate attribution.</p><h3>Acknowledgements</h3><p>Special
230
- thanks to Ojas Sathe for assistance with the fuzzy string matching</p>","published_at":1685768070,"updated_at":1685768070,"indexed_at":1690923223,"authors":[{"url":"https://orcid.org/0000-0003-0449-4469","name":"Tejas
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- S. Sathe"}],"image":"https://www.ideasurg.pub/content/images/2023/06/Frame-2-1.png","tags":["Preprint"],"language":"en","reference":[],"relationships":[],"blog_id":"3cxcm20","blog_name":"I.D.E.A.S.","blog_slug":"ideas","blog":{"id":"3cxcm20","title":"I.D.E.A.S.","description":"Innovation
232
- and Design Experiments in Academic Surgery (I.D.E.A.S.)","language":"en","favicon":"https://www.ideasurg.pub/favicon.png","feed_url":"https://www.ideasurg.pub/rss/","home_page_url":"https://www.ideasurg.pub","user_id":"4cecb4b8-58b5-49fe-9edb-6af638294ef5","created_at":"2023-01-04","feed_format":"application/rss+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Ghost
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- 5.61","category":"clinicalMedicine","prefix":"10.59350","modified_at":"2023-07-29T22:28:28+00:00","version":"https://jsonfeed.org/version/1.1","current_feed_url":null,"status":"active","issn":"2993-1150","backlog":0,"authors":null,"plan":"Starter","slug":"ideas","use_mastodon":false}}'
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- recorded_at: Wed, 06 Sep 2023 14:27:25 GMT
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+ posters and presentations are an important secondary metric.","tags":["Preprint"],"title":"How
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+ to Build an Academic Powerhouse: Let''s Study Who''s Doing it","updated_at":1685768070,"url":"https://www.ideasurg.pub/academic-powerhouse"}
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+
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+ '
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+ recorded_at: Thu, 05 Oct 2023 20:37:41 GMT
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  recorded_with: VCR 6.2.0