commonmeta-ruby 3.5.5 → 3.6

Sign up to get free protection for your applications and to get access to all the features.
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
  187. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_relations_and_funding.yml +55 -133
  188. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_upstream_blog.yml +21 -224
  189. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +134 -330
  190. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/posted_content.yml +19 -19
  191. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_another_science_blog.yml +9 -9
  192. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_front_matter.yml +92 -91
  193. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_upstream_blog.yml +6 -6
  194. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/Another_dataset.yml +8 -8
  195. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/BlogPosting.yml +10 -10
  196. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/BlogPosting_schema_org.yml +146 -147
  197. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/Dataset.yml +10 -10
  198. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/container_title.yml +16 -21
  199. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/interactive_resource_without_dates.yml +8 -8
  200. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/journal_article.yml +16 -16
  201. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/keywords_subject_scheme.yml +8 -8
  202. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/maremma.yml +10 -10
  203. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/missing_creator.yml +15 -15
  204. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/multiple_abstracts.yml +8 -8
  205. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/organization_author.yml +22 -22
  206. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/software.yml +8 -8
  207. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/software_w/version.yml +8 -8
  208. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/with_only_first_page.yml +16 -16
  209. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/with_pages.yml +16 -16
  210. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/climate_data.yml +10 -10
  211. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/maremma.yml +10 -10
  212. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/text.yml +8 -8
  213. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/with_data_citation.yml +16 -16
  214. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/with_pages.yml +16 -16
  215. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/dissertation.yml +20 -20
  216. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/from_schema_org.yml +146 -147
  217. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/journal_article.yml +22 -22
  218. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/maremma.yml +10 -10
  219. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/with_ORCID_ID.yml +16 -16
  220. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/with_data_citation.yml +16 -16
  221. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/Dataset_in_schema_4_0.yml +10 -10
  222. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/Text_pass-thru.yml +8 -8
  223. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/book_chapter.yml +15 -15
  224. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/from_schema_org.yml +146 -147
  225. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/interactive_resource_without_dates.yml +8 -8
  226. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/maremma.yml +10 -10
  227. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_ORCID_ID.yml +16 -16
  228. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_data_citation.yml +16 -16
  229. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_editor.yml +17 -17
  230. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/BlogPosting.yml +10 -10
  231. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/BlogPosting_schema_org.yml +145 -146
  232. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/Dataset.yml +10 -10
  233. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/alternate_name.yml +8 -8
  234. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/journal_article.yml +9 -9
  235. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/keywords_with_subject_scheme.yml +8 -8
  236. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/maremma.yml +10 -10
  237. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/with_pages.yml +10 -10
  238. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Another_Schema_org_JSON.yml +10 -10
  239. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Funding.yml +13 -13
  240. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Funding_OpenAIRE.yml +13 -13
  241. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Schema_org_JSON.yml +8 -8
  242. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Schema_org_JSON_Cyark.yml +13 -13
  243. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/alternate_identifiers.yml +13 -13
  244. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/data_catalog.yml +13 -13
  245. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/geo_location_box.yml +13 -13
  246. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/interactive_resource_without_dates.yml +13 -13
  247. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/journal_article.yml +16 -16
  248. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/maremma_schema_org_JSON.yml +11 -11
  249. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/series_information.yml +17 -16
  250. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/subject_scheme.yml +15 -15
  251. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/subject_scheme_multiple_keywords.yml +13 -13
  252. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/BlogPosting.yml +10 -10
  253. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/Dataset.yml +10 -10
  254. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/journal_article.yml +16 -16
  255. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/with_pages.yml +16 -16
  256. data/spec/readers/cff_reader_spec.rb +2 -20
  257. data/spec/readers/crossref_reader_spec.rb +10 -16
  258. data/spec/readers/crossref_xml_reader_spec.rb +61 -64
  259. data/spec/readers/json_feed_reader_spec.rb +56 -56
  260. data/spec/readers/schema_org_reader_spec.rb +1 -1
  261. data/spec/utils_spec.rb +1 -1
  262. data/spec/writers/crossref_xml_writer_spec.rb +9 -8
  263. data/spec/writers/csv_writer_spec.rb +1 -1
  264. data/spec/writers/ris_writer_spec.rb +2 -2
  265. metadata +2 -11
  266. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_crossref_xml_refresh.yml +0 -107
  267. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/doi_prefix/doi_prefix_by_blog.yml +0 -997
  268. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/doi_prefix/doi_prefix_by_uuid.yml +0 -256
  269. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_uuid.yml +0 -256
  270. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_uuid_unknown_uuid.yml +0 -49
  271. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/missing_creator.yml +0 -307
  272. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_uuid.yml +0 -136
  273. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_uuid_specific_prefix.yml +0 -256
  274. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/book_oup.yml +0 -107
@@ -2,61 +2,9 @@
2
2
  http_interactions:
3
3
  - request:
4
4
  method: get
5
- uri: https://doi.org/ra/10.1186
6
- body:
7
- encoding: UTF-8
8
- string: ''
9
- headers:
10
- Connection:
11
- - close
12
- Host:
13
- - doi.org
14
- User-Agent:
15
- - http.rb/5.1.1
16
- response:
17
- status:
18
- code: 200
19
- message: OK
20
- headers:
21
- Date:
22
- - Sun, 18 Jun 2023 15:21:15 GMT
23
- Content-Type:
24
- - application/json;charset=UTF-8
25
- Transfer-Encoding:
26
- - chunked
27
- Connection:
28
- - close
29
- Permissions-Policy:
30
- - interest-cohort=(),browsing-topics=()
31
- Cf-Cache-Status:
32
- - DYNAMIC
33
- Report-To:
34
- - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=jEbMi2ErrnPyP2Iq6xlESbzkk0Kk4PUNJdk%2FeUk%2FS4%2BAI3xYDcMkNRvB0%2FJgzrRnM7MXGrzvnlUK6mnZY93kQHm6ZPhC7KhXPm1w6FKV4wlPzRJO987DbdQUPyHi%2FfbELIs%2Bddk%3D"}],"group":"cf-nel","max_age":604800}'
35
- Nel:
36
- - '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}'
37
- Strict-Transport-Security:
38
- - max-age=31536000; includeSubDomains; preload
39
- Server:
40
- - cloudflare
41
- Cf-Ray:
42
- - 7d94855eaec2b8d0-AMS
43
- Alt-Svc:
44
- - h3=":443"; ma=86400
45
- body:
46
- encoding: UTF-8
47
- string: |-
48
- [
49
- {
50
- "DOI": "10.1186",
51
- "RA": "Crossref"
52
- }
53
- ]
54
- recorded_at: Sun, 18 Jun 2023 15:21:15 GMT
55
- - request:
56
- method: get
57
- uri: https://api.crossref.org/works/10.1186/1471-2164-7-187
5
+ uri: https://api.crossref.org/works/10.1186/1471-2164-7-187/transform/application/vnd.crossref.unixsd+xml
58
6
  body:
59
- encoding: UTF-8
7
+ encoding: ASCII-8BIT
60
8
  string: ''
61
9
  headers:
62
10
  Connection:
@@ -71,11 +19,15 @@ http_interactions:
71
19
  message: OK
72
20
  headers:
73
21
  Date:
74
- - Sun, 18 Jun 2023 15:21:15 GMT
75
- Content-Type:
76
- - application/json
22
+ - Thu, 05 Oct 2023 19:46:21 GMT
77
23
  Transfer-Encoding:
78
24
  - chunked
25
+ Link:
26
+ - <http://dx.doi.org/10.1186/1471-2164-7-187>; rel="canonical", <http://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf>;
27
+ version="vor"; type="application/pdf"; rel="item", <http://link.springer.com/article/10.1186/1471-2164-7-187/fulltext.html>;
28
+ version="vor"; type="text/html"; rel="item", <https://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf>;
29
+ version="vor"; type="application/pdf"; rel="item", <http://creativecommons.org/licenses/by/2.0>;
30
+ version="tdm"; rel="license"
79
31
  Access-Control-Expose-Headers:
80
32
  - Link
81
33
  Access-Control-Allow-Headers:
@@ -100,491 +52,124 @@ http_interactions:
100
52
  Connection:
101
53
  - close
102
54
  body:
103
- encoding: UTF-8
104
- string: '{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T12:26:22Z","timestamp":1684931182250},"reference-count":38,"publisher":"Springer
105
- Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2006,7,25]],"date-time":"2006-07-25T00:00:00Z","timestamp":1153785600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC
106
- Genomics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n <jats:sec>\n <jats:title>Background<\/jats:title>\n <jats:p>Accurate
107
- evaluation of the quality of genomic or proteomic data and computational methods
108
- is vital to our ability to use them for formulating novel biological hypotheses
109
- and directing further experiments. There is currently no standard approach
110
- to evaluation in functional genomics. Our analysis of existing approaches
111
- shows that they are inconsistent and contain substantial functional biases
112
- that render the resulting evaluations misleading both quantitatively and qualitatively.
113
- These problems make it essentially impossible to compare computational methods
114
- or large-scale experimental datasets and also result in conclusions that generalize
115
- poorly in most biological applications.<\/jats:p>\n <\/jats:sec>\n <jats:sec>\n <jats:title>Results<\/jats:title>\n <jats:p>We
116
- reveal issues with current evaluation methods here and suggest new approaches
117
- to evaluation that facilitate accurate and representative characterization
118
- of genomic methods and data. Specifically, we describe a functional genomics
119
- gold standard based on curation by expert biologists and demonstrate its use
120
- as an effective means of evaluation of genomic approaches. Our evaluation
121
- framework and gold standard are freely available to the community through
122
- our website.<\/jats:p>\n <\/jats:sec>\n <jats:sec>\n <jats:title>Conclusion<\/jats:title>\n <jats:p>Proper
123
- methods for evaluating genomic data and computational approaches will determine
124
- how much we, as a community, are able to learn from the wealth of available
125
- data. We propose one possible solution to this problem here but emphasize
126
- that this topic warrants broader community discussion.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2164-7-187","type":"journal-article","created":{"date-parts":[[2006,7,25]],"date-time":"2006-07-25T18:14:51Z","timestamp":1153851291000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":170,"title":["Finding
127
- function: evaluation methods for functional genomic data"],"prefix":"10.1186","volume":"7","author":[{"given":"Chad
128
- L","family":"Myers","sequence":"first","affiliation":[]},{"given":"Daniel
129
- R","family":"Barrett","sequence":"additional","affiliation":[]},{"given":"Matthew
130
- A","family":"Hibbs","sequence":"additional","affiliation":[]},{"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[]},{"given":"Olga
131
- G","family":"Troyanskaya","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,7,25]]},"reference":[{"key":"570_CR1","volume-title":"Bioinformatics","author":"Z
132
- Barutcuoglu","year":"2006","unstructured":"Barutcuoglu Z, Schapire RE, Troyanskaya
133
- OG: Hierarchical multi-label prediction of gene function. Bioinformatics.
134
- 2006"},{"issue":"Suppl 2","key":"570_CR2","doi-asserted-by":"publisher","first-page":"II42","DOI":"10.1093\/bioinformatics\/btg1058","volume":"19","author":"A
135
- Clare","year":"2003","unstructured":"Clare A, King RD: Predicting gene function
136
- in Saccharomyces cerevisiae. Bioinformatics. 2003, 19 (Suppl 2): II42-II49.","journal-title":"Bioinformatics"},{"key":"570_CR3","first-page":"300","volume-title":"Pac
137
- Symp Biocomput","author":"GR Lanckriet","year":"2004","unstructured":"Lanckriet
138
- GR, Deng M, Cristianini N, Jordan MI, Noble WS: Kernel-based data fusion and
139
- its application to protein function prediction in yeast. Pac Symp Biocomput.
140
- 2004, 300-311."},{"issue":"2","key":"570_CR4","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1089\/10665270252935539","volume":"9","author":"P
141
- Pavlidis","year":"2002","unstructured":"Pavlidis P, Weston J, Cai J, Noble
142
- WS: Learning gene functional classifications from multiple data types. J Comput
143
- Biol. 2002, 9 (2): 401-411. 10.1089\/10665270252935539.","journal-title":"J
144
- Comput Biol"},{"issue":"Suppl 1","key":"570_CR5","doi-asserted-by":"publisher","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","volume":"21","author":"A
145
- Ben-Hur","year":"2005","unstructured":"Ben-Hur A, Noble WS: Kernel methods
146
- for predicting protein-protein interactions. Bioinformatics. 2005, 21 (Suppl
147
- 1): i38-i46. 10.1093\/bioinformatics\/bti1016.","journal-title":"Bioinformatics"},{"issue":"5644","key":"570_CR6","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1126\/science.1087361","volume":"302","author":"R
148
- Jansen","year":"2003","unstructured":"Jansen R, Yu H, Greenbaum D, Kluger
149
- Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian
150
- networks approach for predicting protein-protein interactions from genomic
151
- data. Science. 2003, 302 (5644): 449-453. 10.1126\/science.1087361.","journal-title":"Science"},{"issue":"5701","key":"570_CR7","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1126\/science.1099511","volume":"306","author":"I
152
- Lee","year":"2004","unstructured":"Lee I, Date SV, Adai AT, Marcotte EM: A
153
- probabilistic functional network of yeast genes. Science. 2004, 306 (5701):
154
- 1555-1558. 10.1126\/science.1099511.","journal-title":"Science"},{"issue":"1","key":"570_CR8","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1186\/1471-2105-5-154","volume":"5","author":"N
155
- Lin","year":"2004","unstructured":"Lin N, Wu B, Jansen R, Gerstein M, Zhao
156
- H: Information assessment on predicting protein-protein interactions. BMC
157
- Bioinformatics. 2004, 5 (1): 154-10.1186\/1471-2105-5-154.","journal-title":"BMC
158
- Bioinformatics"},{"issue":"14","key":"570_CR9","doi-asserted-by":"publisher","first-page":"8348","DOI":"10.1073\/pnas.0832373100","volume":"100","author":"OG
159
- Troyanskaya","year":"2003","unstructured":"Troyanskaya OG, Dolinski K, Owen
160
- AB, Altman RB, Botstein D: A Bayesian framework for combining heterogeneous
161
- data sources for gene function prediction (in Saccharomyces cerevisiae). Proc
162
- Natl Acad Sci USA. 2003, 100 (14): 8348-8353. 10.1073\/pnas.0832373100.","journal-title":"Proc
163
- Natl Acad Sci USA"},{"issue":"8","key":"570_CR10","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1016\/j.tig.2005.06.006","volume":"21","author":"SL
164
- Wong","year":"2005","unstructured":"Wong SL, Zhang LV, Roth FP: Discovering
165
- functional relationships: biochemistry versus genetics. Trends Genet. 2005,
166
- 21 (8): 424-427. 10.1016\/j.tig.2005.06.006.","journal-title":"Trends Genet"},{"issue":"1","key":"570_CR11","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M
167
- Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: kyoto encyclopedia
168
- of genes and genomes. Nucleic Acids Res. 2000, 28 (1): 27-30. 10.1093\/nar\/28.1.27.","journal-title":"Nucleic
169
- Acids Res"},{"issue":"Suppl 1","key":"570_CR12","doi-asserted-by":"publisher","first-page":"I363","DOI":"10.1093\/bioinformatics\/bth910","volume":"20","author":"Y
170
- Yamanishi","year":"2004","unstructured":"Yamanishi Y, Vert JP, Kanehisa M:
171
- Protein network inference from multiple genomic data: a supervised approach.
172
- Bioinformatics. 2004, 20 (Suppl 1): I363-I370. 10.1093\/bioinformatics\/bth910.","journal-title":"Bioinformatics"},{"key":"570_CR13","unstructured":"GRIFn
173
- Home Page. [http:\/\/function.princeton.edu\/GRIFn]"},{"issue":"6868","key":"570_CR14","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"AC
174
- Gavin","year":"2002","unstructured":"Gavin AC, Bosche M, Krause R, Grandi
175
- P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM: Functional
176
- organization of the yeast proteome by systematic analysis of protein complexes.
177
- Nature. 2002, 415 (6868): 141-147. 10.1038\/415141a.","journal-title":"Nature"},{"issue":"5","key":"570_CR15","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1016\/S0022-2836(03)00239-0","volume":"327","author":"E
178
- Sprinzak","year":"2003","unstructured":"Sprinzak E, Sattath S, Margalit H:
179
- How reliable are experimental protein-protein interaction data?. J Mol Biol.
180
- 2003, 327 (5): 919-923. 10.1016\/S0022-2836(03)00239-0.","journal-title":"J
181
- Mol Biol"},{"issue":"6770","key":"570_CR16","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P
182
- Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield TA,
183
- Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P: A comprehensive
184
- analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature.
185
- 2000, 403 (6770): 623-627. 10.1038\/35001009.","journal-title":"Nature"},{"issue":"6887","key":"570_CR17","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C
186
- von Mering","year":"2002","unstructured":"von Mering C, Krause R, Snel B,
187
- Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale
188
- data sets of protein-protein interactions. Nature. 2002, 417 (6887): 399-403.
189
- 10.1038\/nature750.","journal-title":"Nature"},{"issue":"3","key":"570_CR18","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1093\/bioinformatics\/btg420","volume":"20","author":"SG
190
- Lee","year":"2004","unstructured":"Lee SG, Hur JU, Kim YS: A graph-theoretic
191
- modeling on GO space for biological interpretation of gene clusters. Bioinformatics.
192
- 2004, 20 (3): 381-388. 10.1093\/bioinformatics\/btg420.","journal-title":"Bioinformatics"},{"issue":"1","key":"570_CR19","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M
193
- Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein
194
- D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology:
195
- tool for the unification of biology. The Gene Ontology Consortium. Nat Genet.
196
- 2000, 25 (1): 25-29. 10.1038\/75556.","journal-title":"Nat Genet"},{"issue":"1","key":"570_CR20","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/nar\/28.1.77","volume":"28","author":"CA
197
- Ball","year":"2000","unstructured":"Ball CA, Dolinski K, Dwight SS, Harris
198
- MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H: Integrating
199
- functional genomic information into the Saccharomyces genome database. Nucleic
200
- Acids Res. 2000, 28 (1): 77-80. 10.1093\/nar\/28.1.77.","journal-title":"Nucleic
201
- Acids Res"},{"issue":"1","key":"570_CR21","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/nar\/30.1.31","volume":"30","author":"HW
202
- Mewes","year":"2002","unstructured":"Mewes HW, Frishman D, Guldener U, Mannhaupt
203
- G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B: MIPS:
204
- a database for genomes and protein sequences. Nucleic Acids Res. 2002, 30
205
- (1): 31-34. 10.1093\/nar\/30.1.31.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"570_CR22","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1093\/nar\/29.1.75","volume":"29","author":"MC
206
- Costanzo","year":"2001","unstructured":"Costanzo MC, Crawford ME, Hirschman
207
- JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu
208
- P: YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library,
209
- an integrated resource for protein information. Nucleic Acids Res. 2001, 29
210
- (1): 75-79. 10.1093\/nar\/29.1.75.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"570_CR23","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.mib.2004.08.012","volume":"7","author":"R
211
- Jansen","year":"2004","unstructured":"Jansen R, Gerstein M: Analyzing protein
212
- function on a genomic scale: the importance of gold-standard positives and
213
- negatives for network prediction. Curr Opin Microbiol. 2004, 7 (5): 535-545.
214
- 10.1016\/j.mib.2004.08.012.","journal-title":"Curr Opin Microbiol"},{"issue":"1","key":"570_CR24","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/1471-2105-6-100","volume":"6","author":"A
215
- Patil","year":"2005","unstructured":"Patil A, Nakamura H: Filtering high-throughput
216
- protein-protein interaction data using a combination of genomic features.
217
- BMC Bioinformatics. 2005, 6 (1): 100-10.1186\/1471-2105-6-100.","journal-title":"BMC
218
- Bioinformatics"},{"issue":"6959","key":"570_CR25","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1038\/nature02026","volume":"425","author":"WK
219
- Huh","year":"2003","unstructured":"Huh WK, Falvo JV, Gerke LC, Carroll AS,
220
- Howson RW, Weissman JS, O''Shea EK: Global analysis of protein localization
221
- in budding yeast. Nature. 2003, 425 (6959): 686-691. 10.1038\/nature02026.","journal-title":"Nature"},{"issue":"5","key":"570_CR26","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1074\/mcp.M100037-MCP200","volume":"1","author":"CM
222
- Deane","year":"2002","unstructured":"Deane CM, Salwinski L, Xenarios I, Eisenberg
223
- D: Protein interactions: two methods for assessment of the reliability of
224
- high throughput observations. Mol Cell Proteomics. 2002, 1 (5): 349-356. 10.1074\/mcp.M100037-MCP200.","journal-title":"Mol
225
- Cell Proteomics"},{"key":"570_CR27","first-page":"531","volume-title":"Pac
226
- Symp Biocomput","author":"Y Qi","year":"2005","unstructured":"Qi Y, Klein-Seetharaman
227
- J, Bar-Joseph Z: Random forest similarity for protein-protein interaction
228
- prediction from multiple sources. Pac Symp Biocomput. 2005, 531-542."},{"issue":"3","key":"570_CR28","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/j.sbi.2004.05.003","volume":"14","author":"P
229
- Bork","year":"2004","unstructured":"Bork P, Jensen LJ, von Mering C, Ramani
230
- AK, Lee I, Marcotte EM: Protein interaction networks from yeast to human.
231
- Curr Opin Struct Biol. 2004, 14 (3): 292-299. 10.1016\/j.sbi.2004.05.003.","journal-title":"Curr
232
- Opin Struct Biol"},{"issue":"1","key":"570_CR29","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/nar\/28.1.289","volume":"28","author":"I
233
- Xenarios","year":"2000","unstructured":"Xenarios I, Rice DW, Salwinski L,
234
- Baron MK, Marcotte EM, Eisenberg D: DIP: the database of interacting proteins.
235
- Nucleic Acids Res. 2000, 28 (1): 289-291. 10.1093\/nar\/28.1.289.","journal-title":"Nucleic
236
- Acids Res"},{"issue":"3","key":"570_CR30","doi-asserted-by":"publisher","first-page":"R23","DOI":"10.1186\/gb-2003-4-3-r23","volume":"4","author":"BJ
237
- Breitkreutz","year":"2003","unstructured":"Breitkreutz BJ, Stark C, Tyers
238
- M: The GRID: the General Repository for Interaction Datasets. Genome Biol.
239
- 2003, 4 (3): R23-10.1186\/gb-2003-4-3-r23.","journal-title":"Genome Biol"},{"key":"570_CR31","doi-asserted-by":"crossref","unstructured":"Alfarano
240
- C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko
241
- B, Boutilier K, Burgess E: The Biomolecular Interaction Network Database and
242
- related tools 2005 update. Nucleic Acids Res. 2005, D418-424. 33 Database","DOI":"10.1093\/nar\/gki051"},{"issue":"10","key":"570_CR32","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","volume":"19","author":"PW
243
- Lord","year":"2003","unstructured":"Lord PW, Stevens RD, Brass A, Goble CA:
244
- Investigating semantic similarity measures across the Gene Ontology: the relationship
245
- between sequence and annotation. Bioinformatics. 2003, 19 (10): 1275-1283.
246
- 10.1093\/bioinformatics\/btg153.","journal-title":"Bioinformatics"},{"issue":"Suppl61","key":"570_CR33","first-page":"S2","volume":"7","author":"A
247
- Ben-Hur","year":"2005","unstructured":"Ben-Hur A, Noble WS: Choosing negative
248
- examples for the prediction of protein-protein interactions. BMC Bioinformatics.
249
- 2005, 7 (Suppl61): S2-","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"570_CR34","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1073\/pnas.061034498","volume":"98","author":"T
250
- Ito","year":"2001","unstructured":"Ito T, Chiba T, Ozawa R, Yoshida M, Hattori
251
- M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein
252
- interactome. Proc Natl Acad Sci U S A. 2001, 98 (8): 4569-4574. 10.1073\/pnas.061034498.","journal-title":"Proc
253
- Natl Acad Sci U S A"},{"issue":"5553","key":"570_CR35","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1126\/science.1064987","volume":"295","author":"AH
254
- Tong","year":"2002","unstructured":"Tong AH, Drees B, Nardelli G, Bader GD,
255
- Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S:
256
- A combined experimental and computational strategy to define protein interaction
257
- networks for peptide recognition modules. Science. 2002, 295 (5553): 321-324.
258
- 10.1126\/science.1064987.","journal-title":"Science"},{"issue":"6868","key":"570_CR36","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/415180a","volume":"415","author":"Y
259
- Ho","year":"2002","unstructured":"Ho Y, Gruhler A, Heilbut A, Bader GD, Moore
260
- L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic identification
261
- of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature.
262
- 2002, 415 (6868): 180-183. 10.1038\/415180a.","journal-title":"Nature"},{"issue":"10","key":"570_CR37","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1091\/mbc.12.10.2987","volume":"12","author":"AP
263
- Gasch","year":"2001","unstructured":"Gasch AP, Huang M, Metzner S, Botstein
264
- D, Elledge SJ, Brown PO: Genomic expression responses to DNA-damaging agents
265
- and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell. 2001,
266
- 12 (10): 2987-3003.","journal-title":"Mol Biol Cell"},{"issue":"12","key":"570_CR38","doi-asserted-by":"publisher","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","volume":"9","author":"PT
267
- Spellman","year":"1998","unstructured":"Spellman PT, Sherlock G, Zhang MQ,
268
- Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive
269
- identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae
270
- by microarray hybridization. Mol Biol Cell. 1998, 9 (12): 3273-3297.","journal-title":"Mol
271
- Biol Cell"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-7-187.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2164-7-187\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-7-187.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:37:43Z","timestamp":1630460263000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-7-187"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,7,25]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["570"],"URL":"http:\/\/dx.doi.org\/10.1186\/1471-2164-7-187","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":["Genetics","Biotechnology"],"published":{"date-parts":[[2006,7,25]]},"assertion":[{"value":"10
272
- May 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article
273
- History"}},{"value":"25 July 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article
274
- History"}},{"value":"25 July 2006","order":3,"name":"first_online","label":"First
275
- Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"187"}}'
276
- recorded_at: Sun, 18 Jun 2023 15:21:15 GMT
277
- - request:
278
- method: get
279
- uri: https://api.crossref.org/members/297
280
- body:
281
- encoding: UTF-8
282
- string: ''
283
- headers:
284
- Connection:
285
- - close
286
- Host:
287
- - api.crossref.org
288
- User-Agent:
289
- - http.rb/5.1.1
290
- response:
291
- status:
292
- code: 200
293
- message: OK
294
- headers:
295
- Date:
296
- - Sun, 18 Jun 2023 15:21:16 GMT
297
- Content-Type:
298
- - application/json
299
- Transfer-Encoding:
300
- - chunked
301
- Access-Control-Expose-Headers:
302
- - Link
303
- Access-Control-Allow-Headers:
304
- - X-Requested-With, Accept, Accept-Encoding, Accept-Charset, Accept-Language,
305
- Accept-Ranges, Cache-Control
306
- Access-Control-Allow-Origin:
307
- - "*"
308
- Server:
309
- - Jetty(9.4.40.v20210413)
310
- X-Ratelimit-Limit:
311
- - '50'
312
- X-Ratelimit-Interval:
313
- - 1s
314
- X-Api-Pool:
315
- - public
316
- X-Rate-Limit-Limit:
317
- - '50'
318
- X-Rate-Limit-Interval:
319
- - 1s
320
- Permissions-Policy:
321
- - interest-cohort=()
322
- Connection:
323
- - close
324
- body:
325
- encoding: UTF-8
326
- string: '{"status":"ok","message-type":"member","message-version":"1.0.0","message":{"last-status-check-time":1687044227035,"primary-name":"Springer
327
- Science and Business Media LLC","counts":{"current-dois":1798782,"backfile-dois":13838189,"total-dois":15636971},"breakdowns":{"dois-by-issued-year":[[2022,738328],[2021,736414],[2020,696998],[2019,637478],[2018,626386],[2017,607295],[2014,594440],[2016,586876],[2013,576773],[2015,524012],[2012,469433],[2011,453240],[2010,415850],[2009,397352],[2023,324022],[2008,322054],[2007,283326],[2006,254697],[2004,251651],[2005,239697],[2003,235979],[2000,234840],[2002,225220],[2001,222769],[1999,205327],[1998,204478],[1997,198548],[1996,184875],[1995,174607],[1994,168404],[1993,166708],[1991,162565],[1992,161494],[1990,157101],[1989,152466],[1988,142595],[1987,135929],[1986,125331],[1985,117258],[1984,114663],[1983,101438],[1982,99014],[1981,96225],[1980,91070],[1979,84436],[1978,83740],[1977,79756],[1976,73466],[1975,69520],[1974,67539],[1973,62912],[1972,59917],[1971,55752],[1970,53101],[1969,49815],[1968,48947],[1967,47186],[1966,42444],[1965,37484],[1964,33194],[1963,30593],[1962,30083],[1961,29432],[1960,28851],[1959,25681],[1958,24481],[1956,21941],[1957,21837],[1955,19907],[1954,16716],[1953,16707],[1932,16468],[1928,16373],[1930,16178],[1927,15870],[1926,15581],[1929,15329],[1931,15286],[1933,15129],[1952,14987],[1936,14706],[1938,14651],[1950,14507],[1935,14396],[1937,14279],[1939,14063],[1951,13951],[1934,13698],[1925,13413],[1924,13128],[1923,12818],[1922,12374],[1949,11829],[1913,11542],[1921,11472],[1940,11277],[1914,10095],[1941,9997],[1920,9970],[1942,9650],[1948,9430],[1912,9290],[1910,9128],[1911,9063],[1943,8570],[1904,8229],[1903,8054],[1909,7961],[1919,7949],[1908,7910],[1905,7554],[1907,7549],[1902,7376],[1906,7298],[1918,7183],[1901,7167],[1915,7030],[1900,7023],[1916,6836],[1897,6815],[1917,6752],[1899,6699],[1887,6682],[1886,6652],[1888,6512],[1947,6407],[1893,6407],[1898,6398],[1889,6361],[1895,6147],[1891,6122],[1894,6116],[1880,6105],[1944,6070],[1892,6068],[1885,6010],[1890,5981],[1896,5963],[1877,5912],[1884,5694],[1883,5675],[1878,5633],[1882,5628],[1881,5603],[1946,5556],[1876,5486],[1879,5427],[1847,5058],[1945,3954],[1848,3882],[1872,3827],[1875,3819],[1873,3761],[1870,3725],[1874,3641],[1871,3604],[1852,3065],[1849,3025],[1869,3021],[1856,2943],[1855,2836],[1857,2796],[1854,2772],[1851,2733],[1850,2690],[1860,2628],[1867,2586],[1859,2530],[1853,2512],[1868,2447],[1858,2433],[1865,2238],[1863,2148],[1864,2145],[1866,2110],[1862,2044],[1846,1920],[1861,1703],[1845,265],[1844,176],[1843,99],[1837,66],[1840,64],[1835,62],[1833,62],[1400,57],[1834,56],[1838,55],[1841,50],[1832,50],[1839,49],[1842,42],[1836,38],[2024,18],[1827,2],[1815,2]]},"prefixes":["10.1208","10.19150","10.1245","10.7603","10.1007","10.17269","10.4076","10.7123","10.1140","10.1381","10.33283","10.4333","10.1186","10.1065","10.1361","10.4056","10.1023","10.1385","10.26778","10.26777","10.5819","10.1617","10.1013","10.1057","10.1379","10.1038","10.1114","10.3758","10.1557","10.3858","10.7759","10.2165","10.1251","10.5052"],"coverage":{"affiliations-current":1.267524358149014E-4,"similarity-checking-current":0.9963225115661598,"descriptions-current":0.0,"ror-ids-current":0.0,"funders-backfile":0.04592559040781998,"licenses-backfile":0.718562811940204,"funders-current":0.2507591247855493,"affiliations-backfile":4.914660437142461E-4,"resource-links-backfile":0.53193282733745,"orcids-backfile":0.05139386374907873,"update-policies-current":0.9279234504236756,"ror-ids-backfile":0.0,"orcids-current":0.3901023025580643,"similarity-checking-backfile":0.9344421441273855,"references-backfile":0.6704000068217019,"descriptions-backfile":0.0,"award-numbers-backfile":0.0372477207819607,"update-policies-backfile":0.2802055962669682,"licenses-current":0.9928040196088243,"award-numbers-current":0.1936743863347532,"abstracts-backfile":0.03308807243491182,"resource-links-current":0.6257840027307368,"abstracts-current":0.2164497976964413,"references-current":0.864806296705215},"prefix":[{"name":"American
328
- Association of Pharmaceutical Scientists","value":"10.1208"},{"name":"Society
329
- for Mining, Metallurgy & Exploration Inc.","value":"10.19150"},{"name":"Springer
330
- - Society of Surgical Oncology","value":"10.1245"},{"name":"Springer - Global
331
- Science Journals","value":"10.7603"},{"name":"Springer-Verlag","value":"10.1007"},{"name":"Canadian
332
- Public Health Association","value":"10.17269"},{"name":"Springer (Cases Network,
333
- Ltd.)","value":"10.4076"},{"name":"Springer Science and Business Media LLC","value":"10.7123"},{"name":"Springer-Verlag","value":"10.1140"},{"name":"Springer
334
- - FD Communications","value":"10.1381"},{"name":"Springer Science and Business
335
- Media LLC","value":"10.33283"},{"name":"Springer - The Korean Society of Pharmaceutical
336
- Sciences and Technology","value":"10.4333"},{"name":"Springer (Biomed Central
337
- Ltd.)","value":"10.1186"},{"name":"Springer - Ecomed Publishers","value":"10.1065"},{"name":"Springer
338
- - ASM International","value":"10.1361"},{"name":"Genomic Standards Consortium","value":"10.4056"},{"name":"Springer
339
- (Kluwer Academic Publishers)","value":"10.1023"},{"name":"Springer - Humana
340
- Press","value":"10.1385"},{"name":"SpringerNature","value":"10.26778"},{"name":"SpringerNature","value":"10.26777"},{"name":"Springer
341
- - (backfiles)","value":"10.5819"},{"name":"Springer - RILEM Publishing","value":"10.1617"},{"name":"Springer
342
- Science and Business Media LLC","value":"10.1013"},{"name":"Springer Science
343
- and Business Media LLC","value":"10.1057"},{"name":"Springer - Cell Stress
344
- Society International","value":"10.1379"},{"name":"Springer Science and Business
345
- Media LLC","value":"10.1038"},{"name":"Springer (Kluwer Academic Publishers
346
- - Biomedical Engineering Society (BMES))","value":"10.1114"},{"name":"Springer
347
- - Psychonomic Society","value":"10.3758"},{"name":"Materials Research Society","value":"10.1557"},{"name":"Springer
348
- Science and Business Media LLC","value":"10.3858"},{"name":"Cureus, Inc.","value":"10.7759"},{"name":"Springer
349
- - Adis","value":"10.2165"},{"name":"Springer (Biological Procedures Online)","value":"10.1251"},{"name":"Springer
350
- - Real Academia de Ciencias Exactas, Fisicas y Naturales","value":"10.5052"}],"id":297,"tokens":["springer","science","and","business","media","llc"],"counts-type":{"all":{"monograph":359,"journal-article":9392043,"book":329229,"reference-entry":85798,"proceedings-article":1149,"journal":2146,"component":4443,"book-chapter":6424734,"reference-book":1007,"journal-issue":1311,"dataset":23415},"backfile":{"monograph":359,"journal-article":8293043,"book":295345,"proceedings-article":1149,"book-chapter":5226129,"reference-book":743,"journal-issue":1311,"dataset":20110},"current":{"journal-article":1098999,"book":33884,"book-chapter":662332,"reference-book":264,"dataset":3303}},"coverage-type":{"all":{"monograph":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.6295264623955432,"references":0.0,"funders":0.0,"similarity-checking":0.6295264623955432,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.6295264623955432,"descriptions":0.0},"journal-article":{"last-status-check-time":1687044227035,"affiliations":7.48399469636159E-4,"abstracts":0.08796701633499761,"orcids":0.1362866417881605,"licenses":0.878906431752921,"references":0.7304443772244228,"funders":0.1138326347100413,"similarity-checking":0.9064530475424782,"award-numbers":0.09181516737093302,"ror-ids":0.0,"update-policies":0.3710155500778691,"resource-links":0.8686014320845848,"descriptions":0.0},"book":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.02600621451937709,"licenses":0.9949093184379262,"references":3.037399500044042E-6,"funders":0.004413341473563993,"similarity-checking":0.9965829255624505,"award-numbers":6.257042970090726E-4,"ror-ids":0.0,"update-policies":3.037399500044042E-6,"resource-links":0.9945174939024205,"descriptions":0.0},"reference-entry":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.005396396186391291,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"proceedings-article":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.006092254134029591,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"journal":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":4.659832246039143E-4,"references":0.0,"funders":0.0,"similarity-checking":0.001863932898415657,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":4.659832246039143E-4,"descriptions":0.0},"component":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":6.75219446320054E-4},"book-chapter":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.003274065509949517,"orcids":0.0184194396219361,"licenses":0.4896562254561823,"references":0.6562951866956671,"funders":0.001361768440529989,"similarity-checking":0.9697749354292333,"award-numbers":1.990743896945772E-4,"ror-ids":0.0,"update-policies":0.3178142472513259,"resource-links":1.556484673139775E-7,"descriptions":0.0},"reference-book":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.02184707050645482,"licenses":0.9910625620655412,"references":0.0,"funders":0.00198609731876862,"similarity-checking":0.9940417080436941,"award-numbers":0.00198609731876862,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.9910625620655412,"descriptions":0.0},"journal-issue":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.03508771929824561,"references":0.0,"funders":0.0,"similarity-checking":0.07704042715484363,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.03508771929824561,"descriptions":0.0},"dataset":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.2550928891736067,"licenses":0.0,"references":0.0,"funders":0.3101857783472133,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.862822976724322,"resource-links":0.0,"descriptions":0.0}},"backfile":{"monograph":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.6295264623955432,"references":0.0,"funders":0.0,"similarity-checking":0.6295264623955432,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.6295264623955432,"descriptions":0.0},"journal-article":{"last-status-check-time":1687044227035,"affiliations":8.200849796630742E-4,"abstracts":0.05472189159033662,"orcids":0.08018745350771725,"licenses":0.8637461544574169,"references":0.7047474612153826,"funders":0.07529335130663135,"similarity-checking":0.8942189254294232,"award-numbers":0.06204272665654815,"ror-ids":0.0,"update-policies":0.2979894111244811,"resource-links":0.8520822814978772,"descriptions":0.0},"book":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.01166432477272343,"licenses":0.9943354382163233,"references":3.385870761313041E-6,"funders":0.001919788721664494,"similarity-checking":0.9964786944082344,"award-numbers":3.589023006991823E-4,"ror-ids":0.0,"update-policies":3.385870761313041E-6,"resource-links":0.9941763022905415,"descriptions":0.0},"proceedings-article":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.006092254134029591,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"book-chapter":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":7.783964000888612E-4,"orcids":0.007472452363881565,"licenses":0.4756572216261788,"references":0.6568188423974992,"funders":9.88111851046922E-4,"similarity-checking":0.9987918400024186,"award-numbers":1.553731260747678E-4,"ror-ids":0.0,"update-policies":0.2652496714107134,"resource-links":1.913462143777928E-7,"descriptions":0.0},"reference-book":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0161507402422611,"licenses":0.9878869448183042,"references":0.0,"funders":0.0,"similarity-checking":0.9919246298788694,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.9878869448183042,"descriptions":0.0},"journal-issue":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.03508771929824561,"references":0.0,"funders":0.0,"similarity-checking":0.07704042715484363,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.03508771929824561,"descriptions":0.0},"dataset":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.1835405271009448,"licenses":0.0,"references":0.0,"funders":0.2677772252610641,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.9979612133267031,"resource-links":0.0,"descriptions":0.0}},"current":{"journal-article":{"last-status-check-time":1687044227035,"affiliations":2.074615172534279E-4,"abstracts":0.3388347032162905,"orcids":0.559611064250286,"licenses":0.9933057263928357,"references":0.9243538893120012,"funders":0.4046500497270698,"similarity-checking":0.9987716094373152,"award-numbers":0.3164779949754276,"ror-ids":0.0,"update-policies":0.9220709027032782,"resource-links":0.9932547709324576,"descriptions":0.0},"book":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.1510152284263959,"licenses":0.9999114626372329,"references":0.0,"funders":0.02614803447054657,"similarity-checking":0.9974914413882658,"award-numbers":0.00295124542556959,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.9974914413882658,"descriptions":0.0},"book-chapter":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.02561706213802142,"orcids":0.1197103567395204,"licenses":0.9965561078130001,"references":0.8148994763955237,"funders":0.005412693332044956,"similarity-checking":0.9971660738119251,"award-numbers":7.050844591534155E-4,"ror-ids":0.0,"update-policies":0.9899008352306699,"resource-links":0.0,"descriptions":0.0},"reference-book":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.03787878787878788,"licenses":1.0,"references":0.0,"funders":0.007575757575757576,"similarity-checking":1.0,"award-numbers":0.007575757575757576,"ror-ids":0.0,"update-policies":0.0,"resource-links":1.0,"descriptions":0.0},"dataset":{"last-status-check-time":1687044227035,"affiliations":0.0,"abstracts":0.0,"orcids":0.690887072358462,"licenses":0.0,"references":0.0,"funders":0.5685740236148955,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.04056917953375719,"resource-links":0.0,"descriptions":0.0}}},"flags":{"deposits-abstracts-current":true,"deposits-orcids-current":true,"deposits":true,"deposits-affiliations-backfile":true,"deposits-update-policies-backfile":true,"deposits-similarity-checking-backfile":true,"deposits-award-numbers-current":true,"deposits-resource-links-current":true,"deposits-ror-ids-current":false,"deposits-articles":true,"deposits-affiliations-current":true,"deposits-funders-current":true,"deposits-references-backfile":true,"deposits-ror-ids-backfile":false,"deposits-abstracts-backfile":true,"deposits-licenses-backfile":true,"deposits-award-numbers-backfile":true,"deposits-descriptions-current":false,"deposits-references-current":true,"deposits-resource-links-backfile":true,"deposits-descriptions-backfile":false,"deposits-orcids-backfile":true,"deposits-funders-backfile":true,"deposits-update-policies-current":true,"deposits-similarity-checking-current":true,"deposits-licenses-current":true},"location":"Dordrecht,
351
- GX, Netherlands","names":["Springer Science and Business Media LLC","American
352
- Association of Pharmaceutical Scientists","Society for Mining, Metallurgy
353
- & Exploration Inc.","Springer - Society of Surgical Oncology","Springer -
354
- Global Science Journals","Springer-Verlag","Canadian Public Health Association","Springer
355
- (Cases Network, Ltd.)","Springer - FD Communications","Springer - The Korean
356
- Society of Pharmaceutical Sciences and Technology","Springer (Biomed Central
357
- Ltd.)","Springer - Ecomed Publishers","Springer - ASM International","Genomic
358
- Standards Consortium","Springer (Kluwer Academic Publishers)","Springer -
359
- Humana Press","SpringerNature","Springer - (backfiles)","Springer - RILEM
360
- Publishing","Springer - Cell Stress Society International","Springer (Kluwer
361
- Academic Publishers - Biomedical Engineering Society (BMES))","Springer -
362
- Psychonomic Society","Materials Research Society","Cureus, Inc.","Springer
363
- - Adis","Springer (Biological Procedures Online)","Springer - Real Academia
364
- de Ciencias Exactas, Fisicas y Naturales"]}}'
365
- recorded_at: Sun, 18 Jun 2023 15:21:16 GMT
366
- - request:
367
- method: get
368
- uri: https://doi.org/ra/10.1186
369
- body:
370
- encoding: UTF-8
371
- string: ''
372
- headers:
373
- Connection:
374
- - close
375
- Host:
376
- - doi.org
377
- User-Agent:
378
- - http.rb/5.1.1
379
- response:
380
- status:
381
- code: 200
382
- message: OK
383
- headers:
384
- Date:
385
- - Sun, 18 Jun 2023 15:21:17 GMT
386
- Content-Type:
387
- - application/json;charset=UTF-8
388
- Transfer-Encoding:
389
- - chunked
390
- Connection:
391
- - close
392
- Permissions-Policy:
393
- - interest-cohort=(),browsing-topics=()
394
- Cf-Cache-Status:
395
- - DYNAMIC
396
- Report-To:
397
- - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=ZyhUsn2WPykfCb347nfY4%2FflaRhetPzN8DIjaBHn9J3K9GUNsYDmNQBq0E7gZd5kkCKJUR4lstdklU2JlBvVf8C6AL5jJOGd8C7BQ6WfRCUmyDzmd5dTKQ7i%2BVfJ4xGFwaFTkSI%3D"}],"group":"cf-nel","max_age":604800}'
398
- Nel:
399
- - '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}'
400
- Strict-Transport-Security:
401
- - max-age=31536000; includeSubDomains; preload
402
- Server:
403
- - cloudflare
404
- Cf-Ray:
405
- - 7d94856918630bd7-AMS
406
- Alt-Svc:
407
- - h3=":443"; ma=86400
408
- body:
409
- encoding: UTF-8
410
- string: |-
411
- [
412
- {
413
- "DOI": "10.1186",
414
- "RA": "Crossref"
415
- }
416
- ]
417
- recorded_at: Sun, 18 Jun 2023 15:21:16 GMT
418
- - request:
419
- method: get
420
- uri: https://api.crossref.org/works/10.1186/1471-2164-7-187/transform/application/vnd.crossref.unixsd+xml
421
- body:
422
- encoding: UTF-8
423
- string: ''
424
- headers:
425
- Connection:
426
- - close
427
- Host:
428
- - api.crossref.org
429
- User-Agent:
430
- - http.rb/5.1.1
431
- response:
432
- status:
433
- code: 200
434
- message: OK
435
- headers:
436
- Date:
437
- - Sun, 18 Jun 2023 15:25:24 GMT
438
- Transfer-Encoding:
439
- - chunked
440
- Link:
441
- - <http://dx.doi.org/10.1186/1471-2164-7-187>; rel="canonical", <http://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf>;
442
- version="vor"; type="application/pdf"; rel="item", <http://link.springer.com/article/10.1186/1471-2164-7-187/fulltext.html>;
443
- version="vor"; type="text/html"; rel="item", <https://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf>;
444
- version="vor"; type="application/pdf"; rel="item", <http://creativecommons.org/licenses/by/2.0>;
445
- version="tdm"; rel="license"
446
- Access-Control-Expose-Headers:
447
- - Link
448
- Access-Control-Allow-Headers:
449
- - X-Requested-With, Accept, Accept-Encoding, Accept-Charset, Accept-Language,
450
- Accept-Ranges, Cache-Control
451
- Access-Control-Allow-Origin:
452
- - "*"
453
- Server:
454
- - Jetty(9.4.40.v20210413)
455
- X-Ratelimit-Limit:
456
- - '50'
457
- X-Ratelimit-Interval:
458
- - 1s
459
- X-Api-Pool:
460
- - public
461
- X-Rate-Limit-Limit:
462
- - '50'
463
- X-Rate-Limit-Interval:
464
- - 1s
465
- Permissions-Policy:
466
- - interest-cohort=()
467
- Connection:
468
- - close
469
- body:
470
- encoding: ASCII-8BIT
471
- string: "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<crossref_result xmlns=\"http://www.crossref.org/qrschema/3.0\"
472
- version=\"3.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.crossref.org/qrschema/3.0
473
- http://www.crossref.org/schemas/crossref_query_output3.0.xsd\">\r\n <query_result>\r\n
474
- \ <head>\r\n <doi_batch_id>none</doi_batch_id>\r\n </head>\r\n <body>\r\n
475
- \ <query status=\"resolved\">\r\n <doi type=\"journal_article\">10.1186/1471-2164-7-187</doi>\r\n
476
- \ <crm-item name=\"publisher-name\" type=\"string\">Springer Science
477
- and Business Media LLC</crm-item>\r\n <crm-item name=\"prefix-name\"
478
- type=\"string\">Springer (Biomed Central Ltd.)</crm-item>\r\n <crm-item
479
- name=\"member-id\" type=\"number\">297</crm-item>\r\n <crm-item name=\"citation-id\"
480
- type=\"number\">22586616</crm-item>\r\n <crm-item name=\"journal-id\"
481
- type=\"number\">5911</crm-item>\r\n <crm-item name=\"deposit-timestamp\"
482
- type=\"number\">20210831173149578</crm-item>\r\n <crm-item name=\"owner-prefix\"
483
- type=\"string\">10.1186</crm-item>\r\n <crm-item name=\"last-update\"
484
- type=\"date\">2021-09-01T01:37:43Z</crm-item>\r\n <crm-item name=\"created\"
485
- type=\"date\">2006-07-25T18:14:51Z</crm-item>\r\n <crm-item name=\"citedby-count\"
486
- type=\"number\">171</crm-item>\r\n <crm-item name=\"relation\" type=\"doi\"
487
- claim=\"isReviewOf\">10.3410/f.1044091.494000</crm-item>\r\n <crm-item
488
- name=\"relation\" type=\"doi\" claim=\"isReviewOf\">10.3410/f.1044091.496329</crm-item>\r\n
489
- \ <doi_record>\r\n <crossref xmlns=\"http://www.crossref.org/xschema/1.1\"
490
- xsi:schemaLocation=\"http://www.crossref.org/xschema/1.1 http://doi.crossref.org/schemas/unixref1.1.xsd\">\r\n
491
- \ <journal>\r\n <journal_metadata language=\"en\">\r\n
492
- \ <full_title>BMC Genomics</full_title>\r\n <abbrev_title>BMC
493
- Genomics</abbrev_title>\r\n <issn media_type=\"electronic\">1471-2164</issn>\r\n
494
- \ </journal_metadata>\r\n <journal_issue>\r\n <publication_date
495
- media_type=\"print\">\r\n <month>12</month>\r\n <year>2006</year>\r\n
496
- \ </publication_date>\r\n <journal_volume>\r\n
497
- \ <volume>7</volume>\r\n </journal_volume>\r\n
498
- \ <issue>1</issue>\r\n </journal_issue>\r\n <journal_article
499
- publication_type=\"full_text\">\r\n <titles>\r\n <title>Finding
500
- function: evaluation methods for functional genomic data</title>\r\n </titles>\r\n
501
- \ <contributors>\r\n <person_name sequence=\"first\"
502
- contributor_role=\"author\">\r\n <given_name>Chad L</given_name>\r\n
503
- \ <surname>Myers</surname>\r\n </person_name>\r\n
504
- \ <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
505
- \ <given_name>Daniel R</given_name>\r\n <surname>Barrett</surname>\r\n
506
- \ </person_name>\r\n <person_name sequence=\"additional\"
507
- contributor_role=\"author\">\r\n <given_name>Matthew A</given_name>\r\n
508
- \ <surname>Hibbs</surname>\r\n </person_name>\r\n
509
- \ <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
510
- \ <given_name>Curtis</given_name>\r\n <surname>Huttenhower</surname>\r\n
511
- \ </person_name>\r\n <person_name sequence=\"additional\"
512
- contributor_role=\"author\">\r\n <given_name>Olga G</given_name>\r\n
513
- \ <surname>Troyanskaya</surname>\r\n </person_name>\r\n
514
- \ </contributors>\r\n <jats:abstract xmlns:jats=\"http://www.ncbi.nlm.nih.gov/JATS1\"
515
- xml:lang=\"en\">\r\n <jats:title>Abstract</jats:title>\r\n
516
- \ <jats:sec>\r\n <jats:title>Background</jats:title>\r\n
517
- \ <jats:p>Accurate evaluation of the quality of genomic
518
- or proteomic data and computational methods is vital to our ability to use
519
- them for formulating novel biological hypotheses and directing further experiments.
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
526
- \ </jats:sec>\r\n <jats:sec>\r\n <jats:title>Results</jats:title>\r\n
527
- \ <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
- biologists and demonstrate its use as an effective means of evaluation of
532
- genomic approaches. Our evaluation framework and gold standard are freely
533
- available to the community through our website.</jats:p>\r\n </jats:sec>\r\n
534
- \ <jats:sec>\r\n <jats:title>Conclusion</jats:title>\r\n
535
- \ <jats:p>Proper methods for evaluating genomic data and
536
- computational approaches will determine how much we, as a community, are able
537
- to learn from the wealth of available data. We propose one possible solution
538
- to this problem here but emphasize that this topic warrants broader community
539
- discussion.</jats:p>\r\n </jats:sec>\r\n </jats:abstract>\r\n
540
- \ <publication_date media_type=\"online\">\r\n <month>07</month>\r\n
541
- \ <day>25</day>\r\n <year>2006</year>\r\n
542
- \ </publication_date>\r\n <publication_date media_type=\"print\">\r\n
543
- \ <month>12</month>\r\n <year>2006</year>\r\n
544
- \ </publication_date>\r\n <publisher_item>\r\n
545
- \ <item_number item_number_type=\"article-number\">187</item_number>\r\n
546
- \ <identifier id_type=\"pii\">570</identifier>\r\n </publisher_item>\r\n
547
- \ <crossmark>\r\n <crossmark_version>1</crossmark_version>\r\n
548
- \ <crossmark_policy>10.1007/springer_crossmark_policy</crossmark_policy>\r\n
549
- \ <crossmark_domains>\r\n <crossmark_domain>\r\n
550
- \ <domain>link.springer.com</domain>\r\n </crossmark_domain>\r\n
551
- \ </crossmark_domains>\r\n <crossmark_domain_exclusive>false</crossmark_domain_exclusive>\r\n
552
- \ <custom_metadata>\r\n <assertion group_label=\"Article
553
- History\" group_name=\"ArticleHistory\" order=\"1\" label=\"Received\" name=\"received\">10
554
- May 2006</assertion>\r\n <assertion group_label=\"Article
555
- History\" group_name=\"ArticleHistory\" order=\"2\" label=\"Accepted\" name=\"accepted\">25
556
- July 2006</assertion>\r\n <assertion group_label=\"Article
557
- History\" group_name=\"ArticleHistory\" order=\"3\" label=\"First Online\"
558
- name=\"first_online\">25 July 2006</assertion>\r\n <ai:program
559
- xmlns:ai=\"http://www.crossref.org/AccessIndicators.xsd\" name=\"AccessIndicators\">\r\n
560
- \ <ai:license_ref applies_to=\"tdm\">http://creativecommons.org/licenses/by/2.0</ai:license_ref>\r\n
561
- \ </ai:program>\r\n </custom_metadata>\r\n
562
- \ </crossmark>\r\n <doi_data>\r\n <doi>10.1186/1471-2164-7-187</doi>\r\n
563
- \ <timestamp>20210831173149578</timestamp>\r\n <resource
564
- content_version=\"vor\">https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-187</resource>\r\n
565
- \ <collection property=\"crawler-based\">\r\n <item
566
- crawler=\"iParadigms\">\r\n <resource mime_type=\"application/pdf\">https://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf</resource>\r\n
567
- \ </item>\r\n </collection>\r\n <collection
568
- property=\"text-mining\">\r\n <item>\r\n <resource
569
- mime_type=\"application/pdf\">http://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf</resource>\r\n
570
- \ </item>\r\n <item>\r\n <resource
571
- mime_type=\"text/html\">http://link.springer.com/article/10.1186/1471-2164-7-187/fulltext.html</resource>\r\n
572
- \ </item>\r\n </collection>\r\n </doi_data>\r\n
573
- \ <citation_list>\r\n <citation key=\"570_CR1\">\r\n
574
- \ <author>Z Barutcuoglu</author>\r\n <cYear>2006</cYear>\r\n
575
- \ <volume_title>Bioinformatics</volume_title>\r\n <unstructured_citation>Barutcuoglu
576
- Z, Schapire RE, Troyanskaya OG: Hierarchical multi-label prediction of gene
577
- function. Bioinformatics. 2006</unstructured_citation>\r\n </citation>\r\n
578
- \ <citation key=\"570_CR2\">\r\n <journal_title>Bioinformatics</journal_title>\r\n
579
- \ <author>A Clare</author>\r\n <volume>19</volume>\r\n
580
- \ <issue>Suppl 2</issue>\r\n <first_page>II42</first_page>\r\n
581
- \ <cYear>2003</cYear>\r\n <doi>10.1093/bioinformatics/btg1058</doi>\r\n
582
- \ <unstructured_citation>Clare A, King RD: Predicting gene
583
- function in Saccharomyces cerevisiae. Bioinformatics. 2003, 19 (Suppl 2):
584
- II42-II49.</unstructured_citation>\r\n </citation>\r\n <citation
585
- key=\"570_CR3\">\r\n <author>GR Lanckriet</author>\r\n
586
- \ <first_page>300</first_page>\r\n <cYear>2004</cYear>\r\n
587
- \ <volume_title>Pac Symp Biocomput</volume_title>\r\n <unstructured_citation>Lanckriet
55
+ encoding: ASCII-8BIT
56
+ string: "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<crossref_result xmlns=\"http://www.crossref.org/qrschema/3.0\"
57
+ version=\"3.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.crossref.org/qrschema/3.0
58
+ http://www.crossref.org/schemas/crossref_query_output3.0.xsd\">\r\n <query_result>\r\n
59
+ \ <head>\r\n <doi_batch_id>none</doi_batch_id>\r\n </head>\r\n <body>\r\n
60
+ \ <query status=\"resolved\">\r\n <doi type=\"journal_article\">10.1186/1471-2164-7-187</doi>\r\n
61
+ \ <crm-item name=\"publisher-name\" type=\"string\">Springer Science
62
+ and Business Media LLC</crm-item>\r\n <crm-item name=\"prefix-name\"
63
+ type=\"string\">Springer (Biomed Central Ltd.)</crm-item>\r\n <crm-item
64
+ name=\"member-id\" type=\"number\">297</crm-item>\r\n <crm-item name=\"citation-id\"
65
+ type=\"number\">22586616</crm-item>\r\n <crm-item name=\"journal-id\"
66
+ type=\"number\">5911</crm-item>\r\n <crm-item name=\"deposit-timestamp\"
67
+ type=\"number\">20210831173149578</crm-item>\r\n <crm-item name=\"owner-prefix\"
68
+ type=\"string\">10.1186</crm-item>\r\n <crm-item name=\"last-update\"
69
+ type=\"date\">2021-09-01T01:37:43Z</crm-item>\r\n <crm-item name=\"created\"
70
+ type=\"date\">2006-07-25T18:14:51Z</crm-item>\r\n <crm-item name=\"citedby-count\"
71
+ type=\"number\">172</crm-item>\r\n <crm-item name=\"relation\" type=\"doi\"
72
+ claim=\"isReviewOf\">10.3410/f.1044091.494000</crm-item>\r\n <crm-item
73
+ name=\"relation\" type=\"doi\" claim=\"isReviewOf\">10.3410/f.1044091.496329</crm-item>\r\n
74
+ \ <doi_record>\r\n <crossref xmlns=\"http://www.crossref.org/xschema/1.1\"
75
+ xsi:schemaLocation=\"http://www.crossref.org/xschema/1.1 http://doi.crossref.org/schemas/unixref1.1.xsd\">\r\n
76
+ \ <journal>\r\n <journal_metadata language=\"en\">\r\n
77
+ \ <full_title>BMC Genomics</full_title>\r\n <abbrev_title>BMC
78
+ Genomics</abbrev_title>\r\n <issn media_type=\"electronic\">1471-2164</issn>\r\n
79
+ \ </journal_metadata>\r\n <journal_issue>\r\n <publication_date
80
+ media_type=\"print\">\r\n <month>12</month>\r\n <year>2006</year>\r\n
81
+ \ </publication_date>\r\n <journal_volume>\r\n
82
+ \ <volume>7</volume>\r\n </journal_volume>\r\n
83
+ \ <issue>1</issue>\r\n </journal_issue>\r\n <journal_article
84
+ publication_type=\"full_text\">\r\n <titles>\r\n <title>Finding
85
+ function: evaluation methods for functional genomic data</title>\r\n </titles>\r\n
86
+ \ <contributors>\r\n <person_name sequence=\"first\"
87
+ contributor_role=\"author\">\r\n <given_name>Chad L</given_name>\r\n
88
+ \ <surname>Myers</surname>\r\n </person_name>\r\n
89
+ \ <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
90
+ \ <given_name>Daniel R</given_name>\r\n <surname>Barrett</surname>\r\n
91
+ \ </person_name>\r\n <person_name sequence=\"additional\"
92
+ contributor_role=\"author\">\r\n <given_name>Matthew A</given_name>\r\n
93
+ \ <surname>Hibbs</surname>\r\n </person_name>\r\n
94
+ \ <person_name sequence=\"additional\" contributor_role=\"author\">\r\n
95
+ \ <given_name>Curtis</given_name>\r\n <surname>Huttenhower</surname>\r\n
96
+ \ </person_name>\r\n <person_name sequence=\"additional\"
97
+ contributor_role=\"author\">\r\n <given_name>Olga G</given_name>\r\n
98
+ \ <surname>Troyanskaya</surname>\r\n </person_name>\r\n
99
+ \ </contributors>\r\n <jats:abstract xmlns:jats=\"http://www.ncbi.nlm.nih.gov/JATS1\"
100
+ xml:lang=\"en\">\r\n <jats:title>Abstract</jats:title>\r\n
101
+ \ <jats:sec>\r\n <jats:title>Background</jats:title>\r\n
102
+ \ <jats:p>Accurate evaluation of the quality of genomic
103
+ or proteomic data and computational methods is vital to our ability to use
104
+ them for formulating novel biological hypotheses and directing further experiments.
105
+ There is currently no standard approach to evaluation in functional genomics.
106
+ Our analysis of existing approaches shows that they are inconsistent and contain
107
+ substantial functional biases that render the resulting evaluations misleading
108
+ both quantitatively and qualitatively. These problems make it essentially
109
+ impossible to compare computational methods or large-scale experimental datasets
110
+ and also result in conclusions that generalize poorly in most biological applications.</jats:p>\r\n
111
+ \ </jats:sec>\r\n <jats:sec>\r\n <jats:title>Results</jats:title>\r\n
112
+ \ <jats:p>We reveal issues with current evaluation methods
113
+ here and suggest new approaches to evaluation that facilitate accurate and
114
+ representative characterization of genomic methods and data. Specifically,
115
+ we describe a functional genomics gold standard based on curation by expert
116
+ biologists and demonstrate its use as an effective means of evaluation of
117
+ genomic approaches. Our evaluation framework and gold standard are freely
118
+ available to the community through our website.</jats:p>\r\n </jats:sec>\r\n
119
+ \ <jats:sec>\r\n <jats:title>Conclusion</jats:title>\r\n
120
+ \ <jats:p>Proper methods for evaluating genomic data and
121
+ computational approaches will determine how much we, as a community, are able
122
+ to learn from the wealth of available data. We propose one possible solution
123
+ to this problem here but emphasize that this topic warrants broader community
124
+ discussion.</jats:p>\r\n </jats:sec>\r\n </jats:abstract>\r\n
125
+ \ <publication_date media_type=\"online\">\r\n <month>07</month>\r\n
126
+ \ <day>25</day>\r\n <year>2006</year>\r\n
127
+ \ </publication_date>\r\n <publication_date media_type=\"print\">\r\n
128
+ \ <month>12</month>\r\n <year>2006</year>\r\n
129
+ \ </publication_date>\r\n <publisher_item>\r\n
130
+ \ <item_number item_number_type=\"article-number\">187</item_number>\r\n
131
+ \ <identifier id_type=\"pii\">570</identifier>\r\n </publisher_item>\r\n
132
+ \ <crossmark>\r\n <crossmark_version>1</crossmark_version>\r\n
133
+ \ <crossmark_policy>10.1007/springer_crossmark_policy</crossmark_policy>\r\n
134
+ \ <crossmark_domains>\r\n <crossmark_domain>\r\n
135
+ \ <domain>link.springer.com</domain>\r\n </crossmark_domain>\r\n
136
+ \ </crossmark_domains>\r\n <crossmark_domain_exclusive>false</crossmark_domain_exclusive>\r\n
137
+ \ <custom_metadata>\r\n <assertion group_label=\"Article
138
+ History\" group_name=\"ArticleHistory\" order=\"1\" label=\"Received\" name=\"received\">10
139
+ May 2006</assertion>\r\n <assertion group_label=\"Article
140
+ History\" group_name=\"ArticleHistory\" order=\"2\" label=\"Accepted\" name=\"accepted\">25
141
+ July 2006</assertion>\r\n <assertion group_label=\"Article
142
+ History\" group_name=\"ArticleHistory\" order=\"3\" label=\"First Online\"
143
+ name=\"first_online\">25 July 2006</assertion>\r\n <ai:program
144
+ xmlns:ai=\"http://www.crossref.org/AccessIndicators.xsd\" name=\"AccessIndicators\">\r\n
145
+ \ <ai:license_ref applies_to=\"tdm\">http://creativecommons.org/licenses/by/2.0</ai:license_ref>\r\n
146
+ \ </ai:program>\r\n </custom_metadata>\r\n
147
+ \ </crossmark>\r\n <doi_data>\r\n <doi>10.1186/1471-2164-7-187</doi>\r\n
148
+ \ <timestamp>20210831173149578</timestamp>\r\n <resource
149
+ content_version=\"vor\">https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-187</resource>\r\n
150
+ \ <collection property=\"crawler-based\">\r\n <item
151
+ crawler=\"iParadigms\">\r\n <resource mime_type=\"application/pdf\">https://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf</resource>\r\n
152
+ \ </item>\r\n </collection>\r\n <collection
153
+ property=\"text-mining\">\r\n <item>\r\n <resource
154
+ mime_type=\"application/pdf\">http://link.springer.com/content/pdf/10.1186/1471-2164-7-187.pdf</resource>\r\n
155
+ \ </item>\r\n <item>\r\n <resource
156
+ mime_type=\"text/html\">http://link.springer.com/article/10.1186/1471-2164-7-187/fulltext.html</resource>\r\n
157
+ \ </item>\r\n </collection>\r\n </doi_data>\r\n
158
+ \ <citation_list>\r\n <citation key=\"570_CR1\">\r\n
159
+ \ <author>Z Barutcuoglu</author>\r\n <cYear>2006</cYear>\r\n
160
+ \ <volume_title>Bioinformatics</volume_title>\r\n <unstructured_citation>Barutcuoglu
161
+ Z, Schapire RE, Troyanskaya OG: Hierarchical multi-label prediction of gene
162
+ function. Bioinformatics. 2006</unstructured_citation>\r\n </citation>\r\n
163
+ \ <citation key=\"570_CR2\">\r\n <journal_title>Bioinformatics</journal_title>\r\n
164
+ \ <author>A Clare</author>\r\n <volume>19</volume>\r\n
165
+ \ <issue>Suppl 2</issue>\r\n <first_page>II42</first_page>\r\n
166
+ \ <cYear>2003</cYear>\r\n <doi>10.1093/bioinformatics/btg1058</doi>\r\n
167
+ \ <unstructured_citation>Clare A, King RD: Predicting gene
168
+ function in Saccharomyces cerevisiae. Bioinformatics. 2003, 19 (Suppl 2):
169
+ II42-II49.</unstructured_citation>\r\n </citation>\r\n <citation
170
+ key=\"570_CR3\">\r\n <author>GR Lanckriet</author>\r\n
171
+ \ <first_page>300</first_page>\r\n <cYear>2004</cYear>\r\n
172
+ \ <volume_title>Pac Symp Biocomput</volume_title>\r\n <unstructured_citation>Lanckriet
588
173
  GR, Deng M, Cristianini N, Jordan MI, Noble WS: Kernel-based data fusion and
589
174
  its application to protein function prediction in yeast. Pac Symp Biocomput.
590
175
  2004, 300-311.</unstructured_citation>\r\n </citation>\r\n
@@ -827,34 +412,449 @@ http_interactions:
827
412
  GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi
828
413
  S: A combined experimental and computational strategy to define protein interaction
829
414
  networks for peptide recognition modules. Science. 2002, 295 (5553): 321-324.
830
- 10.1126/science.1064987.</unstructured_citation>\r\n </citation>\r\n
831
- \ <citation key=\"570_CR36\">\r\n <journal_title>Nature</journal_title>\r\n
832
- \ <author>Y Ho</author>\r\n <volume>415</volume>\r\n
833
- \ <issue>6868</issue>\r\n <first_page>180</first_page>\r\n
834
- \ <cYear>2002</cYear>\r\n <doi>10.1038/415180a</doi>\r\n
835
- \ <unstructured_citation>Ho Y, Gruhler A, Heilbut A, Bader
836
- GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic
837
- identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
838
- Nature. 2002, 415 (6868): 180-183. 10.1038/415180a.</unstructured_citation>\r\n
839
- \ </citation>\r\n <citation key=\"570_CR37\">\r\n
840
- \ <journal_title>Mol Biol Cell</journal_title>\r\n <author>AP
841
- Gasch</author>\r\n <volume>12</volume>\r\n <issue>10</issue>\r\n
842
- \ <first_page>2987</first_page>\r\n <cYear>2001</cYear>\r\n
843
- \ <doi>10.1091/mbc.12.10.2987</doi>\r\n <unstructured_citation>Gasch
844
- AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression
845
- responses to DNA-damaging agents and the regulatory role of the yeast ATR
846
- homolog Mec1p. Mol Biol Cell. 2001, 12 (10): 2987-3003.</unstructured_citation>\r\n
847
- \ </citation>\r\n <citation key=\"570_CR38\">\r\n
848
- \ <journal_title>Mol Biol Cell</journal_title>\r\n <author>PT
849
- Spellman</author>\r\n <volume>9</volume>\r\n <issue>12</issue>\r\n
850
- \ <first_page>3273</first_page>\r\n <cYear>1998</cYear>\r\n
851
- \ <doi>10.1091/mbc.9.12.3273</doi>\r\n <unstructured_citation>Spellman
852
- PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein
853
- D, Futcher B: Comprehensive identification of cell cycle-regulated genes of
854
- the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell.
855
- 1998, 9 (12): 3273-3297.</unstructured_citation>\r\n </citation>\r\n
856
- \ </citation_list>\r\n </journal_article>\r\n </journal>\r\n
857
- \ </crossref>\r\n </doi_record>\r\n </query>\r\n </body>\r\n
858
- \ </query_result>\r\n</crossref_result>"
859
- recorded_at: Sun, 18 Jun 2023 15:25:24 GMT
860
- recorded_with: VCR 6.1.0
415
+ 10.1126/science.1064987.</unstructured_citation>\r\n </citation>\r\n
416
+ \ <citation key=\"570_CR36\">\r\n <journal_title>Nature</journal_title>\r\n
417
+ \ <author>Y Ho</author>\r\n <volume>415</volume>\r\n
418
+ \ <issue>6868</issue>\r\n <first_page>180</first_page>\r\n
419
+ \ <cYear>2002</cYear>\r\n <doi>10.1038/415180a</doi>\r\n
420
+ \ <unstructured_citation>Ho Y, Gruhler A, Heilbut A, Bader
421
+ GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic
422
+ identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
423
+ Nature. 2002, 415 (6868): 180-183. 10.1038/415180a.</unstructured_citation>\r\n
424
+ \ </citation>\r\n <citation key=\"570_CR37\">\r\n
425
+ \ <journal_title>Mol Biol Cell</journal_title>\r\n <author>AP
426
+ Gasch</author>\r\n <volume>12</volume>\r\n <issue>10</issue>\r\n
427
+ \ <first_page>2987</first_page>\r\n <cYear>2001</cYear>\r\n
428
+ \ <doi>10.1091/mbc.12.10.2987</doi>\r\n <unstructured_citation>Gasch
429
+ AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression
430
+ responses to DNA-damaging agents and the regulatory role of the yeast ATR
431
+ homolog Mec1p. Mol Biol Cell. 2001, 12 (10): 2987-3003.</unstructured_citation>\r\n
432
+ \ </citation>\r\n <citation key=\"570_CR38\">\r\n
433
+ \ <journal_title>Mol Biol Cell</journal_title>\r\n <author>PT
434
+ Spellman</author>\r\n <volume>9</volume>\r\n <issue>12</issue>\r\n
435
+ \ <first_page>3273</first_page>\r\n <cYear>1998</cYear>\r\n
436
+ \ <doi>10.1091/mbc.9.12.3273</doi>\r\n <unstructured_citation>Spellman
437
+ PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein
438
+ D, Futcher B: Comprehensive identification of cell cycle-regulated genes of
439
+ the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell.
440
+ 1998, 9 (12): 3273-3297.</unstructured_citation>\r\n </citation>\r\n
441
+ \ </citation_list>\r\n </journal_article>\r\n </journal>\r\n
442
+ \ </crossref>\r\n </doi_record>\r\n </query>\r\n </body>\r\n
443
+ \ </query_result>\r\n</crossref_result>"
444
+ recorded_at: Thu, 05 Oct 2023 19:46:21 GMT
445
+ - request:
446
+ method: get
447
+ uri: https://doi.org/ra/10.1186
448
+ body:
449
+ encoding: ASCII-8BIT
450
+ string: ''
451
+ headers:
452
+ Connection:
453
+ - close
454
+ Host:
455
+ - doi.org
456
+ User-Agent:
457
+ - http.rb/5.1.1
458
+ response:
459
+ status:
460
+ code: 200
461
+ message: OK
462
+ headers:
463
+ Date:
464
+ - Thu, 05 Oct 2023 19:46:21 GMT
465
+ Content-Type:
466
+ - application/json;charset=UTF-8
467
+ Transfer-Encoding:
468
+ - chunked
469
+ Connection:
470
+ - close
471
+ Permissions-Policy:
472
+ - interest-cohort=(),browsing-topics=()
473
+ Cf-Cache-Status:
474
+ - DYNAMIC
475
+ Report-To:
476
+ - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=jMTdlN9PoDfJU7hGLwHOwvk9%2BKLxSp2UYYvLbil8kHEwhhR4fDQyWkZTKakp7MzWDoxZXin6w5sBTjyocZYMXkYx33IIftsGCQkUN2aYbJrqKjOlGyi24bmweyxMWHS9Q7HXYZw%3D"}],"group":"cf-nel","max_age":604800}'
477
+ Nel:
478
+ - '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}'
479
+ Strict-Transport-Security:
480
+ - max-age=31536000; includeSubDomains; preload
481
+ Server:
482
+ - cloudflare
483
+ Cf-Ray:
484
+ - 81182b950bb4b7d3-AMS
485
+ Alt-Svc:
486
+ - h3=":443"; ma=86400
487
+ body:
488
+ encoding: UTF-8
489
+ string: |-
490
+ [
491
+ {
492
+ "DOI": "10.1186",
493
+ "RA": "Crossref"
494
+ }
495
+ ]
496
+ recorded_at: Thu, 05 Oct 2023 19:46:21 GMT
497
+ - request:
498
+ method: get
499
+ uri: https://api.crossref.org/works/10.1186/1471-2164-7-187
500
+ body:
501
+ encoding: ASCII-8BIT
502
+ string: ''
503
+ headers:
504
+ Connection:
505
+ - close
506
+ Host:
507
+ - api.crossref.org
508
+ User-Agent:
509
+ - http.rb/5.1.1
510
+ response:
511
+ status:
512
+ code: 200
513
+ message: OK
514
+ headers:
515
+ Date:
516
+ - Thu, 05 Oct 2023 19:48:56 GMT
517
+ Content-Type:
518
+ - application/json
519
+ Transfer-Encoding:
520
+ - chunked
521
+ Access-Control-Expose-Headers:
522
+ - Link
523
+ Access-Control-Allow-Headers:
524
+ - X-Requested-With, Accept, Accept-Encoding, Accept-Charset, Accept-Language,
525
+ Accept-Ranges, Cache-Control
526
+ Access-Control-Allow-Origin:
527
+ - "*"
528
+ Server:
529
+ - Jetty(9.4.40.v20210413)
530
+ X-Ratelimit-Limit:
531
+ - '50'
532
+ X-Ratelimit-Interval:
533
+ - 1s
534
+ X-Api-Pool:
535
+ - public
536
+ X-Rate-Limit-Limit:
537
+ - '50'
538
+ X-Rate-Limit-Interval:
539
+ - 1s
540
+ Permissions-Policy:
541
+ - interest-cohort=()
542
+ Connection:
543
+ - close
544
+ body:
545
+ encoding: UTF-8
546
+ string: '{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,26]],"date-time":"2023-09-26T12:00:57Z","timestamp":1695729657408},"reference-count":38,"publisher":"Springer
547
+ Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2006,7,25]],"date-time":"2006-07-25T00:00:00Z","timestamp":1153785600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC
548
+ Genomics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n <jats:sec>\n <jats:title>Background<\/jats:title>\n <jats:p>Accurate
549
+ evaluation of the quality of genomic or proteomic data and computational methods
550
+ is vital to our ability to use them for formulating novel biological hypotheses
551
+ and directing further experiments. There is currently no standard approach
552
+ to evaluation in functional genomics. Our analysis of existing approaches
553
+ shows that they are inconsistent and contain substantial functional biases
554
+ that render the resulting evaluations misleading both quantitatively and qualitatively.
555
+ These problems make it essentially impossible to compare computational methods
556
+ or large-scale experimental datasets and also result in conclusions that generalize
557
+ poorly in most biological applications.<\/jats:p>\n <\/jats:sec>\n <jats:sec>\n <jats:title>Results<\/jats:title>\n <jats:p>We
558
+ reveal issues with current evaluation methods here and suggest new approaches
559
+ to evaluation that facilitate accurate and representative characterization
560
+ of genomic methods and data. Specifically, we describe a functional genomics
561
+ gold standard based on curation by expert biologists and demonstrate its use
562
+ as an effective means of evaluation of genomic approaches. Our evaluation
563
+ framework and gold standard are freely available to the community through
564
+ our website.<\/jats:p>\n <\/jats:sec>\n <jats:sec>\n <jats:title>Conclusion<\/jats:title>\n <jats:p>Proper
565
+ methods for evaluating genomic data and computational approaches will determine
566
+ how much we, as a community, are able to learn from the wealth of available
567
+ data. We propose one possible solution to this problem here but emphasize
568
+ that this topic warrants broader community discussion.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2164-7-187","type":"journal-article","created":{"date-parts":[[2006,7,25]],"date-time":"2006-07-25T18:14:51Z","timestamp":1153851291000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":172,"title":["Finding
569
+ function: evaluation methods for functional genomic data"],"prefix":"10.1186","volume":"7","author":[{"given":"Chad
570
+ L","family":"Myers","sequence":"first","affiliation":[]},{"given":"Daniel
571
+ R","family":"Barrett","sequence":"additional","affiliation":[]},{"given":"Matthew
572
+ A","family":"Hibbs","sequence":"additional","affiliation":[]},{"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[]},{"given":"Olga
573
+ G","family":"Troyanskaya","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,7,25]]},"reference":[{"key":"570_CR1","volume-title":"Bioinformatics","author":"Z
574
+ Barutcuoglu","year":"2006","unstructured":"Barutcuoglu Z, Schapire RE, Troyanskaya
575
+ OG: Hierarchical multi-label prediction of gene function. Bioinformatics.
576
+ 2006"},{"issue":"Suppl 2","key":"570_CR2","doi-asserted-by":"publisher","first-page":"II42","DOI":"10.1093\/bioinformatics\/btg1058","volume":"19","author":"A
577
+ Clare","year":"2003","unstructured":"Clare A, King RD: Predicting gene function
578
+ in Saccharomyces cerevisiae. Bioinformatics. 2003, 19 (Suppl 2): II42-II49.","journal-title":"Bioinformatics"},{"key":"570_CR3","first-page":"300","volume-title":"Pac
579
+ Symp Biocomput","author":"GR Lanckriet","year":"2004","unstructured":"Lanckriet
580
+ GR, Deng M, Cristianini N, Jordan MI, Noble WS: Kernel-based data fusion and
581
+ its application to protein function prediction in yeast. Pac Symp Biocomput.
582
+ 2004, 300-311."},{"issue":"2","key":"570_CR4","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1089\/10665270252935539","volume":"9","author":"P
583
+ Pavlidis","year":"2002","unstructured":"Pavlidis P, Weston J, Cai J, Noble
584
+ WS: Learning gene functional classifications from multiple data types. J Comput
585
+ Biol. 2002, 9 (2): 401-411. 10.1089\/10665270252935539.","journal-title":"J
586
+ Comput Biol"},{"issue":"Suppl 1","key":"570_CR5","doi-asserted-by":"publisher","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","volume":"21","author":"A
587
+ Ben-Hur","year":"2005","unstructured":"Ben-Hur A, Noble WS: Kernel methods
588
+ for predicting protein-protein interactions. Bioinformatics. 2005, 21 (Suppl
589
+ 1): i38-i46. 10.1093\/bioinformatics\/bti1016.","journal-title":"Bioinformatics"},{"issue":"5644","key":"570_CR6","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1126\/science.1087361","volume":"302","author":"R
590
+ Jansen","year":"2003","unstructured":"Jansen R, Yu H, Greenbaum D, Kluger
591
+ Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian
592
+ networks approach for predicting protein-protein interactions from genomic
593
+ data. Science. 2003, 302 (5644): 449-453. 10.1126\/science.1087361.","journal-title":"Science"},{"issue":"5701","key":"570_CR7","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1126\/science.1099511","volume":"306","author":"I
594
+ Lee","year":"2004","unstructured":"Lee I, Date SV, Adai AT, Marcotte EM: A
595
+ probabilistic functional network of yeast genes. Science. 2004, 306 (5701):
596
+ 1555-1558. 10.1126\/science.1099511.","journal-title":"Science"},{"issue":"1","key":"570_CR8","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1186\/1471-2105-5-154","volume":"5","author":"N
597
+ Lin","year":"2004","unstructured":"Lin N, Wu B, Jansen R, Gerstein M, Zhao
598
+ H: Information assessment on predicting protein-protein interactions. BMC
599
+ Bioinformatics. 2004, 5 (1): 154-10.1186\/1471-2105-5-154.","journal-title":"BMC
600
+ Bioinformatics"},{"issue":"14","key":"570_CR9","doi-asserted-by":"publisher","first-page":"8348","DOI":"10.1073\/pnas.0832373100","volume":"100","author":"OG
601
+ Troyanskaya","year":"2003","unstructured":"Troyanskaya OG, Dolinski K, Owen
602
+ AB, Altman RB, Botstein D: A Bayesian framework for combining heterogeneous
603
+ data sources for gene function prediction (in Saccharomyces cerevisiae). Proc
604
+ Natl Acad Sci USA. 2003, 100 (14): 8348-8353. 10.1073\/pnas.0832373100.","journal-title":"Proc
605
+ Natl Acad Sci USA"},{"issue":"8","key":"570_CR10","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1016\/j.tig.2005.06.006","volume":"21","author":"SL
606
+ Wong","year":"2005","unstructured":"Wong SL, Zhang LV, Roth FP: Discovering
607
+ functional relationships: biochemistry versus genetics. Trends Genet. 2005,
608
+ 21 (8): 424-427. 10.1016\/j.tig.2005.06.006.","journal-title":"Trends Genet"},{"issue":"1","key":"570_CR11","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M
609
+ Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: kyoto encyclopedia
610
+ of genes and genomes. Nucleic Acids Res. 2000, 28 (1): 27-30. 10.1093\/nar\/28.1.27.","journal-title":"Nucleic
611
+ Acids Res"},{"issue":"Suppl 1","key":"570_CR12","doi-asserted-by":"publisher","first-page":"I363","DOI":"10.1093\/bioinformatics\/bth910","volume":"20","author":"Y
612
+ Yamanishi","year":"2004","unstructured":"Yamanishi Y, Vert JP, Kanehisa M:
613
+ Protein network inference from multiple genomic data: a supervised approach.
614
+ Bioinformatics. 2004, 20 (Suppl 1): I363-I370. 10.1093\/bioinformatics\/bth910.","journal-title":"Bioinformatics"},{"key":"570_CR13","unstructured":"GRIFn
615
+ Home Page. [http:\/\/function.princeton.edu\/GRIFn]"},{"issue":"6868","key":"570_CR14","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"AC
616
+ Gavin","year":"2002","unstructured":"Gavin AC, Bosche M, Krause R, Grandi
617
+ P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM: Functional
618
+ organization of the yeast proteome by systematic analysis of protein complexes.
619
+ Nature. 2002, 415 (6868): 141-147. 10.1038\/415141a.","journal-title":"Nature"},{"issue":"5","key":"570_CR15","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1016\/S0022-2836(03)00239-0","volume":"327","author":"E
620
+ Sprinzak","year":"2003","unstructured":"Sprinzak E, Sattath S, Margalit H:
621
+ How reliable are experimental protein-protein interaction data?. J Mol Biol.
622
+ 2003, 327 (5): 919-923. 10.1016\/S0022-2836(03)00239-0.","journal-title":"J
623
+ Mol Biol"},{"issue":"6770","key":"570_CR16","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P
624
+ Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield TA,
625
+ Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P: A comprehensive
626
+ analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature.
627
+ 2000, 403 (6770): 623-627. 10.1038\/35001009.","journal-title":"Nature"},{"issue":"6887","key":"570_CR17","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C
628
+ von Mering","year":"2002","unstructured":"von Mering C, Krause R, Snel B,
629
+ Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale
630
+ data sets of protein-protein interactions. Nature. 2002, 417 (6887): 399-403.
631
+ 10.1038\/nature750.","journal-title":"Nature"},{"issue":"3","key":"570_CR18","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1093\/bioinformatics\/btg420","volume":"20","author":"SG
632
+ Lee","year":"2004","unstructured":"Lee SG, Hur JU, Kim YS: A graph-theoretic
633
+ modeling on GO space for biological interpretation of gene clusters. Bioinformatics.
634
+ 2004, 20 (3): 381-388. 10.1093\/bioinformatics\/btg420.","journal-title":"Bioinformatics"},{"issue":"1","key":"570_CR19","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M
635
+ Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein
636
+ D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology:
637
+ tool for the unification of biology. The Gene Ontology Consortium. Nat Genet.
638
+ 2000, 25 (1): 25-29. 10.1038\/75556.","journal-title":"Nat Genet"},{"issue":"1","key":"570_CR20","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/nar\/28.1.77","volume":"28","author":"CA
639
+ Ball","year":"2000","unstructured":"Ball CA, Dolinski K, Dwight SS, Harris
640
+ MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H: Integrating
641
+ functional genomic information into the Saccharomyces genome database. Nucleic
642
+ Acids Res. 2000, 28 (1): 77-80. 10.1093\/nar\/28.1.77.","journal-title":"Nucleic
643
+ Acids Res"},{"issue":"1","key":"570_CR21","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/nar\/30.1.31","volume":"30","author":"HW
644
+ Mewes","year":"2002","unstructured":"Mewes HW, Frishman D, Guldener U, Mannhaupt
645
+ G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B: MIPS:
646
+ a database for genomes and protein sequences. Nucleic Acids Res. 2002, 30
647
+ (1): 31-34. 10.1093\/nar\/30.1.31.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"570_CR22","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1093\/nar\/29.1.75","volume":"29","author":"MC
648
+ Costanzo","year":"2001","unstructured":"Costanzo MC, Crawford ME, Hirschman
649
+ JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu
650
+ P: YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library,
651
+ an integrated resource for protein information. Nucleic Acids Res. 2001, 29
652
+ (1): 75-79. 10.1093\/nar\/29.1.75.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"570_CR23","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1016\/j.mib.2004.08.012","volume":"7","author":"R
653
+ Jansen","year":"2004","unstructured":"Jansen R, Gerstein M: Analyzing protein
654
+ function on a genomic scale: the importance of gold-standard positives and
655
+ negatives for network prediction. Curr Opin Microbiol. 2004, 7 (5): 535-545.
656
+ 10.1016\/j.mib.2004.08.012.","journal-title":"Curr Opin Microbiol"},{"issue":"1","key":"570_CR24","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/1471-2105-6-100","volume":"6","author":"A
657
+ Patil","year":"2005","unstructured":"Patil A, Nakamura H: Filtering high-throughput
658
+ protein-protein interaction data using a combination of genomic features.
659
+ BMC Bioinformatics. 2005, 6 (1): 100-10.1186\/1471-2105-6-100.","journal-title":"BMC
660
+ Bioinformatics"},{"issue":"6959","key":"570_CR25","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1038\/nature02026","volume":"425","author":"WK
661
+ Huh","year":"2003","unstructured":"Huh WK, Falvo JV, Gerke LC, Carroll AS,
662
+ Howson RW, Weissman JS, O''Shea EK: Global analysis of protein localization
663
+ in budding yeast. Nature. 2003, 425 (6959): 686-691. 10.1038\/nature02026.","journal-title":"Nature"},{"issue":"5","key":"570_CR26","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1074\/mcp.M100037-MCP200","volume":"1","author":"CM
664
+ Deane","year":"2002","unstructured":"Deane CM, Salwinski L, Xenarios I, Eisenberg
665
+ D: Protein interactions: two methods for assessment of the reliability of
666
+ high throughput observations. Mol Cell Proteomics. 2002, 1 (5): 349-356. 10.1074\/mcp.M100037-MCP200.","journal-title":"Mol
667
+ Cell Proteomics"},{"key":"570_CR27","first-page":"531","volume-title":"Pac
668
+ Symp Biocomput","author":"Y Qi","year":"2005","unstructured":"Qi Y, Klein-Seetharaman
669
+ J, Bar-Joseph Z: Random forest similarity for protein-protein interaction
670
+ prediction from multiple sources. Pac Symp Biocomput. 2005, 531-542."},{"issue":"3","key":"570_CR28","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/j.sbi.2004.05.003","volume":"14","author":"P
671
+ Bork","year":"2004","unstructured":"Bork P, Jensen LJ, von Mering C, Ramani
672
+ AK, Lee I, Marcotte EM: Protein interaction networks from yeast to human.
673
+ Curr Opin Struct Biol. 2004, 14 (3): 292-299. 10.1016\/j.sbi.2004.05.003.","journal-title":"Curr
674
+ Opin Struct Biol"},{"issue":"1","key":"570_CR29","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/nar\/28.1.289","volume":"28","author":"I
675
+ Xenarios","year":"2000","unstructured":"Xenarios I, Rice DW, Salwinski L,
676
+ Baron MK, Marcotte EM, Eisenberg D: DIP: the database of interacting proteins.
677
+ Nucleic Acids Res. 2000, 28 (1): 289-291. 10.1093\/nar\/28.1.289.","journal-title":"Nucleic
678
+ Acids Res"},{"issue":"3","key":"570_CR30","doi-asserted-by":"publisher","first-page":"R23","DOI":"10.1186\/gb-2003-4-3-r23","volume":"4","author":"BJ
679
+ Breitkreutz","year":"2003","unstructured":"Breitkreutz BJ, Stark C, Tyers
680
+ M: The GRID: the General Repository for Interaction Datasets. Genome Biol.
681
+ 2003, 4 (3): R23-10.1186\/gb-2003-4-3-r23.","journal-title":"Genome Biol"},{"key":"570_CR31","doi-asserted-by":"crossref","unstructured":"Alfarano
682
+ C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko
683
+ B, Boutilier K, Burgess E: The Biomolecular Interaction Network Database and
684
+ related tools 2005 update. Nucleic Acids Res. 2005, D418-424. 33 Database","DOI":"10.1093\/nar\/gki051"},{"issue":"10","key":"570_CR32","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","volume":"19","author":"PW
685
+ Lord","year":"2003","unstructured":"Lord PW, Stevens RD, Brass A, Goble CA:
686
+ Investigating semantic similarity measures across the Gene Ontology: the relationship
687
+ between sequence and annotation. Bioinformatics. 2003, 19 (10): 1275-1283.
688
+ 10.1093\/bioinformatics\/btg153.","journal-title":"Bioinformatics"},{"issue":"Suppl61","key":"570_CR33","first-page":"S2","volume":"7","author":"A
689
+ Ben-Hur","year":"2005","unstructured":"Ben-Hur A, Noble WS: Choosing negative
690
+ examples for the prediction of protein-protein interactions. BMC Bioinformatics.
691
+ 2005, 7 (Suppl61): S2-","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"570_CR34","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1073\/pnas.061034498","volume":"98","author":"T
692
+ Ito","year":"2001","unstructured":"Ito T, Chiba T, Ozawa R, Yoshida M, Hattori
693
+ M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein
694
+ interactome. Proc Natl Acad Sci U S A. 2001, 98 (8): 4569-4574. 10.1073\/pnas.061034498.","journal-title":"Proc
695
+ Natl Acad Sci U S A"},{"issue":"5553","key":"570_CR35","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1126\/science.1064987","volume":"295","author":"AH
696
+ Tong","year":"2002","unstructured":"Tong AH, Drees B, Nardelli G, Bader GD,
697
+ Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S:
698
+ A combined experimental and computational strategy to define protein interaction
699
+ networks for peptide recognition modules. Science. 2002, 295 (5553): 321-324.
700
+ 10.1126\/science.1064987.","journal-title":"Science"},{"issue":"6868","key":"570_CR36","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/415180a","volume":"415","author":"Y
701
+ Ho","year":"2002","unstructured":"Ho Y, Gruhler A, Heilbut A, Bader GD, Moore
702
+ L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic identification
703
+ of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature.
704
+ 2002, 415 (6868): 180-183. 10.1038\/415180a.","journal-title":"Nature"},{"issue":"10","key":"570_CR37","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1091\/mbc.12.10.2987","volume":"12","author":"AP
705
+ Gasch","year":"2001","unstructured":"Gasch AP, Huang M, Metzner S, Botstein
706
+ D, Elledge SJ, Brown PO: Genomic expression responses to DNA-damaging agents
707
+ and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell. 2001,
708
+ 12 (10): 2987-3003.","journal-title":"Mol Biol Cell"},{"issue":"12","key":"570_CR38","doi-asserted-by":"publisher","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","volume":"9","author":"PT
709
+ Spellman","year":"1998","unstructured":"Spellman PT, Sherlock G, Zhang MQ,
710
+ Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive
711
+ identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae
712
+ by microarray hybridization. Mol Biol Cell. 1998, 9 (12): 3273-3297.","journal-title":"Mol
713
+ Biol Cell"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-7-187.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2164-7-187\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-7-187.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:37:43Z","timestamp":1630460263000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-7-187"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,7,25]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["570"],"URL":"http:\/\/dx.doi.org\/10.1186\/1471-2164-7-187","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":["Genetics","Biotechnology"],"published":{"date-parts":[[2006,7,25]]},"assertion":[{"value":"10
714
+ May 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article
715
+ History"}},{"value":"25 July 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article
716
+ History"}},{"value":"25 July 2006","order":3,"name":"first_online","label":"First
717
+ Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"187"}}'
718
+ recorded_at: Thu, 05 Oct 2023 19:48:56 GMT
719
+ - request:
720
+ method: get
721
+ uri: https://api.crossref.org/members/297
722
+ body:
723
+ encoding: ASCII-8BIT
724
+ string: ''
725
+ headers:
726
+ Connection:
727
+ - close
728
+ Host:
729
+ - api.crossref.org
730
+ User-Agent:
731
+ - http.rb/5.1.1
732
+ response:
733
+ status:
734
+ code: 200
735
+ message: OK
736
+ headers:
737
+ Date:
738
+ - Thu, 05 Oct 2023 19:48:57 GMT
739
+ Content-Type:
740
+ - application/json
741
+ Transfer-Encoding:
742
+ - chunked
743
+ Access-Control-Expose-Headers:
744
+ - Link
745
+ Access-Control-Allow-Headers:
746
+ - X-Requested-With, Accept, Accept-Encoding, Accept-Charset, Accept-Language,
747
+ Accept-Ranges, Cache-Control
748
+ Access-Control-Allow-Origin:
749
+ - "*"
750
+ Server:
751
+ - Jetty(9.4.40.v20210413)
752
+ X-Ratelimit-Limit:
753
+ - '50'
754
+ X-Ratelimit-Interval:
755
+ - 1s
756
+ X-Api-Pool:
757
+ - public
758
+ X-Rate-Limit-Limit:
759
+ - '50'
760
+ X-Rate-Limit-Interval:
761
+ - 1s
762
+ Permissions-Policy:
763
+ - interest-cohort=()
764
+ Connection:
765
+ - close
766
+ body:
767
+ encoding: UTF-8
768
+ string: '{"status":"ok","message-type":"member","message-version":"1.0.0","message":{"last-status-check-time":1696462315722,"primary-name":"Springer
769
+ Science and Business Media LLC","counts":{"current-dois":2032926,"backfile-dois":13845713,"total-dois":15878639},"breakdowns":{"dois-by-issued-year":[[2022,738697],[2021,736641],[2020,697200],[2019,637628],[2018,626498],[2017,607344],[2014,594488],[2016,586868],[2013,576898],[2023,557382],[2015,524075],[2012,469541],[2011,453210],[2010,415852],[2009,397477],[2008,322290],[2007,283545],[2006,254889],[2004,251758],[2005,239917],[2003,236134],[2000,234944],[2002,225415],[2001,222802],[1999,205539],[1998,204688],[1997,198738],[1996,185252],[1995,174987],[1994,168734],[1993,167014],[1991,162873],[1992,161821],[1990,157387],[1989,152727],[1988,142846],[1987,136059],[1986,125472],[1985,117421],[1984,114755],[1983,101536],[1982,99089],[1981,96284],[1980,91121],[1979,84520],[1978,83762],[1977,79778],[1976,73482],[1975,69575],[1974,67550],[1973,62944],[1972,59939],[1971,55787],[1970,53125],[1969,49815],[1968,48955],[1967,47205],[1966,42454],[1965,37501],[1964,33205],[1963,30595],[1962,30097],[1961,29432],[1960,28854],[1959,25681],[1958,24491],[1956,21941],[1957,21848],[1955,19912],[1954,16716],[1953,16708],[1932,16468],[1928,16373],[1930,16195],[1927,15870],[1926,15584],[1929,15329],[1931,15287],[1933,15129],[1952,14994],[1936,14706],[1938,14651],[1950,14507],[1935,14397],[1937,14279],[1939,14063],[1951,13951],[1934,13698],[1925,13413],[1924,13128],[1923,12818],[1922,12374],[1949,11829],[1913,11542],[1921,11472],[1940,11281],[1914,10095],[1941,9997],[1920,9970],[1942,9650],[1948,9430],[1912,9290],[1910,9128],[1911,9063],[1943,8590],[1904,8229],[1903,8054],[1909,7961],[1919,7949],[1908,7910],[1905,7554],[1907,7549],[1902,7376],[1906,7298],[1918,7183],[1901,7167],[1915,7030],[1900,7023],[1916,6836],[1897,6815],[1917,6752],[1887,6742],[1886,6713],[1899,6699],[1888,6512],[1947,6407],[1893,6407],[1898,6398],[1889,6361],[1895,6147],[1891,6122],[1894,6116],[1880,6105],[1944,6080],[1885,6076],[1892,6068],[1890,5981],[1896,5963],[1877,5912],[1884,5771],[1883,5732],[1878,5633],[1882,5628],[1881,5603],[1946,5556],[1876,5486],[1879,5427],[1847,5058],[1945,3954],[1848,3882],[1872,3827],[1875,3819],[1873,3761],[1870,3725],[1874,3641],[1871,3604],[1852,3065],[1849,3025],[1869,3021],[1856,2943],[1855,2836],[1857,2796],[1854,2772],[1851,2733],[1850,2690],[1860,2628],[1867,2601],[1859,2530],[1853,2512],[1868,2447],[1858,2433],[1865,2238],[1863,2148],[1864,2145],[1866,2110],[1862,2044],[1846,1920],[1861,1703],[1845,278],[2024,206],[1844,176],[1843,99],[1837,66],[1840,64],[1836,62],[1835,62],[1833,62],[1400,57],[1834,56],[1838,55],[1841,50],[1832,50],[1839,49],[1842,42],[1827,2],[1815,2]]},"prefixes":["10.1208","10.19150","10.1245","10.7603","10.1007","10.17269","10.4076","10.7123","10.1140","10.1381","10.33283","10.4333","10.1186","10.1065","10.1361","10.4056","10.1023","10.1385","10.26778","10.26777","10.5819","10.1617","10.1013","10.1057","10.1379","10.1038","10.1114","10.3758","10.1557","10.3858","10.7759","10.2165","10.1251","10.5052"],"coverage":{"affiliations-current":1.116617132153359E-4,"similarity-checking-current":0.9964356794098752,"descriptions-current":0.0,"ror-ids-current":0.0,"funders-backfile":0.04590951726357465,"licenses-backfile":0.7187580011228024,"funders-current":0.2501512598097521,"affiliations-backfile":4.914156461281552E-4,"resource-links-backfile":0.5320717683516912,"orcids-backfile":0.05136384092317962,"update-policies-current":0.9261217575061758,"ror-ids-backfile":0.0,"orcids-current":0.3873869486641422,"similarity-checking-backfile":0.9344034503676336,"references-backfile":0.6703077696323765,"descriptions-backfile":0.0,"award-numbers-backfile":0.03723087427855828,"update-policies-backfile":0.2806135733132703,"licenses-current":0.9904787483656562,"award-numbers-current":0.1925293886742557,"abstracts-backfile":0.03314506085746541,"resource-links-current":0.6217284839684278,"abstracts-current":0.217546039550874,"references-current":0.8660187335889254},"prefix":[{"name":"American
770
+ Association of Pharmaceutical Scientists","value":"10.1208"},{"name":"Society
771
+ for Mining, Metallurgy & Exploration Inc.","value":"10.19150"},{"name":"Springer
772
+ - Society of Surgical Oncology","value":"10.1245"},{"name":"Springer - Global
773
+ Science Journals","value":"10.7603"},{"name":"Springer-Verlag","value":"10.1007"},{"name":"Canadian
774
+ Public Health Association","value":"10.17269"},{"name":"Springer (Cases Network,
775
+ Ltd.)","value":"10.4076"},{"name":"Springer Science and Business Media LLC","value":"10.7123"},{"name":"Springer-Verlag","value":"10.1140"},{"name":"Springer
776
+ - FD Communications","value":"10.1381"},{"name":"Springer Science and Business
777
+ Media LLC","value":"10.33283"},{"name":"Springer - The Korean Society of Pharmaceutical
778
+ Sciences and Technology","value":"10.4333"},{"name":"Springer (Biomed Central
779
+ Ltd.)","value":"10.1186"},{"name":"Springer - Ecomed Publishers","value":"10.1065"},{"name":"Springer
780
+ - ASM International","value":"10.1361"},{"name":"Genomic Standards Consortium","value":"10.4056"},{"name":"Springer
781
+ (Kluwer Academic Publishers)","value":"10.1023"},{"name":"Springer - Humana
782
+ Press","value":"10.1385"},{"name":"SpringerNature","value":"10.26778"},{"name":"SpringerNature","value":"10.26777"},{"name":"Springer
783
+ - (backfiles)","value":"10.5819"},{"name":"Springer - RILEM Publishing","value":"10.1617"},{"name":"Springer
784
+ Science and Business Media LLC","value":"10.1013"},{"name":"Springer Science
785
+ and Business Media LLC","value":"10.1057"},{"name":"Springer - Cell Stress
786
+ Society International","value":"10.1379"},{"name":"Springer Science and Business
787
+ Media LLC","value":"10.1038"},{"name":"Springer (Kluwer Academic Publishers
788
+ - Biomedical Engineering Society (BMES))","value":"10.1114"},{"name":"Springer
789
+ - Psychonomic Society","value":"10.3758"},{"name":"Materials Research Society","value":"10.1557"},{"name":"Springer
790
+ Science and Business Media LLC","value":"10.3858"},{"name":"Cureus, Inc.","value":"10.7759"},{"name":"Springer
791
+ - Adis","value":"10.2165"},{"name":"Springer (Biological Procedures Online)","value":"10.1251"},{"name":"Springer
792
+ - Real Academia de Ciencias Exactas, Fisicas y Naturales","value":"10.5052"}],"id":297,"tokens":["springer","science","and","business","media","llc"],"counts-type":{"all":{"monograph":359,"journal-article":9538976,"book":333443,"reference-entry":85798,"proceedings-article":1149,"journal":2144,"component":5270,"book-chapter":6514303,"reference-book":1047,"journal-issue":1311,"dataset":23869},"backfile":{"monograph":359,"journal-article":8299935,"book":295341,"proceedings-article":1149,"book-chapter":5226764,"reference-book":744,"journal-issue":1311,"dataset":20110},"current":{"journal-article":1239040,"book":38102,"book-chapter":751724,"reference-book":303,"dataset":3757}},"coverage-type":{"all":{"monograph":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.6295264623955432,"references":0.0,"funders":0.0,"similarity-checking":0.6295264623955432,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.6295264623955432,"descriptions":0.0},"journal-article":{"last-status-check-time":1696462315722,"affiliations":7.37081212910065E-4,"abstracts":0.09197035405058153,"orcids":0.1414656038551727,"licenses":0.8800411071377053,"references":0.733224090300678,"funders":0.118032480635238,"similarity-checking":0.9077871670921491,"award-numbers":0.09490903426111985,"ror-ids":0.0,"update-policies":0.3790063000473007,"resource-links":0.869894839865411,"descriptions":0.0},"book":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.02808875879835534,"licenses":0.9949586586013202,"references":2.999013324616201E-6,"funders":0.00470545190632282,"similarity-checking":0.9965841238232621,"award-numbers":6.357908248186347E-4,"ror-ids":0.0,"update-policies":2.999013324616201E-6,"resource-links":0.9945477937758477,"descriptions":0.0},"reference-entry":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.005396396186391291,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"proceedings-article":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.006092254134029591,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"journal":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":4.664179104477612E-4,"references":0.0,"funders":0.0,"similarity-checking":0.001865671641791045,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":4.664179104477612E-4,"descriptions":0.0},"component":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":5.692599620493359E-4},"book-chapter":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.003664091154494963,"orcids":0.02050641488429384,"licenses":0.4969893171993995,"references":0.6587463002565278,"funders":0.001408285736785655,"similarity-checking":0.9701639607491392,"award-numbers":2.052406834622215E-4,"ror-ids":0.0,"update-policies":0.327355973463316,"resource-links":1.535083645940325E-7,"descriptions":0.0},"reference-book":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.02578796561604585,"licenses":0.9914040114613181,"references":0.0,"funders":0.001910219675262655,"similarity-checking":0.994269340974212,"award-numbers":0.001910219675262655,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.9914040114613181,"descriptions":0.0},"journal-issue":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.03508771929824561,"references":0.0,"funders":0.0,"similarity-checking":0.07704042715484363,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.03508771929824561,"descriptions":0.0},"dataset":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.2632284553186141,"licenses":0.0,"references":0.0,"funders":0.3156814277933722,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.8464116636641669,"resource-links":0.0,"descriptions":0.0}},"backfile":{"monograph":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.6295264623955432,"references":0.0,"funders":0.0,"similarity-checking":0.6295264623955432,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.6295264623955432,"descriptions":0.0},"journal-article":{"last-status-check-time":1696462315722,"affiliations":8.197654559945349E-4,"abstracts":0.05477982658900341,"orcids":0.0801156876529756,"licenses":0.8637439931758502,"references":0.7045625056099837,"funders":0.07523167350105754,"similarity-checking":0.8941902557068218,"award-numbers":0.06199181077924104,"ror-ids":0.0,"update-policies":0.2983495653881627,"resource-links":0.8520898055225734,"descriptions":0.0},"book":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.01171527149972405,"licenses":0.9943319755807692,"references":3.385916618417355E-6,"funders":0.00191981472264264,"similarity-checking":0.996454945300517,"award-numbers":3.589071615522396E-4,"ror-ids":0.0,"update-policies":3.385916618417355E-6,"resource-links":0.9941559079166116,"descriptions":0.0},"proceedings-article":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.0,"references":0.0,"funders":0.0,"similarity-checking":0.006092254134029591,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.0,"descriptions":0.0},"book-chapter":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":8.127399668322503E-4,"orcids":0.007471353212044776,"licenses":0.4760161354138048,"references":0.6568241841414688,"funders":0.001010185269509012,"similarity-checking":0.9987814640186548,"award-numbers":1.633898144243742E-4,"ror-ids":0.0,"update-policies":0.2657366967400862,"resource-links":1.913229677100401E-7,"descriptions":0.0},"reference-book":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.01612903225806452,"licenses":0.9879032258064516,"references":0.0,"funders":0.0,"similarity-checking":0.9919354838709677,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.9879032258064516,"descriptions":0.0},"journal-issue":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0,"licenses":0.03508771929824561,"references":0.0,"funders":0.0,"similarity-checking":0.07704042715484363,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.03508771929824561,"descriptions":0.0},"dataset":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.1835405271009448,"licenses":0.0,"references":0.0,"funders":0.2677772252610641,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.9979612133267031,"resource-links":0.0,"descriptions":0.0}},"current":{"journal-article":{"last-status-check-time":1696462315722,"affiliations":1.832063533057851E-4,"abstracts":0.3410979467975207,"orcids":0.5524293001033058,"licenses":0.9892101949896694,"references":0.9252195247933884,"funders":0.4047415741219008,"similarity-checking":0.998868478822314,"award-numbers":0.3154111247417355,"ror-ids":0.0,"update-policies":0.9193004261363636,"resource-links":0.9891649987086777,"descriptions":0.0},"book":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.1550049866148759,"licenses":0.9998162826098368,"references":0.0,"funders":0.02629783213479607,"similarity-checking":0.9975854285864258,"award-numbers":0.002782006193900583,"ror-ids":0.0,"update-policies":0.0,"resource-links":0.9975854285864258,"descriptions":0.0},"book-chapter":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.02610133506446515,"orcids":0.1257562616066535,"licenses":0.9970427976225317,"references":0.8170126269747939,"funders":0.00518009269359499,"similarity-checking":0.9973461004304771,"award-numbers":6.425230536739548E-4,"ror-ids":0.0,"update-policies":0.9891303191064806,"resource-links":0.0,"descriptions":0.0},"reference-book":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.0495049504950495,"licenses":1.0,"references":0.0,"funders":0.006600660066006601,"similarity-checking":1.0,"award-numbers":0.006600660066006601,"ror-ids":0.0,"update-policies":0.0,"resource-links":1.0,"descriptions":0.0},"dataset":{"last-status-check-time":1696462315722,"affiliations":0.0,"abstracts":0.0,"orcids":0.689912163960607,"licenses":0.0,"references":0.0,"funders":0.5722651051370775,"similarity-checking":0.0,"award-numbers":0.0,"ror-ids":0.0,"update-policies":0.03566675538993878,"resource-links":0.0,"descriptions":0.0}}},"flags":{"deposits-abstracts-current":true,"deposits-orcids-current":true,"deposits":true,"deposits-affiliations-backfile":true,"deposits-update-policies-backfile":true,"deposits-similarity-checking-backfile":true,"deposits-award-numbers-current":true,"deposits-resource-links-current":true,"deposits-ror-ids-current":false,"deposits-articles":true,"deposits-affiliations-current":true,"deposits-funders-current":true,"deposits-references-backfile":true,"deposits-ror-ids-backfile":false,"deposits-abstracts-backfile":true,"deposits-licenses-backfile":true,"deposits-award-numbers-backfile":true,"deposits-descriptions-current":false,"deposits-references-current":true,"deposits-resource-links-backfile":true,"deposits-descriptions-backfile":false,"deposits-orcids-backfile":true,"deposits-funders-backfile":true,"deposits-update-policies-current":true,"deposits-similarity-checking-current":true,"deposits-licenses-current":true},"location":"Dordrecht,
793
+ GX, Netherlands","names":["Springer Science and Business Media LLC","American
794
+ Association of Pharmaceutical Scientists","Society for Mining, Metallurgy
795
+ & Exploration Inc.","Springer - Society of Surgical Oncology","Springer -
796
+ Global Science Journals","Springer-Verlag","Canadian Public Health Association","Springer
797
+ (Cases Network, Ltd.)","Springer - FD Communications","Springer - The Korean
798
+ Society of Pharmaceutical Sciences and Technology","Springer (Biomed Central
799
+ Ltd.)","Springer - Ecomed Publishers","Springer - ASM International","Genomic
800
+ Standards Consortium","Springer (Kluwer Academic Publishers)","Springer -
801
+ Humana Press","SpringerNature","Springer - (backfiles)","Springer - RILEM
802
+ Publishing","Springer - Cell Stress Society International","Springer (Kluwer
803
+ Academic Publishers - Biomedical Engineering Society (BMES))","Springer -
804
+ Psychonomic Society","Materials Research Society","Cureus, Inc.","Springer
805
+ - Adis","Springer (Biological Procedures Online)","Springer - Real Academia
806
+ de Ciencias Exactas, Fisicas y Naturales"]}}'
807
+ recorded_at: Thu, 05 Oct 2023 19:48:57 GMT
808
+ - request:
809
+ method: get
810
+ uri: https://doi.org/ra/10.1186
811
+ body:
812
+ encoding: ASCII-8BIT
813
+ string: ''
814
+ headers:
815
+ Connection:
816
+ - close
817
+ Host:
818
+ - doi.org
819
+ User-Agent:
820
+ - http.rb/5.1.1
821
+ response:
822
+ status:
823
+ code: 200
824
+ message: OK
825
+ headers:
826
+ Date:
827
+ - Thu, 05 Oct 2023 19:48:57 GMT
828
+ Content-Type:
829
+ - application/json;charset=UTF-8
830
+ Transfer-Encoding:
831
+ - chunked
832
+ Connection:
833
+ - close
834
+ Permissions-Policy:
835
+ - interest-cohort=(),browsing-topics=()
836
+ Cf-Cache-Status:
837
+ - DYNAMIC
838
+ Report-To:
839
+ - '{"endpoints":[{"url":"https:\/\/a.nel.cloudflare.com\/report\/v3?s=PwdN4XilmXN%2BLiKvtzVBdsUDk4MIh7nHmAtDQWrJdlwTbzoa0tYAlIJ0byd193aQ9Fvqti04l2w8TVgNn2HxU36zz0x2r2sy6lFgM6k2jI8GkAA2F3sxCpr%2Fi8W0CT6vT5ks%2FaA%3D"}],"group":"cf-nel","max_age":604800}'
840
+ Nel:
841
+ - '{"success_fraction":0,"report_to":"cf-nel","max_age":604800}'
842
+ Strict-Transport-Security:
843
+ - max-age=31536000; includeSubDomains; preload
844
+ Server:
845
+ - cloudflare
846
+ Cf-Ray:
847
+ - 81182f64ba3fd0c5-AMS
848
+ Alt-Svc:
849
+ - h3=":443"; ma=86400
850
+ body:
851
+ encoding: UTF-8
852
+ string: |-
853
+ [
854
+ {
855
+ "DOI": "10.1186",
856
+ "RA": "Crossref"
857
+ }
858
+ ]
859
+ recorded_at: Thu, 05 Oct 2023 19:48:57 GMT
860
+ recorded_with: VCR 6.2.0