commonmeta-ruby 3.0.0

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Files changed (791) hide show
  1. checksums.yaml +7 -0
  2. data/.github/workflows/build.yml +38 -0
  3. data/.github/workflows/changelog.yml +36 -0
  4. data/.github/workflows/codeql-analysis.yml +72 -0
  5. data/.github/workflows/rubocop.yml +50 -0
  6. data/.gitignore +59 -0
  7. data/.rubocop.yml +182 -0
  8. data/.rubocop_todo.yml +76 -0
  9. data/.tool-versions +1 -0
  10. data/CHANGELOG.md +124 -0
  11. data/CITATION +16 -0
  12. data/CITATION.cff +20 -0
  13. data/Gemfile +5 -0
  14. data/Gemfile.lock +270 -0
  15. data/LICENSE.md +21 -0
  16. data/README.md +733 -0
  17. data/Rakefile +13 -0
  18. data/bin/commonmeta +9 -0
  19. data/commonmeta.gemspec +68 -0
  20. data/lib/commonmeta/array.rb +13 -0
  21. data/lib/commonmeta/author_utils.rb +172 -0
  22. data/lib/commonmeta/cli.rb +70 -0
  23. data/lib/commonmeta/crossref_utils.rb +343 -0
  24. data/lib/commonmeta/doi_utils.rb +81 -0
  25. data/lib/commonmeta/metadata.rb +269 -0
  26. data/lib/commonmeta/metadata_utils.rb +184 -0
  27. data/lib/commonmeta/pubmed.rb +36 -0
  28. data/lib/commonmeta/readers/bibtex_reader.rb +62 -0
  29. data/lib/commonmeta/readers/cff_reader.rb +146 -0
  30. data/lib/commonmeta/readers/codemeta_reader.rb +90 -0
  31. data/lib/commonmeta/readers/crossref_reader.rb +186 -0
  32. data/lib/commonmeta/readers/crossref_xml_reader.rb +379 -0
  33. data/lib/commonmeta/readers/csl_reader.rb +85 -0
  34. data/lib/commonmeta/readers/datacite_reader.rb +169 -0
  35. data/lib/commonmeta/readers/npm_reader.rb +94 -0
  36. data/lib/commonmeta/readers/ris_reader.rb +66 -0
  37. data/lib/commonmeta/readers/schema_org_reader.rb +300 -0
  38. data/lib/commonmeta/schema_utils.rb +19 -0
  39. data/lib/commonmeta/string.rb +7 -0
  40. data/lib/commonmeta/utils.rb +1351 -0
  41. data/lib/commonmeta/version.rb +5 -0
  42. data/lib/commonmeta/whitelist_scrubber.rb +54 -0
  43. data/lib/commonmeta/writers/bibtex_writer.rb +36 -0
  44. data/lib/commonmeta/writers/cff_writer.rb +63 -0
  45. data/lib/commonmeta/writers/citation_writer.rb +14 -0
  46. data/lib/commonmeta/writers/codemeta_writer.rb +33 -0
  47. data/lib/commonmeta/writers/crossref_xml_writer.rb +11 -0
  48. data/lib/commonmeta/writers/csl_writer.rb +11 -0
  49. data/lib/commonmeta/writers/csv_writer.rb +26 -0
  50. data/lib/commonmeta/writers/datacite_writer.rb +94 -0
  51. data/lib/commonmeta/writers/jats_writer.rb +138 -0
  52. data/lib/commonmeta/writers/rdf_xml_writer.rb +11 -0
  53. data/lib/commonmeta/writers/ris_writer.rb +41 -0
  54. data/lib/commonmeta/writers/schema_org_writer.rb +61 -0
  55. data/lib/commonmeta/writers/turtle_writer.rb +11 -0
  56. data/lib/commonmeta/xml_converter.rb +14 -0
  57. data/lib/commonmeta.rb +35 -0
  58. data/resources/2008/09/xsd.xsl +997 -0
  59. data/resources/cff.json +1827 -0
  60. data/resources/commonmeta_v0.9.json +393 -0
  61. data/resources/crossref/AccessIndicators.xsd +47 -0
  62. data/resources/crossref/JATS-journalpublishing1-3d2-mathml3-elements.xsd +10130 -0
  63. data/resources/crossref/JATS-journalpublishing1-3d2-mathml3.xsd +48 -0
  64. data/resources/crossref/JATS-journalpublishing1-elements.xsd +8705 -0
  65. data/resources/crossref/JATS-journalpublishing1-mathml3-elements.xsd +8608 -0
  66. data/resources/crossref/JATS-journalpublishing1-mathml3.xsd +49 -0
  67. data/resources/crossref/JATS-journalpublishing1.xsd +6176 -0
  68. data/resources/crossref/clinicaltrials.xsd +61 -0
  69. data/resources/crossref/common5.3.1.xsd +1530 -0
  70. data/resources/crossref/crossref5.3.1.xsd +1949 -0
  71. data/resources/crossref/crossref_query_output3.0.xsd +1097 -0
  72. data/resources/crossref/fundref.xsd +49 -0
  73. data/resources/crossref/module-ali.xsd +39 -0
  74. data/resources/crossref/relations.xsd +444 -0
  75. data/resources/datacite-contributorType-v4.xsd +35 -0
  76. data/resources/datacite-dateType-v4.xsd +25 -0
  77. data/resources/datacite-descriptionType-v4.xsd +19 -0
  78. data/resources/datacite-funderIdentifierType-v4.xsd +15 -0
  79. data/resources/datacite-nameType-v4.xsd +10 -0
  80. data/resources/datacite-relatedIdentifierType-v4.xsd +34 -0
  81. data/resources/datacite-relationType-v4.xsd +49 -0
  82. data/resources/datacite-resourceType-v4.xsd +28 -0
  83. data/resources/datacite-titleType-v4.xsd +14 -0
  84. data/resources/datacite-v3.json +508 -0
  85. data/resources/datacite-v4.json +512 -0
  86. data/resources/kernel-3.0/include/datacite-contributorType-v3.xsd +33 -0
  87. data/resources/kernel-3.0/include/datacite-dateType-v3.xsd +21 -0
  88. data/resources/kernel-3.0/include/datacite-descriptionType-v3.xsd +17 -0
  89. data/resources/kernel-3.0/include/datacite-relatedIdentifierType-v3.xsd +27 -0
  90. data/resources/kernel-3.0/include/datacite-relationType-v3.xsd +33 -0
  91. data/resources/kernel-3.0/include/datacite-resourceType-v3.xsd +26 -0
  92. data/resources/kernel-3.0/include/datacite-titleType-v3.xsd +12 -0
  93. data/resources/kernel-3.0/include/xml.xsd +286 -0
  94. data/resources/kernel-3.0/metadata.xsd +377 -0
  95. data/resources/kernel-4/include/datacite-contributorType-v4.xsd +35 -0
  96. data/resources/kernel-4/include/datacite-dateType-v4.xsd +25 -0
  97. data/resources/kernel-4/include/datacite-descriptionType-v4.xsd +19 -0
  98. data/resources/kernel-4/include/datacite-funderIdentifierType-v4.xsd +16 -0
  99. data/resources/kernel-4/include/datacite-nameType-v4.xsd +10 -0
  100. data/resources/kernel-4/include/datacite-numberType-v4.xsd +12 -0
  101. data/resources/kernel-4/include/datacite-relatedIdentifierType-v4.xsd +34 -0
  102. data/resources/kernel-4/include/datacite-relationType-v4.xsd +51 -0
  103. data/resources/kernel-4/include/datacite-resourceType-v4.xsd +43 -0
  104. data/resources/kernel-4/include/datacite-titleType-v4.xsd +14 -0
  105. data/resources/kernel-4/include/xml.xsd +286 -0
  106. data/resources/kernel-4/metadata.xsd +707 -0
  107. data/resources/oecd/dfg-mappings.json +1866 -0
  108. data/resources/oecd/for-mappings.json +1099 -0
  109. data/resources/oecd/fos-mappings.json +198 -0
  110. data/resources/schema_org/jsonldcontext.json +7477 -0
  111. data/resources/spdx/licenses.json +5297 -0
  112. data/resources/xml.xsd +286 -0
  113. data/rubocop.sarif +0 -0
  114. data/sonar-project.properties +11 -0
  115. data/spec/array_spec.rb +22 -0
  116. data/spec/author_utils_spec.rb +132 -0
  117. data/spec/cli_spec.rb +309 -0
  118. data/spec/doi_utils_spec.rb +318 -0
  119. data/spec/find_from_format_spec.rb +144 -0
  120. data/spec/fixtures/CITATION.cff +83 -0
  121. data/spec/fixtures/aida.json +82 -0
  122. data/spec/fixtures/cgimp_package.json +18 -0
  123. data/spec/fixtures/cit_package.json +19 -0
  124. data/spec/fixtures/citeproc-no-author.json +26 -0
  125. data/spec/fixtures/citeproc-no-categories.json +21 -0
  126. data/spec/fixtures/citeproc.json +30 -0
  127. data/spec/fixtures/codemeta.json +86 -0
  128. data/spec/fixtures/codemeta_v2.json +86 -0
  129. data/spec/fixtures/crosscite.json +63 -0
  130. data/spec/fixtures/crossref.bib +14 -0
  131. data/spec/fixtures/crossref.json +572 -0
  132. data/spec/fixtures/crossref.ris +15 -0
  133. data/spec/fixtures/crossref.xml +606 -0
  134. data/spec/fixtures/datacite.json +86 -0
  135. data/spec/fixtures/datacite_software.json +21 -0
  136. data/spec/fixtures/datacite_software_missing_comma.json +18 -0
  137. data/spec/fixtures/datacite_software_overlapping_keys.json +18 -0
  138. data/spec/fixtures/datacite_software_version.json +74 -0
  139. data/spec/fixtures/edam_package.json +12 -0
  140. data/spec/fixtures/maremma/codemeta.json +36 -0
  141. data/spec/fixtures/pure.bib +14 -0
  142. data/spec/fixtures/pure.ris +15 -0
  143. data/spec/fixtures/pure.xml +188 -0
  144. data/spec/fixtures/ris_bug.ris +9 -0
  145. data/spec/fixtures/schema_4.0.xml +140 -0
  146. data/spec/fixtures/schema_org.json +49 -0
  147. data/spec/fixtures/schema_org_front-matter.json +32 -0
  148. data/spec/fixtures/schema_org_geolocation.json +82 -0
  149. data/spec/fixtures/schema_org_geoshape.json +550 -0
  150. data/spec/fixtures/schema_org_gtex.json +75 -0
  151. data/spec/fixtures/schema_org_list.json +12623 -0
  152. data/spec/fixtures/schema_org_tdl_iodp_invalid_authors.json +25 -0
  153. data/spec/fixtures/schema_org_topmed.json +53 -0
  154. data/spec/fixtures/schema_org_type_as_array.json +41 -0
  155. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/default.yml +110 -0
  156. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_bibtex.yml +110 -0
  157. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_crossref_xml.yml +110 -0
  158. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_datacite.yml +110 -0
  159. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_schema_org.yml +110 -0
  160. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/default.yml +55 -0
  161. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_bibtex.yml +55 -0
  162. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_crossref_xml.yml +55 -0
  163. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_datacite.yml +55 -0
  164. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_schema_org.yml +55 -0
  165. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/default.yml +299 -0
  166. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_bibtex.yml +299 -0
  167. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_citation.yml +299 -0
  168. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_crossref_xml.yml +299 -0
  169. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_datacite.yml +299 -0
  170. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_jats.yml +299 -0
  171. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_schema_org.yml +299 -0
  172. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/default.yml +172 -0
  173. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_bibtex.yml +172 -0
  174. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_citation.yml +172 -0
  175. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_datacite.yml +172 -0
  176. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_jats.yml +172 -0
  177. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_schema_org.yml +172 -0
  178. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/default.yml +1098 -0
  179. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/to_datacite.yml +1098 -0
  180. data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/to_schema_org.yml +1100 -0
  181. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/crossref.yml +55 -0
  182. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/datacite.yml +55 -0
  183. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/jalc.yml +55 -0
  184. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/kisti.yml +55 -0
  185. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/medra.yml +55 -0
  186. data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/op.yml +55 -0
  187. data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/author.yml +164 -0
  188. data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/no_author.yml +164 -0
  189. data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/single_author.yml +164 -0
  190. data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/with_organization.yml +164 -0
  191. data/spec/fixtures/vcr_cassettes/Briard_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +247 -0
  192. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/crossref.yml +55 -0
  193. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/datacite.yml +55 -0
  194. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/jalc.yml +55 -0
  195. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/kisti.yml +55 -0
  196. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/medra.yml +55 -0
  197. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/not_found.yml +55 -0
  198. data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/op.yml +55 -0
  199. data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/crossref.yml +55 -0
  200. data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +55 -0
  201. data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/datacite.yml +55 -0
  202. data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/datacite_doi_http.yml +55 -0
  203. data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +55 -0
  204. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_for_match.yml +221 -0
  205. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_for_with_schemeUri_in_hash.yml +221 -0
  206. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_match.yml +221 -0
  207. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_no_match.yml +221 -0
  208. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/name_to_fos_for_match.yml +221 -0
  209. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/name_to_fos_match.yml +221 -0
  210. data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/name_to_fos_no_match.yml +221 -0
  211. data/spec/fixtures/vcr_cassettes/Briard_Metadata/from_schema_org/with_id.yml +221 -0
  212. data/spec/fixtures/vcr_cassettes/Briard_Metadata/from_schema_org_creators/with_affiliation.yml +221 -0
  213. data/spec/fixtures/vcr_cassettes/Briard_Metadata/from_schema_org_creators/without_affiliation.yml +221 -0
  214. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_cff_metadata/cff-converter-python.yml +200 -0
  215. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_cff_metadata/ruby-cff.yml +154 -0
  216. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +154 -0
  217. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_codemeta_metadata/maremma.yml +86 -0
  218. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_codemeta_metadata/metadata_reports.yml +93 -0
  219. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +337 -0
  220. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +347 -0
  221. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +359 -0
  222. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/JaLC.yml +384 -0
  223. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/KISTI.yml +330 -0
  224. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/OP.yml +969 -0
  225. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/affiliation_is_space.yml +358 -0
  226. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/another_book.yml +312 -0
  227. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/another_book_chapter.yml +465 -0
  228. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/article_id_as_page_number.yml +276 -0
  229. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/author_literal.yml +492 -0
  230. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book.yml +523 -0
  231. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book_chapter.yml +377 -0
  232. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +336 -0
  233. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book_oup.yml +289 -0
  234. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/component.yml +289 -0
  235. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/dataset.yml +299 -0
  236. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/dataset_usda.yml +341 -0
  237. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/date_in_future.yml +570 -0
  238. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/dissertation.yml +301 -0
  239. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/empty_given_name.yml +303 -0
  240. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/invalid_date.yml +307 -0
  241. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article.yml +461 -0
  242. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +276 -0
  243. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_with.yml +470 -0
  244. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +519 -0
  245. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_with_funding.yml +456 -0
  246. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_issue.yml +270 -0
  247. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/mEDRA.yml +310 -0
  248. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/markup.yml +329 -0
  249. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/missing_creator.yml +307 -0
  250. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/multiple_issn.yml +393 -0
  251. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/multiple_titles.yml +265 -0
  252. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +860 -0
  253. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/not_found_error.yml +209 -0
  254. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/peer_review.yml +287 -0
  255. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/posted_content.yml +326 -0
  256. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/posted_content_copernicus.yml +297 -0
  257. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/report_osti.yml +315 -0
  258. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/vor_with_url.yml +451 -0
  259. data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/yet_another_book.yml +816 -0
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205
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206
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+ \ </div>\n </div>\n </header>\n\n \n<main class=\"gh-main\">\n
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+ \ <article class=\"gh-article post tag-interview\">\n\n <header
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+ class=\"gh-article-header gh-canvas\">\n <a class=\"gh-article-tag\"
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+ href=\"https://blog.front-matter.io/tag/interview/\">Interview</a>\n\n <h1
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+ class=\"gh-article-title\">Dryad: Interview with Jen Gibson</h1>\n\n <aside
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+ class=\"gh-article-sidebar\">\n\n <div class=\"gh-author-image-list\">\n
276
+ \ <a class=\"gh-author-image\" href=\"/author/martin/\">\n <img
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+ src=\"https://www.gravatar.com/avatar/8adea77ad740876f5cb832f92d49f08d?s&#x3D;250&amp;r&#x3D;x&amp;d&#x3D;mp\"
278
+ alt=\"Martin Fenner\">\n </a>\n </div>\n\n <div
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+ class=\"gh-author-name-list\">\n <h4 class=\"gh-author-name\">\n
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+ \ <a href=\"/author/martin/\">Martin Fenner</a>\n </h4>\n
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+ \ \n </div>\n\n <div class=\"gh-article-meta\">\n
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+ \ <div class=\"gh-article-meta-inner\">\n <time class=\"gh-article-date\"
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+ datetime=\"2021-11-15\">Nov 15, 2021</time>\n <span class=\"gh-article-meta-sep\"></span>\n
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+ \ <span class=\"gh-article-length\">4 min</span>\n </div>\n
285
+ \ <a class=\"gh-card-link\" href=\"https://doi.org/10.53731/rceh7pn-tzg61kj-7zv63\">https://doi.org/10.53731/rceh7pn-tzg61kj-7zv63</a>\n
286
+ \ </div>\n\n </aside>\n\n\n <figure class=\"gh-article-image\">\n
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+ \ <img\n srcset=\"/content/images/size/w300/2022/07/jgibson.png
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+ 300w,\n /content/images/size/w720/2022/07/jgibson.png 720w,\n
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+ \ /content/images/size/w960/2022/07/jgibson.png 960w,\n
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+ \ /content/images/size/w1200/2022/07/jgibson.png 1200w,\n
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+ \ /content/images/size/w2000/2022/07/jgibson.png 2000w\"\n
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+ \ sizes=\"(max-width: 1200px) 100vw, 1200px\"\n src=\"/content/images/size/w1200/2022/07/jgibson.png\"\n
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+ \ alt=\"Dryad: Interview with Jen Gibson\"\n >\n <figcaption>Jennifer
294
+ Gibson</figcaption>\n </figure>\n </header>\n\n <section
295
+ class=\"gh-content gh-canvas\">\n <p>In October Jen Gibson
296
+ started as the new Executive Director for the Dryad Data Repository. I used
297
+ the opportunity to ask Jen a few questions about Dryad, challenges with data
298
+ sharing, and ideas about moving Dryad forward. I was particularly interested
299
+ in the interview as I served on the Dryad Board of Directors from 2013 to
300
+ 2016. In fact, one post on this blog is about a presentation I gave in 2013
301
+ (<a href=\"https://doi.org/10.53731/r294649-6f79289-8cw1x\">Metrics and attribution:
302
+ my thoughts for the panel at the ORCID-Dryad symposium on research attribution</a>).</p><h3
303
+ id=\"1-can-you-describe-what-dryad-is\">1. Can you describe what Dryad is?</h3><p>Dryad
304
+ is an open data publishing platform and community committed to the open availability
305
+ and routine re-use of all research data. We’re a generalist, curated data
306
+ repository – working with researchers across disciplines to assemble details
307
+ about their work and their data to increase its discoverability and use by
308
+ others. We’re a non-profit initiative working in partnership with other systems
309
+ and communities working to advance open research.</p><h3 id=\"2-are-there-data-that-should-not-be-submitted-to-dryad\">2.
310
+ Are there data that should not be submitted to Dryad?</h3><p>Dryad is designed
311
+ to support openly accessible and fully re-usable data, and publishes under
312
+ a Creative Commons Public Domain License (CC0). So, we’re not able to publish
313
+ data with incompatible licensing terms. We also don’t accept datasets that
314
+ contain personally identifiable human subject information or specific locations
315
+ for endangered species – but our team of curators will work with researchers
316
+ to see if the data can be made appropriate for sharing. </p><h3 id=\"3-are-there-limits-in-the-number-or-size-of-files-in-a-data-submission\">3.
317
+ Are there limits in the number or size of files in a data submission?</h3><p>We
318
+ can accept up to 300GB per dataset and thousands of files, but curators are
319
+ looking for the most accessible file types and downloads to support re-use.
320
+ So, we ask that files be small and zipped when possible. Users with files
321
+ larger than 300GB are asked simply to contact us to coordinate. </p><h3 id=\"4-does-dryad-also-accept-software-submissions\">4.
322
+ Does Dryad also accept software submissions?</h3><p>No, Dryad only publishes
323
+ data. So, we’ve partnered with <a href=\"https://zenodo.org\">Zenodo</a> so
324
+ that users can load software and other supplementary information at the same
325
+ time that they load data to Dryad. Software can then be made available under
326
+ a different, more appropriate license and be given its own citation, but is
327
+ also linked from the data publication at Dryad.</p><h3 id=\"5-does-a-data-submission-to-dryad-cost-money\">5.
328
+ Does a data submission to Dryad cost money?</h3><p>Yes. Often the cost to
329
+ researchers is covered or discounted through an arrangement with their institution,
330
+ publisher, or funder. Where there is not yet an arrangement in place, the
331
+ submitting researcher is asked to pay $120 – with overage fees if the data
332
+ is larger than 300GB. Waivers are, of course, available. Publication fees,
333
+ memberships, and partnerships with institutions, publishers and funders help
334
+ cover our costs for data curation and long-term preservation.</p><h3 id=\"6-what-are-the-main-challenges-for-authors\">6.
335
+ What are the main challenges for authors?</h3><p>There are so many challenges
336
+ for researchers with respect to open sharing of data – and they’re different
337
+ in every discipline. There are behaviour changes, and workflow changes and
338
+ culture changes to overcome – although several disciplines have carved a path,
339
+ including astronomy and ecology. I hope that the open data-sharing around
340
+ COVID will help inspire more people to follow suit.</p><p>Dryad helps to overcome
341
+ these challenges, of course. We help first of all by helping to make it <em>possible</em>
342
+ to share data properly – openly, with a CC0 license, and second by making
343
+ it <em>easy</em> to share data through our friendly user interface and our
344
+ integrations with publishers and partners such as Zenodo. (With the terms
345
+ ‘possible, easy, rewarding and normative,’ I’m invoking Brian Nosek’s <a href=\"https://www.cos.io/blog/strategy-for-culture-change\">Strategy
346
+ for Culture Change</a>).</p><p>We’re helping to make data sharing <em>rewarding</em>
347
+ by standardising usage metrics (through <a href=\"https://makedatacount.org/\">Make
348
+ Data Count</a> – an important, community-led initiative to develop metrics
349
+ for open research data assessment) and encouraging citation, though these
350
+ are just a couple of the pieces needed to put data and data sharing at the
351
+ centre of research assessment.</p><p>Finally, what I’m very much looking forward
352
+ to doing with Dryad is supporting and building communities that share and
353
+ re-use data to make this practice <em>normative</em>. Connecting people with
354
+ people – and people with data – is key in nurturing and normalising the regular
355
+ exchange and re-use of data. </p><h3 id=\"7-why-should-authors-submit-their-data-to-dryad\">7.
356
+ Why should authors submit their data to Dryad?</h3><p>Authors whose communities
357
+ don’t already rely on a domain repository for data, such as WormBase or the
358
+ Protein Data Bank, should publish their data with Dryad because:</p><ul><li>Our
359
+ curation service increases the quality and discoverability of new data, by
360
+ ensuring key descriptive information (metadata) is available alongside the
361
+ data itself</li><li>Our curation service increases the integrity of new data,
362
+ by ensuring it’s readable and usable by other users</li><li>We put data in
363
+ context, with links to publications, software, institutions, funders and more</li><li>Data
364
+ published in Dryad is citable and accessible via a persistent DOI</li><li>As
365
+ a non-profit and open-source initiative, our values are closely aligned with
366
+ the research community</li><li>It’s easy, and affordable </li></ul><h3 id=\"8-how-can-authors-give-feedback-eg-to-report-problems-or-request-features\">8.
367
+ How can authors give feedback, e.g. to report problems or request features?</h3><p>We
368
+ are an open source project and our work is driven by researchers' needs. Get
369
+ in touch with the help desk to discuss feature needs with our product team
370
+ or leave a ticket on our public <a href=\"https://github.com/CDL-Dryad/dryad-product-roadmap/projects/1\">Github
371
+ product board</a>.</p><h3 id=\"9-what-did-you-do-before-starting-to-work-for-dryad\">9.
372
+ What did you do before starting to work for Dryad?</h3><p>I’ve worked in open
373
+ research since 2005, when I joined <a href=\"https://sparcopen.org/\">SPARC</a>
374
+ – the Scholarly Publishing and Academic Resources Coalition – to work on open-access
375
+ advocacy and policy efforts. Immediately before Dryad I was a founding member
376
+ of the team for eLife – the open-access journal for biology and medicine and
377
+ initiative from three of the largest, most prestigious, private biomedical
378
+ research funders to put science publishing back in the hands of science. I’d
379
+ say my main contributions so far have been in building communities (among
380
+ librarians, open science advocates, students, early-career or late-stage researchers,
381
+ and others), advocacy (for open research practice at different levels of practice
382
+ and policy), and adoption strategies (for researchers in particular). </p><h3
383
+ id=\"10-do-you-want-to-talk-about-future-plans-for-dryad\">10. Do you want
384
+ to talk about future plans for Dryad?</h3><p>Absolutely. Beyond my near-term
385
+ objectives for optimising operations, I expect us to be:</p><ul><li>Leveraging
386
+ support from institutions and expanding our membership program.</li><li>Working
387
+ with our publisher partners to attract as much data as possible.</li><li>More
388
+ actively diversifying our profile – specifically reaching out to different
389
+ geographic and disciplinary communities.</li><li>Expanding our roadmap for
390
+ modeling data publishing into the future, building on our progress over the
391
+ last couple of years.</li></ul><p>Longer term, I’m enthusiastic about the
392
+ potential for pushing data to the forefront of discovery, and taking steps
393
+ to facilitate re-use and extend credit. Like Make Data Count, Dryad is committed
394
+ to making data a first-class citizen in research and research assessment,
395
+ and I'll be really pleased if we’re able to help properly reward researchers
396
+ for their data publications. We’re going to need to, to really accelerate
397
+ discovery and build that open, global network for the exchange of research
398
+ objects.</p>\n <div class=\"gh-license\">\n Copyright
399
+ © 2021 Martin Fenner. Distributed under the terms of the\n <a\n
400
+ \ class=\"gh-license-link\"\n href=\"https://creativecommons.org/licenses/by/4.0/legalcode\"\n
401
+ \ >\n Creative Commons
402
+ Attribution 4.0 License.\n </a>\n </div>\n
403
+ \ </section> \n </section>\n\n </article>\n\n
404
+ \ <div class=\"gh-read-next gh-canvas\">\n <section
405
+ class=\"gh-pagehead\">\n <h4 class=\"gh-pagehead-title\">Read
406
+ next</h4>\n </section>\n\n <div class=\"gh-topic
407
+ gh-topic-grid\">\n <div class=\"gh-topic-content\">\n <article
408
+ class=\"gh-card post\">\n <a class=\"gh-card-link\" href=\"/posts/conference-blogging-interview-with-alex-knoll/\">\n
409
+ \ <figure class=\"gh-card-image\">\n <img\n srcset=\"/content/images/size/w300/2022/08/knoll.jpeg
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+ 300w,\n /content/images/size/w720/2022/08/knoll.jpeg
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+ 720w,\n /content/images/size/w960/2022/08/knoll.jpeg
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+ 960w,\n /content/images/size/w1200/2022/08/knoll.jpeg
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+ 1200w,\n /content/images/size/w2000/2022/08/knoll.jpeg
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+ 2000w\"\n sizes=\"(max-width: 1200px) 100vw, 1200px\"\n
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+ \ src=\"/content/images/size/w720/2022/08/knoll.jpeg\"\n
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+ \ alt=\"Conference Blogging: Interview with Alex Knoll\"\n
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+ \ >\n </figure>\n\n <div class=\"gh-card-wrapper\">\n
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+ \ <header class=\"gh-card-header\">\n <h3 class=\"gh-card-title\">Conference
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+ Blogging: Interview with Alex Knoll</h3>\n </header>\n\n <div
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+ class=\"gh-card-excerpt\">Blogging is a great way to report from a scientific
421
+ conference. This could be done either with regular blog posts written in the
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+ evening or after the conference, and/or live-blogging using tools such as
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+ Friendfeed or Twitter. One or more blogging scientists can not only add a
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+ unique perspective</div>\n\n <footer class=\"gh-card-footer\">\n
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+ \ <span class=\"gh-card-author\">Martin Fenner</span>\n <time
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+ class=\"gh-card-date\" datetime=\"2009-10-01\">Oct 1, 2009</time>\n <script\n
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+ \ data-ghost-comment-count-autowrap=\"true\"\n>\n</script>\n </footer>\n
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+ \ </div>\n </a>\n</article> <article class=\"gh-card
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+ post\">\n <a class=\"gh-card-link\" href=\"/posts/plos-article-level-metrics-interview-with-martin-fenner/\">\n
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+ \ <figure class=\"gh-card-image\">\n <img\n srcset=\"/content/images/size/w300/2022/08/429781913_9524791cff_c-1.jpg
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+ 300w,\n /content/images/size/w720/2022/08/429781913_9524791cff_c-1.jpg
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+ 720w,\n /content/images/size/w960/2022/08/429781913_9524791cff_c-1.jpg
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+ 960w,\n /content/images/size/w1200/2022/08/429781913_9524791cff_c-1.jpg
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+ 1200w,\n /content/images/size/w2000/2022/08/429781913_9524791cff_c-1.jpg
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+ 2000w\"\n sizes=\"(max-width: 1200px) 100vw, 1200px\"\n
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+ \ src=\"/content/images/size/w720/2022/08/429781913_9524791cff_c-1.jpg\"\n
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+ \ alt=\"PLoS Article-Level Metrics: Interview with Martin
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+ Fenner\"\n >\n </figure>\n\n <div class=\"gh-card-wrapper\">\n
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+ \ <header class=\"gh-card-header\">\n <h3 class=\"gh-card-title\">PLoS
443
+ Article-Level Metrics: Interview with Martin Fenner</h3>\n </header>\n\n
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+ \ <div class=\"gh-card-excerpt\">This blog occasionally
445
+ does interviews with people providing interesting tools for scholars. These
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+ interviews have always been among my favorite blog posts. This now is obviously
447
+ an interview with myself, but I felt this is the best format to explain some
448
+ important news.\n\nStarting May 16 I will be working</div>\n\n <footer
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+ class=\"gh-card-footer\">\n <span class=\"gh-card-author\">Martin
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+ Fenner</span>\n <time class=\"gh-card-date\" datetime=\"2012-04-23\">Apr
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+ 23, 2012</time>\n <script\n data-ghost-comment-count=\"62d42bbd41e317003df48dad\"\n
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+ \ data-ghost-comment-count-class-name=\"gh-card-comments\"\n data-ghost-comment-count-autowrap=\"true\"\n>\n</script>\n
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+ \ </footer>\n </div>\n </a>\n</article> <article
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+ class=\"gh-card post\">\n <a class=\"gh-card-link\" href=\"/posts/figshare-interview-with-mark-hahnel/\">\n
457
+ \ <figure class=\"gh-card-image\">\n <img\n srcset=\"/content/images/size/w300/2022/08/me1.png
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+ 300w,\n /content/images/size/w720/2022/08/me1.png
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+ 720w,\n /content/images/size/w960/2022/08/me1.png
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+ 2000w\"\n sizes=\"(max-width: 1200px) 100vw, 1200px\"\n
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+ \ src=\"/content/images/size/w720/2022/08/me1.png\"\n alt=\"Figshare:
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+ Interview with Mark Hahnel\"\n >\n </figure>\n\n
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+ \ <div class=\"gh-card-wrapper\">\n <header class=\"gh-card-header\">\n
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+ \ <h3 class=\"gh-card-title\">Figshare: Interview with Mark
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+ Hahnel</h3>\n </header>\n\n <div class=\"gh-card-excerpt\">figshare
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+ allows researchers to publish all of their research outputs in seconds in
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+ an easily citable, sharable and discoverable manner. The service was started
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+ by Mark Hahnel last year while still a PhD student. Mark joined Digital Science
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+ to work on figshare in September and last month relaunched a much</div>\n\n
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+ \ <footer class=\"gh-card-footer\">\n <span class=\"gh-card-author\">Martin
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+ Fenner</span>\n <time class=\"gh-card-date\" datetime=\"2012-02-16\">Feb
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+ 16, 2012</time>\n <script\n data-ghost-comment-count=\"62d42bbd41e317003df48db3\"\n
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+ \ data-ghost-comment-count-class-name=\"\"\n data-ghost-comment-count-autowrap=\"true\"\n>\n</script>)</h3>\n
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