commonmeta-ruby 3.3.2 → 3.3.4
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- checksums.yaml +4 -4
- data/Gemfile.lock +3 -1
- data/bin/commonmeta +1 -1
- data/commonmeta.gemspec +1 -0
- data/lib/commonmeta/cli.rb +10 -0
- data/lib/commonmeta/readers/json_feed_reader.rb +1 -1
- data/lib/commonmeta/utils.rb +55 -1
- data/lib/commonmeta/version.rb +1 -1
- data/lib/commonmeta.rb +1 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/crossref.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/datacite.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/jalc.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/kisti.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/medra.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/not_found.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/op.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite_doi_http.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/cff-converter-python.yml +9 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff.yml +16 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +14 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/maremma.yml +10 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/metadata_reports.yml +9 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +74 -74
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +73 -73
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +70 -70
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/JaLC.yml +159 -159
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/KISTI.yml +128 -128
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/OP.yml +72 -72
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/affiliation_is_space.yml +73 -73
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book.yml +109 -109
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book_chapter.yml +71 -71
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/article_id_as_page_number.yml +74 -74
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/author_literal.yml +82 -82
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book.yml +71 -71
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter.yml +72 -72
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +70 -70
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_oup.yml +69 -69
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/component.yml +91 -91
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset.yml +101 -102
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset_usda.yml +133 -133
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/date_in_future.yml +78 -78
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dissertation.yml +100 -100
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/empty_given_name.yml +72 -72
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/invalid_date.yml +73 -73
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article.yml +72 -72
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +70 -70
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with.yml +76 -514
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +70 -70
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_funding.yml +73 -73
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_issue.yml +69 -69
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/mEDRA.yml +69 -69
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/markup.yml +78 -78
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/missing_creator.yml +73 -73
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_issn.yml +72 -72
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles.yml +71 -70
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +716 -716
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/not_found_error.yml +63 -63
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/peer_review.yml +74 -74
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content.yml +71 -71
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content_copernicus.yml +73 -73
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/report_osti.yml +117 -117
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/vor_with_url.yml +75 -75
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book.yml +69 -69
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book_chapter.yml +70 -70
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_raw/journal_article.yml +10 -10
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/dissertation.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/funding_references.yml +11 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/subject_scheme.yml +20 -20
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_id.yml +6 -419
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_uuid.yml +7 -260
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_uuid_specific_prefix.yml +3 -136
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +225 -1432
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +1380 -2112
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +6 -172
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +8 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_organizational_author.yml +3 -3
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +8 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +8 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +90 -176
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +25 -25
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +61 -61
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +8 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +20 -20
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_familyName.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_name_in_display-order_with_ORCID.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/name_with_affiliation_crossref.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/only_familyName_and_givenName.yml +43 -36
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting.yml +158 -158
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml +162 -162
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/get_schema_org_metadata_front_matter/BlogPosting.yml +178 -180
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/harvard_dataverse.yml +226 -230
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/pangaea.yml +43 -36
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/upstream_blog.yml +94 -94
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/zenodo.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/unknown_DOI_prefix.yml +5 -5
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_schema_errors/is_valid.yml +13 -13
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/BlogPosting.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/Dataset.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/authors_with_affiliations.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/climate_data.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/from_schema_org.yml +159 -159
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/keywords_subject_scheme.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/maremma.yml +12 -10
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/text.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_data_citation.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_pages.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/Collection_of_Jupyter_notebooks.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_Zenodo.yml +17 -17
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_also_Zenodo.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/ruby-cff.yml +16 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Dataset.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article_vancouver_style.yml +19 -19
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Missing_author.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/interactive_resource_without_dates.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml +27 -27
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_from_datacite.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +8 -54
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_organizational_author.yml +3 -3
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_upstream_blog.yml +10 -53
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +62 -62
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/posted_content.yml +15 -15
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_another_science_blog.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_front_matter.yml +29 -29
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/schema_org_from_upstream_blog.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/Another_dataset.yml +28 -28
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/BlogPosting.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/BlogPosting_schema_org.yml +158 -158
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/Dataset.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/container_title.yml +11 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/interactive_resource_without_dates.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/journal_article.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/keywords_subject_scheme.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/maremma.yml +9 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/missing_creator.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/multiple_abstracts.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/organization_author.yml +19 -19
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/software.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/software_w/version.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/with_only_first_page.yml +13 -13
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csl/with_pages.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/climate_data.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/maremma.yml +10 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/text.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/with_data_citation.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_csv/with_pages.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/dissertation.yml +17 -17
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/from_schema_org.yml +158 -158
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/journal_article.yml +18 -18
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/maremma.yml +10 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/with_ORCID_ID.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_datacite/with_data_citation.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/Dataset_in_schema_4_0.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/Text_pass-thru.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/book_chapter.yml +15 -13
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/from_schema_org.yml +158 -158
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/interactive_resource_without_dates.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/maremma.yml +12 -10
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_ORCID_ID.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_data_citation.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_jats_xml/with_editor.yml +13 -13
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/BlogPosting.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/BlogPosting_schema_org.yml +159 -159
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/Dataset.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/alternate_name.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/journal_article.yml +8 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/keywords_with_subject_scheme.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/maremma.yml +9 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_ris/with_pages.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Another_Schema_org_JSON.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Funding.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Funding_OpenAIRE.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Schema_org_JSON.yml +17 -17
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/Schema_org_JSON_Cyark.yml +33 -33
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/alternate_identifiers.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/data_catalog.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/geo_location_box.yml +12 -12
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/interactive_resource_without_dates.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/journal_article.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/maremma_schema_org_JSON.yml +10 -8
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/series_information.yml +9 -9
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/subject_scheme.yml +11 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_schema_org/subject_scheme_multiple_keywords.yml +11 -11
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/BlogPosting.yml +4 -4
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/Dataset.yml +6 -6
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/journal_article.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_turtle/with_pages.yml +12 -12
- data/spec/readers/cff_reader_spec.rb +6 -6
- data/spec/readers/crossref_reader_spec.rb +3 -3
- data/spec/readers/crossref_xml_reader_spec.rb +7 -7
- data/spec/readers/json_feed_reader_spec.rb +13 -13
- data/spec/readers/schema_org_reader_spec.rb +2 -3
- data/spec/spec_helper.rb +1 -0
- data/spec/utils_spec.rb +1 -1
- data/spec/writers/cff_writer_spec.rb +3 -3
- data/spec/writers/ris_writer_spec.rb +2 -2
- data/spec/writers/schema_org_writer_spec.rb +1 -1
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- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/default.yml +0 -110
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_bibtex.yml +0 -110
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_crossref_xml.yml +0 -110
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_datacite.yml +0 -110
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref/to_schema_org.yml +0 -110
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/default.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_bibtex.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_crossref_xml.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_datacite.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_file/crossref_xml/to_schema_org.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/default.yml +0 -299
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_bibtex.yml +0 -299
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_citation.yml +0 -299
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- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/crossref/to_jats.yml +0 -299
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- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/default.yml +0 -172
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_bibtex.yml +0 -172
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_citation.yml +0 -172
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_datacite.yml +0 -172
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/datacite/to_jats.yml +0 -172
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- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/to_datacite.yml +0 -1098
- data/spec/fixtures/vcr_cassettes/Briard_CLI/convert_from_id/schema_org/to_schema_org.yml +0 -1100
- data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/crossref.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/datacite.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/jalc.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/kisti.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/medra.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_CLI/find_from_format_by_id/op.yml +0 -55
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- data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/no_author.yml +0 -164
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/single_author.yml +0 -164
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/authors_as_string/with_organization.yml +0 -164
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +0 -247
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/crossref.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/datacite.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/jalc.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/kisti.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/medra.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/not_found.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/doi_registration_agency/op.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/crossref.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/datacite.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/datacite_doi_http.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_for_match.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_for_with_schemeUri_in_hash.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_match.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/hsh_to_fos_no_match.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/name_to_fos_for_match.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/name_to_fos_match.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/fos/name_to_fos_no_match.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/from_schema_org/with_id.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/from_schema_org_creators/with_affiliation.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/from_schema_org_creators/without_affiliation.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_cff_metadata/cff-converter-python.yml +0 -200
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_cff_metadata/ruby-cff.yml +0 -154
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +0 -154
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_codemeta_metadata/maremma.yml +0 -86
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_codemeta_metadata/metadata_reports.yml +0 -93
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +0 -337
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +0 -347
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +0 -359
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/JaLC.yml +0 -384
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/KISTI.yml +0 -330
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/OP.yml +0 -969
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/affiliation_is_space.yml +0 -358
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/another_book.yml +0 -312
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/another_book_chapter.yml +0 -465
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/article_id_as_page_number.yml +0 -276
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/author_literal.yml +0 -492
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book.yml +0 -523
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book_chapter.yml +0 -377
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +0 -336
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/book_oup.yml +0 -289
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/component.yml +0 -289
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/dataset.yml +0 -299
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/dataset_usda.yml +0 -341
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/date_in_future.yml +0 -570
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/dissertation.yml +0 -301
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/empty_given_name.yml +0 -303
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/invalid_date.yml +0 -307
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article.yml +0 -461
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +0 -276
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_with.yml +0 -470
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +0 -519
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_article_with_funding.yml +0 -456
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/journal_issue.yml +0 -270
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/mEDRA.yml +0 -310
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/markup.yml +0 -329
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/missing_creator.yml +0 -307
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/multiple_issn.yml +0 -393
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/multiple_titles.yml +0 -265
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +0 -860
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/not_found_error.yml +0 -209
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/peer_review.yml +0 -287
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/posted_content.yml +0 -326
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/posted_content_copernicus.yml +0 -297
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/report_osti.yml +0 -315
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/vor_with_url.yml +0 -451
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/yet_another_book.yml +0 -816
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_metadata/yet_another_book_chapter.yml +0 -324
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_crossref_raw/journal_article.yml +0 -110
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_datacite_metadata/dissertation.yml +0 -152
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_datacite_metadata/funding_references.yml +0 -175
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_datacite_metadata/subject_scheme.yml +0 -328
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date/publication_date.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_from_date_parts/date.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_from_date_parts/year-month.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_from_date_parts/year.yml +0 -221
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- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_from_parts/year-month.yml +0 -221
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- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_parts/date.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_parts/year-month.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_date_parts/year.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_datetime_from_time/future.yml +0 -221
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- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_datetime_from_time/present.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_one_author/has_familyName.yml +0 -133
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_one_author/has_name_in_display-order_with_ORCID.yml +0 -153
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_one_author/is_organization.yml +0 -164
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_one_author/name_with_affiliation_crossref.yml +0 -247
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_one_author/only_familyName_and_givenName.yml +0 -468
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/BlogPosting.yml +0 -530
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml +0 -530
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/get_schema_org_metadata_front_matter/BlogPosting.yml +0 -534
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/harvard_dataverse.yml +0 -1838
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/pangaea.yml +0 -468
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/upstream_blog.yml +0 -885
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_schema_org_metadata/zenodo.yml +0 -583
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_series_information/only_title.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_series_information/title_and_pages.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_series_information/title_volume_and_pages.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/get_series_information/title_volume_issue_and_pages.yml +0 -221
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/github/github_as_cff_url.yml +0 -221
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- data/spec/fixtures/vcr_cassettes/Briard_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/handle_input/unknown_DOI_prefix.yml +0 -55
- data/spec/fixtures/vcr_cassettes/Briard_Metadata/is_personal_name_/has_comma.yml +0 -164
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evaluation of the quality of genomic or proteomic data and computational methods
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methods for evaluating genomic data and computational approaches will determine
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how much we, as a community, are able to learn from the wealth of available
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data. We propose one possible solution to this problem here but emphasize
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xml:lang=\"en\">\r\n <jats:title>Abstract</jats:title>\r\n
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\ <jats:sec>\r\n <jats:title>Background</jats:title>\r\n
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\ <jats:p>Accurate evaluation of the quality of genomic
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or proteomic data and computational methods is vital to our ability to use
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them for formulating novel biological hypotheses and directing further experiments.
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There is currently no standard approach to evaluation in functional genomics.
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Our analysis of existing approaches shows that they are inconsistent and contain
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substantial functional biases that render the resulting evaluations misleading
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both quantitatively and qualitatively. These problems make it essentially
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impossible to compare computational methods or large-scale experimental datasets
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and also result in conclusions that generalize poorly in most biological applications.</jats:p>\r\n
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here and suggest new approaches to evaluation that facilitate accurate and
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representative characterization of genomic methods and data. Specifically,
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we describe a functional genomics gold standard based on curation by expert
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biologists and demonstrate its use as an effective means of evaluation of
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genomic approaches. Our evaluation framework and gold standard are freely
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\ <jats:sec>\r\n <jats:title>Conclusion</jats:title>\r\n
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\ <jats:p>Proper methods for evaluating genomic data and
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computational approaches will determine how much we, as a community, are able
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to learn from the wealth of available data. We propose one possible solution
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to this problem here but emphasize that this topic warrants broader community
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