{"id":10972,"date":"2013-07-31T10:51:29","date_gmt":"2013-07-31T09:51:29","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10972"},"modified":"2013-07-31T14:39:58","modified_gmt":"2013-07-31T13:39:58","slug":"the-amsterdam-manifesto-on-data-citation-principles","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10972","title":{"rendered":"The Amsterdam Manifesto on Data Citation Principles"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"10972\">\n<p>The <a href=\"http:\/\/www.force11.org\/AmsterdamManifesto\" target=\"_blank\">Amsterdam manifesto<\/a>\u00a0espouses the principles of citable open data. It is a short document, and it is worth re-stating its eight points here:<\/p>\n<ol>\n<li><em>Data should be considered citable products of research.<\/em><\/li>\n<li><em>Such data should be held in persistent public repositories.<\/em><\/li>\n<li><em>If a publication is based on data not included with the article, those data should be cited in the publication.<\/em><\/li>\n<li><em>A data citation in a publication should resemble a bibliographic citation and be located in the publication\u2019s reference list.<\/em><\/li>\n<li><em>Such a data citation should include a unique persistent identifier (a DataCite DOI recommended, or other persistent identifiers already in use within the community).<\/em><\/li>\n<li><em>The identifier should resolve to a page that either provides direct access to the data or information concerning its accessibility. Ideally, that landing page should be machine-actionable to promote interoperability of the data.<\/em><\/li>\n<li><em>If the data are available in different versions, the identifier should provide a method to access the previous or related versions.<\/em><\/li>\n<li><em>Data citation should facilitate\u00a0attribution of credit to all contributors.<\/em><\/li>\n<\/ol>\n<p>The manifesto itself is dated\u00a0\u00a020 March 2013, but the principles above go back far earlier, and most of the articles above have been implemented in this blog for a little while now. But its best illustrated with an example<span id=\"cite_ITEM-10972-0\" name=\"citation\"><a href=\"#ITEM-10972-0\">[1]<\/a><\/span>. Here I have used the excellent wordpress extension <a title=\"The blog post as a scientific article: citation management\" href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=6341\" target=\"_blank\">Kcite<\/a>\u00a0to adhere to<strong> points 1-5 and 8<\/strong> above. <strong>Point 6<\/strong> is the most interesting perhaps, and it is illustrated below. If you click on the graphic, it will load the log file associated with the calculation described in the<a title=\"VSEPR Theory: A closer look at chlorine trifluoride, ClF3.\" href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10937\" target=\"_blank\"> previous post<\/a> to convert the data to a rotatable 3D model, using Jmol.<\/p>\n<div id=\"attachment_10948\" style=\"width: 332px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-10948\" class=\" wp-image-10948 \" onclick=\"jmolInitialize('..\/Jmol\/',true);jmolSetAppletColor('white');jmolApplet([450,450],'load http:\/\/files.figshare.com\/1134372\/logfile.log;frame 27;vectors on;vectors 4;vectors scale 5.0; color vectors orange; vibration 10;animation mode loop;');\" alt=\"Click for  3D\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/ClF3.jpg\" width=\"322\" height=\"245\" \/><p id=\"caption-attachment-10948\" class=\"wp-caption-text\">Click to load from Figshare<\/p><\/div>\n<p>This actually represents a departure from how I normally invoke data on this blog. I have hitherto done it by uploading the data to the WordPress uploads directory (it is thus in effect a local copy of the data). Here in this post I have not done that; it&#8217;s coming directly from the citable data repository, using <em>e.g.<\/em><\/p>\n<p style=\"font-size: xx-small;\"><code>onclick=\"jmolInitialize('..\/Jmol\/',true);jmolSetAppletColor('white');jmolApplet([450,450],'load http:\/\/files.figshare.com\/1134372\/logfile.log;frame 27;vectors on;vectors 4;vectors scale 5.0; color vectors orange; vibration 10;animation mode loop;');\"<\/code><\/p>\n<p>Well, almost. The URL of the actual dataset (<code>http:\/\/files.figshare.com\/1134372\/logfile.log<\/code>) is derived from the doi (10.6084\/m9.figshare.757728) by an internal process which has no exposed algorithm. As it happens, the DSpace digital repository<span id=\"cite_ITEM-10972-1\" name=\"citation\"><a href=\"#ITEM-10972-1\">[2]<\/a><\/span> is a bit better in this regard.<\/p>\n<div id=\"attachment_10948\" style=\"width: 332px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-10948\" class=\" wp-image-10948 \" onclick=\"jmolInitialize('..\/Jmol\/',true);jmolSetAppletColor('white');jmolApplet([450,450],'load https:\/\/spectradspace.lib.imperial.ac.uk:8443\/dspace\/bitstream\/handle\/10042\/24916\/logfile.log;frame 27;vectors on;vectors 4;vectors scale 5.0; color vectors orange; vibration 10;animation mode loop;');\" alt=\"Click for  3D\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/ClF3.jpg\" width=\"322\" height=\"245\" \/><p id=\"caption-attachment-10948\" class=\"wp-caption-text\">Click to load from DSpace<\/p><\/div>\n<p>This is loaded using<\/p>\n<p style=\"font-size: xx-small;\"><code> https:\/\/spectradspace.lib.imperial.ac.uk:8443\/dspace\/bitstream\/handle\/10042\/24916\/logfile.log;<\/code><\/p>\n<p>which is directly derived from the handle itself (although again that algorithm has to be worked out by a human).<\/p>\n<p><strong>Point 7<\/strong> above is also implemented (sort of). If you look at the Figshare repository, you will notice an additional link there which points to the Dspace repository. As it happens, the two datasets are identical (they are not different versions) and these semantics are currently NOT handled well. You could probably work this out from the date stamps of the two depositions (which are respectively\u00a0<strong>Published on\u00a029 Jul 2013 &#8211; 05:58 (GMT)<\/strong> and\u00a0<strong>2013-07-29T05:58:11Z<\/strong> for Figshare and DSpace respectively).\u00a0<\/p>\n<p>Whereas the Amsterdam manifesto is here implemented on a blog post, I think the grander aspiration is that the principles are to be followed in ALL scientific publications. We are some way away yet from achieving this. But watch this space for an upcoming example!\u00a0<\/p>\n<p>So can I urge all scientists who care about data to promulgate the principles of the Amsterdam manifesto, and wherever possible to practice what they preach!\u00a0<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-10972-0\">H.S. Rzepa, \"Gaussian Job Archive for ClF3\", 2013. <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.757728\">https:\/\/doi.org\/10.6084\/m9.figshare.757728<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 10972 -->","protected":false},"excerpt":{"rendered":"<p>The Amsterdam manifesto\u00a0espouses the principles of citable open data. It is a short document, and it is worth re-stating its eight points here: Data should be considered citable products of research. Such data should be held in persistent public repositories. If a publication is based on data not included with the article, those data should [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2],"tags":[1109,1112,1108,1110,1111],"ppma_author":[2661],"class_list":["post-10972","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-amsterdam","tag-exposed-algorithm","tag-opendata","tag-rotatable-3d-model","tag-using-jmol"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>The Amsterdam Manifesto on Data Citation Principles - Henry Rzepa&#039;s Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10972\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Amsterdam Manifesto on Data Citation Principles - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The Amsterdam manifesto\u00a0espouses the principles of citable open data. 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It is worth repeating the eight simple principles: Data should be considered citable products of research. Such data should be held in persistent public repositories. If a publication is based on data not included with the article, those data should\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"doi-x2","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x2.jpg?resize=350%2C200","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x2.jpg?resize=350%2C200 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x2.jpg?resize=525%2C300 1.5x"},"classes":[]},{"id":10998,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10998","url_meta":{"origin":10972,"position":1},"title":"A two-publisher model for the scientific article: narrative+shared data.","author":"Henry Rzepa","date":"September 15, 2013","format":false,"excerpt":"I do go on rather a lot about enabling or\u00a0hyper-activating data. So do others. Why is sharing data important? Reproducibility is a cornerstone in science, To achieve this, it is important that scientific research be\u00a0open and transparent. Openly available research data is central to achieving this. It is estimated that\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":26883,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26883","url_meta":{"origin":10972,"position":2},"title":"Data Citation &#8211; a snapshot of the chemical landscape.","author":"Henry Rzepa","date":"February 26, 2024","format":false,"excerpt":"The recent release of the DataCite Data Citation corpus, which has the stated aim of providing \"a trusted central aggregate of all data citations to further our understanding of data usage and advance meaningful data metrics\" made me want to investigate what the current state of citing data in the\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/02\/DOIs-v-AN.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":27169,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27169","url_meta":{"origin":10972,"position":3},"title":"How should data  be cited in journal articles?  A Crossref request for public comment!","author":"Henry Rzepa","date":"July 18, 2024","format":false,"excerpt":"Metadata is something that goes on behind the scenes and is rarely of concern to either author or readers of scientific articles. Here I tell a story where it has rather greater exposure. For journals in science and chemistry, each article published has a corresponding metadata record, associated with the\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":20634,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20634","url_meta":{"origin":10972,"position":4},"title":"Questions about the (metadata) components of a scientific article.","author":"Henry Rzepa","date":"April 8, 2019","format":false,"excerpt":"The conventional procedures for reporting analysis or new results in science is to compose an \"article\", augment that perhaps with \"supporting information\" or \"SI\", submit to a journal which undertakes peer review, with revision as necessary for acceptance and finally publication. If errors in the original are later identified, a\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":17107,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17107","url_meta":{"origin":10972,"position":5},"title":"OpenCon (2016)","author":"Henry Rzepa","date":"November 25, 2016","format":false,"excerpt":"Another conference, a Cambridge satellite meeting of OpenCon, and I quote here its mission: \"OpenCon is a platform for the next generation to learn about Open Access, Open Education, and Open Data, develop critical skills, and catalyze action toward a more open system of research and education\" targeted at\u00a0students and\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"orcid","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/orcid.png?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10972","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=10972"}],"version-history":[{"count":15,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10972\/revisions"}],"predecessor-version":[{"id":10985,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10972\/revisions\/10985"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10972"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=10972"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=10972"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=10972"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}