{"id":7553,"date":"2012-08-13T18:33:21","date_gmt":"2012-08-13T17:33:21","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=7553"},"modified":"2013-07-19T17:13:51","modified_gmt":"2013-07-19T16:13:51","slug":"digital-repositories-an-update-to-the-update","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7553","title":{"rendered":"Digital repositories. An update to the update."},"content":{"rendered":"
\n

A third digital repository has been added to the two<\/a> I described before. Chempound<\/a> is a free open-source repository which (unlike DSpace and Figshare) was developed specifically for chemistry.<\/p>\n

\"\"<\/a><\/p>\n

It carries more semantic information (in the form of an RDF triple declaration<\/a>), which allows SPARQL<\/a> queries on the entry to be performed.<\/p>\n

Our original DSpace repository<\/a>\u00a0is also being tweaked to allow additional information to be added to existing entries; in particular if an entry is linked to in a journal publication, the DOI of that article is inserted into the DSpace descriptions. It is also relatively simply to duplicate the information in one repository by re-depositing it into another. Thus it becomes feasible to clone the information about the 600+ entries in our DSpace that have been subsequently published in peer-reviewed journal articles, thus adding a measure of confidence to their provenance.<\/p>\n

To compare how the three repositories carry information about the same molecule, invoke any of the links below:<\/p>\n

    \n
  1. DSpace<\/a><\/li>\n
  2. Figshare<\/a><\/li>\n
  3. Chempound\u00a0<\/a><\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    A third digital repository has been added to the two I described before. Chempound is a free open-source repository which (unlike DSpace and Figshare) was developed specifically for chemistry. It carries more semantic information (in the form of an RDF triple declaration), which allows SPARQL queries on the entry to be performed. Our original DSpace […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[2],"tags":[1108,894],"ppma_author":[2661],"class_list":["post-7553","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-opendata","tag-skolnik"],"yoast_head":"\nDigital repositories. An update to the update. - 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=7553\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Digital repositories. An update to the update. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A third digital repository has been added to the two I described before. Chempound is a free open-source repository which (unlike DSpace and Figshare) was developed specifically for chemistry. It carries more semantic information (in the form of an RDF triple declaration), which allows SPARQL queries on the entry to be performed. Our original DSpace […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7553\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2012-08-13T17:33:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-07-19T16:13:51+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/08\/chempound.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=\"1 minute\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Digital repositories. 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An update.","author":"Henry Rzepa","date":"July 21, 2012","format":false,"excerpt":"I blogged about this two years ago\u00a0and thought a brief update might be in order now. To support the discussions here, I often perform calculations, and most of these are then deposited into a DSpace digital repository, along with metadata. Anyone wishing to have the full details of any calculation\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":10972,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10972","url_meta":{"origin":7553,"position":1},"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":1967,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1967","url_meta":{"origin":7553,"position":2},"title":"A Digital chemical repository – is it being used?","author":"Henry Rzepa","date":"May 4, 2010","format":false,"excerpt":"In this previous blog post I wrote about one way in which we have enhanced the journal article. Associated with that enhancement, and also sprinkled liberally throughout this blog, are links to a Digital Repository (if you want to read all about it, see DOI: 10.1021\/ci7004737). It is a fairly\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":14183,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14183","url_meta":{"origin":7553,"position":3},"title":"Personal web pages on digital repositories.","author":"Henry Rzepa","date":"June 20, 2015","format":false,"excerpt":"The university sector in the UK has quality inspections of its research outputs conducted every seven years, going by the name of REF or Research Excellence Framework. The next one is due around 2020, and already preparations are under way! Here I describe how I have interpreted one of its\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":7601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601","url_meta":{"origin":7553,"position":4},"title":"The Sn2 reaction: followed up.","author":"Henry Rzepa","date":"September 12, 2012","format":false,"excerpt":"An obvious issue to follow-up my last post on the (solvated) intrinisic reaction coordinate for the Sn2 reaction is how variation of the halogen (X) impacts upon the nature of the potential. X=FX=Cl X=BrX=I X=FX=Cl X=BrX=I The change in slope of the gradient norm along the IRC is hardly noticeable\u2026","rel":"","context":"In \"potential energy surfaces\"","block_context":{"text":"potential energy surfaces","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=potential-energy-surfaces"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":10825,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10825","url_meta":{"origin":7553,"position":5},"title":"150,000,000 DFT calculations on 2,300,000 compounds!","author":"Henry Rzepa","date":"July 5, 2013","format":false,"excerpt":"The title of this post summarises the contents of a new molecular database:\u00a0www.molecularspace.org and I picked up on it by following the post by Jan Jensen at\u00a0www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called \"The Harvard Clean Energy Project: Large-scale computational\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":[]}],"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\/7553","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=7553"}],"version-history":[{"count":7,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7553\/revisions"}],"predecessor-version":[{"id":10927,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7553\/revisions\/10927"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=7553"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=7553"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=7553"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=7553"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}