{"id":12182,"date":"2014-03-18T15:49:52","date_gmt":"2014-03-18T15:49:52","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12182"},"modified":"2014-03-31T17:11:13","modified_gmt":"2014-03-31T16:11:13","slug":"the-amsterdam-manifesto-and-crystal-structures","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182","title":{"rendered":"The Amsterdam Manifesto and crystal structures."},"content":{"rendered":"
\n

I have mentioned the Amsterdam manifesto<\/a> before on these pages. It is worth repeating the eight simple principles:<\/p>\n

    \n
  1. Data should be considered citable products of research.<\/li>\n
  2. Such data should be held in persistent public repositories.<\/li>\n
  3. If a publication is based on data not included with the article, those data should be cited in the publication.<\/li>\n
  4. A data citation in a publication should resemble a bibliographic citation and be located in the publication’s reference list.<\/li>\n
  5. Such a data citation should include a unique persistent identifier (a DataCite DOI recommended, or other persistent identifiers already in use within the community).<\/li>\n
  6. 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\u00a0machine-actionable to promote interoperability of the data<\/b>.<\/li>\n
  7. If the data are available in different versions, the identifier should provide a method to access the previous or related versions.<\/li>\n
  8. Data citation should facilitate attribution of credit to all contributors<\/li>\n<\/ol>\n

    I just gave a talk at the ACS meeting in Dallas which touched upon the need to emancipate data according to these principles. My talk, in case you are interested, focused particularly upon item 6 above.[1]<\/a><\/span><\/p>\n

    Just after my talk I heard that crystallographic data was about to be emancipated (my phrase) and so I was interested to find out what this might mean, and how many of the above principles were being adhered to. Indeed, it is an interesting test to apply to any chemistry data that you might find out there. Thus 10.5517\/cc10ftfp[2]<\/a><\/span> is the DOI of a recently published crystal data structure. This adheres to points 1-3 and 5 above, and probably also 8. As I have already noted, 6 is the interesting one! So let’s go to the landing page and see what we find.<\/p>\n

    \"doi-x1\"<\/a><\/p>\n

     <\/p>\n

    Firstly, note that you do not need any sort of access code to get to this page, it is open to all. But it is after all just a landing page, not actual data. Next, click on the\u00a0Download<\/strong> button, and you get asked to identify yourself by providing a name, email address and affiliation as mandatory<\/strong> fields, as well as agreeing to conditions of use.\u00a0I reproduce these conditions here:<\/p>\n

    “Individual CIF data sets are provided freely by the CCDC on the understanding that they are used for bona fide research purposes only. They may contain copyright material of the CCDC or of third parties, and may not be copied or further disseminated in any form, whether machine-readable or not, except for the purpose of generating routine backup copies on your local computer system<\/em>“.<\/p>\n

    As with most such conditions, it is what one cannot do that is most interesting.<\/p>\n

      \n
    1. Teach, as for example incorporating the data into lecture notes<\/li>\n
    2. Make a copy, e.g.<\/em> to place into this blog (is this for research purposes?)<\/li>\n
    3. Do bona fide<\/em> research purposes in fact allow a copy to be made, or does the second sentence over-ride the first in this regard, since it lists exclusions and research copying is not an exclusion.<\/li>\n
    4. Judging from the landing page, it is pretty much impossible for any machine action to take place (item 6 in the Amsterdam manifesto). Even though the data is machine actionable, the landing page pretty much prevents this from happening.\u00a0<\/li>\n<\/ol>\n

      What did cause my eyebrows to shoot up was that I have to reveal my full identity and affiliation (which appears not to be actually checked) in order to get the data. Think about this. Do journals ask for this information when you download an article from them? (OK, they probably know your affiliation). Which scientist is reading which article (or viewing which data) could be construed as sensitive information after all. So why in order to acquire crystal data do you have to provide personal information? Surely, looking at data should be a private process if one wants it to be?<\/p>\n

      \"doi-x2\"<\/a><\/p>\n

      The release of crystal data in this manner, with a decent partial adherence to the Amsterdam Manifesto is an excellent start; this data after all is well curated and of high value. But I must call upon CCDC to rethink that landing page, the conditions of use and the mandatory gathering of personal information. Not quite there yet!<\/p>\n

      References<\/h2>\n
      1. Sowa, Micha\u0142., \u015alepokura, Katarzyna., and Matczak-Jon, Ewa., \"CCDC 936802: Experimental Crystal Structure Determination\", 2014. https:\/\/doi.org\/10.5517\/cc10ftfp<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        I have mentioned the Amsterdam manifesto before on these pages. 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 be cited in the publication. […]<\/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":[32,1109,1168,1195,437],"ppma_author":[2661],"class_list":["post-12182","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-acs","tag-amsterdam","tag-amsterdam-manifesto","tag-dallas","tag-scientist"],"yoast_head":"\nThe Amsterdam Manifesto and crystal structures. - Henry Rzepa'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=12182\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Amsterdam Manifesto and crystal structures. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I have mentioned the Amsterdam manifesto before on these pages. 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 be cited in the publication. […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2014-03-18T15:49:52+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2014-03-31T16:11:13+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x1.jpg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"The Amsterdam Manifesto and crystal structures. - Henry Rzepa's Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182","og_locale":"en_GB","og_type":"article","og_title":"The Amsterdam Manifesto and crystal structures. - Henry Rzepa's Blog","og_description":"I have mentioned the Amsterdam manifesto before on these pages. 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 be cited in the publication. […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182","og_site_name":"Henry Rzepa's Blog","article_published_time":"2014-03-18T15:49:52+00:00","article_modified_time":"2014-03-31T16:11:13+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x1.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"The Amsterdam Manifesto and crystal structures.","datePublished":"2014-03-18T15:49:52+00:00","dateModified":"2014-03-31T16:11:13+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182"},"wordCount":726,"commentCount":2,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x1.jpg","keywords":["ACS","Amsterdam","Amsterdam Manifesto","Dallas","scientist"],"articleSection":["Chemical IT"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182","name":"The Amsterdam Manifesto and crystal structures. - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x1.jpg","datePublished":"2014-03-18T15:49:52+00:00","dateModified":"2014-03-31T16:11:13+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#primaryimage","url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x1.jpg","contentUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/doi-x1.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12182#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"The Amsterdam Manifesto and crystal structures."}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-3au","jetpack-related-posts":[{"id":10972,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10972","url_meta":{"origin":12182,"position":0},"title":"The Amsterdam Manifesto on Data Citation Principles","author":"Henry Rzepa","date":"July 31, 2013","format":false,"excerpt":"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\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/ClF3.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26883,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26883","url_meta":{"origin":12182,"position":1},"title":"Data Citation – 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":12182,"position":2},"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 "Interesting chemistry"","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":14437,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14437","url_meta":{"origin":12182,"position":3},"title":"Single Figure (nano)publications, reddit AMAs and other new approaches to research reporting","author":"Henry Rzepa","date":"August 5, 2015","format":false,"excerpt":"I recently received two emails each with a subject line\u00a0new approaches to research reporting. The traditional 350 year-old model of the (scientific) journal is undergoing upheavals at the moment with the introduction of APCs (article processing charges), a refereeing crisis and much more. Some argue that brand new thinking is\u2026","rel":"","context":"In "Chemical IT"","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":20634,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20634","url_meta":{"origin":12182,"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 "Chemical IT"","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":26941,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26941","url_meta":{"origin":12182,"position":5},"title":"Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry.","author":"Henry Rzepa","date":"March 21, 2024","format":false,"excerpt":"In the mid to late 1990s as the Web developed, it was becoming more obvious that one area it would revolutionise was of scholarly journal publishing. Since the days of the very first scientific journals in the 1650s, the medium had been firmly rooted in paper. Even printed colour only\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\/03\/Screenshot-297-1024x698.jpg?resize=350%2C200&ssl=1","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\/12182","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=12182"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12182\/revisions"}],"predecessor-version":[{"id":12198,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12182\/revisions\/12198"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=12182"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=12182"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=12182"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=12182"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}